diff --git a/coverage/class_index.html b/coverage/class_index.html
index f361b6c..71c5b0c 100644
--- a/coverage/class_index.html
+++ b/coverage/class_index.html
@@ -55,7 +55,7 @@ <h2>
         </h2>
         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </header>
@@ -443,10 +443,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html#t15">biobb_structure_utils/utils/cat_pdb.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html#t15"><data value='CatPDB'>CatPDB</data></a></td>
-                <td>34</td>
+                <td>33</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="33 34">97%</td>
+                <td class="right" data-ratio="32 33">97%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html">biobb_structure_utils/utils/cat_pdb.py</a></td>
@@ -459,10 +459,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html#t24">biobb_structure_utils/utils/closest_residues.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html#t24"><data value='ClosestResidues'>ClosestResidues</data></a></td>
-                <td>59</td>
+                <td>58</td>
                 <td>7</td>
                 <td>0</td>
-                <td class="right" data-ratio="52 59">88%</td>
+                <td class="right" data-ratio="51 58">88%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html">biobb_structure_utils/utils/closest_residues.py</a></td>
@@ -483,10 +483,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html#t19">biobb_structure_utils/utils/extract_atoms.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html#t19"><data value='ExtractAtoms'>ExtractAtoms</data></a></td>
-                <td>40</td>
+                <td>39</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="36 40">90%</td>
+                <td class="right" data-ratio="35 39">90%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html">biobb_structure_utils/utils/extract_atoms.py</a></td>
@@ -499,10 +499,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html#t21">biobb_structure_utils/utils/extract_chain.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html#t21"><data value='ExtractChain'>ExtractChain</data></a></td>
-                <td>33</td>
+                <td>32</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="29 33">88%</td>
+                <td class="right" data-ratio="28 32">88%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html">biobb_structure_utils/utils/extract_chain.py</a></td>
@@ -515,10 +515,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html#t24">biobb_structure_utils/utils/extract_heteroatoms.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html#t24"><data value='ExtractHeteroAtoms'>ExtractHeteroAtoms</data></a></td>
-                <td>43</td>
+                <td>42</td>
                 <td>7</td>
                 <td>0</td>
-                <td class="right" data-ratio="36 43">84%</td>
+                <td class="right" data-ratio="35 42">83%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html">biobb_structure_utils/utils/extract_heteroatoms.py</a></td>
@@ -563,10 +563,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html#t24">biobb_structure_utils/utils/extract_residues.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html#t24"><data value='ExtractResidues'>ExtractResidues</data></a></td>
-                <td>38</td>
+                <td>37</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="34 38">89%</td>
+                <td class="right" data-ratio="33 37">89%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html">biobb_structure_utils/utils/extract_residues.py</a></td>
@@ -579,10 +579,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html#t17">biobb_structure_utils/utils/remove_ligand.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html#t17"><data value='RemoveLigand'>RemoveLigand</data></a></td>
-                <td>29</td>
+                <td>28</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="28 29">97%</td>
+                <td class="right" data-ratio="27 28">96%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html">biobb_structure_utils/utils/remove_ligand.py</a></td>
@@ -595,10 +595,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html#t24">biobb_structure_utils/utils/remove_molecules.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html#t24"><data value='RemoveMolecules'>RemoveMolecules</data></a></td>
-                <td>41</td>
+                <td>40</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="37 41">90%</td>
+                <td class="right" data-ratio="36 40">90%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html">biobb_structure_utils/utils/remove_molecules.py</a></td>
@@ -611,10 +611,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html#t13">biobb_structure_utils/utils/remove_pdb_water.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html#t13"><data value='RemovePdbWater'>RemovePdbWater</data></a></td>
-                <td>17</td>
+                <td>16</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="16 17">94%</td>
+                <td class="right" data-ratio="15 16">94%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html">biobb_structure_utils/utils/remove_pdb_water.py</a></td>
@@ -627,10 +627,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html#t19">biobb_structure_utils/utils/renumber_structure.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html#t19"><data value='RenumberStructure'>RenumberStructure</data></a></td>
-                <td>59</td>
+                <td>58</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="58 59">98%</td>
+                <td class="right" data-ratio="57 58">98%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html">biobb_structure_utils/utils/renumber_structure.py</a></td>
@@ -643,10 +643,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html#t16">biobb_structure_utils/utils/sort_gro_residues.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html#t16"><data value='SortGroResidues'>SortGroResidues</data></a></td>
-                <td>20</td>
+                <td>19</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="19 20">95%</td>
+                <td class="right" data-ratio="18 19">95%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html">biobb_structure_utils/utils/sort_gro_residues.py</a></td>
@@ -659,10 +659,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html#t19">biobb_structure_utils/utils/str_check_add_hydrogens.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html#t19"><data value='StrCheckAddHydrogens'>StrCheckAddHydrogens</data></a></td>
-                <td>40</td>
+                <td>39</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="36 40">90%</td>
+                <td class="right" data-ratio="35 39">90%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html">biobb_structure_utils/utils/str_check_add_hydrogens.py</a></td>
@@ -693,10 +693,10 @@ <h2>
             <tr class="total">
                 <td class="name left">Total</td>
                 <td class="name left">&nbsp;</td>
-                <td>1567</td>
+                <td>1555</td>
                 <td>297</td>
                 <td>0</td>
-                <td class="right" data-ratio="1270 1567">81%</td>
+                <td class="right" data-ratio="1258 1555">81%</td>
             </tr>
         </tfoot>
     </table>
@@ -708,7 +708,7 @@ <h2>
     <div class="content">
         <p>
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/coverage.xml b/coverage/coverage.xml
index 7dd1fb5..f6343f6 100644
--- a/coverage/coverage.xml
+++ b/coverage/coverage.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" ?>
-<coverage version="7.6.10" timestamp="1737480356324" lines-valid="1567" lines-covered="1270" line-rate="0.8105" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
+<coverage version="7.6.10" timestamp="1738065037636" lines-valid="1555" lines-covered="1258" line-rate="0.809" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
 	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.10 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
-		<source>/home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils</source>
+		<source>/home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils</source>
 	</sources>
 	<packages>
 		<package name="biobb_structure_utils" line-rate="1" branch-rate="0" complexity="0">
@@ -599,7 +599,7 @@
 				</class>
 			</classes>
 		</package>
-		<package name="biobb_structure_utils.utils" line-rate="0.7852" branch-rate="0" complexity="0">
+		<package name="biobb_structure_utils.utils" line-rate="0.7828" branch-rate="0" complexity="0">
 			<classes>
 				<class name="__init__.py" filename="biobb_structure_utils/utils/__init__.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
@@ -609,7 +609,7 @@
 						<line number="20" hits="1"/>
 					</lines>
 				</class>
-				<class name="cat_pdb.py" filename="biobb_structure_utils/utils/cat_pdb.py" complexity="0" line-rate="0.7966" branch-rate="0">
+				<class name="cat_pdb.py" filename="biobb_structure_utils/utils/cat_pdb.py" complexity="0" line-rate="0.7931" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -652,28 +652,27 @@
 						<line number="127" hits="1"/>
 						<line number="128" hits="1"/>
 						<line number="131" hits="1"/>
-						<line number="134" hits="1"/>
 						<line number="135" hits="1"/>
 						<line number="137" hits="1"/>
 						<line number="139" hits="1"/>
 						<line number="142" hits="1"/>
 						<line number="152" hits="1"/>
-						<line number="161" hits="1"/>
-						<line number="163" hits="0"/>
-						<line number="167" hits="0"/>
-						<line number="175" hits="0"/>
-						<line number="176" hits="0"/>
-						<line number="182" hits="0"/>
-						<line number="188" hits="0"/>
-						<line number="195" hits="0"/>
-						<line number="196" hits="0"/>
+						<line number="163" hits="1"/>
+						<line number="165" hits="0"/>
+						<line number="169" hits="0"/>
+						<line number="177" hits="0"/>
+						<line number="178" hits="0"/>
+						<line number="184" hits="0"/>
+						<line number="190" hits="0"/>
 						<line number="197" hits="0"/>
-						<line number="200" hits="0"/>
-						<line number="208" hits="1"/>
-						<line number="209" hits="0"/>
+						<line number="198" hits="0"/>
+						<line number="199" hits="0"/>
+						<line number="202" hits="0"/>
+						<line number="210" hits="1"/>
+						<line number="211" hits="0"/>
 					</lines>
 				</class>
-				<class name="closest_residues.py" filename="biobb_structure_utils/utils/closest_residues.py" complexity="0" line-rate="0.8" branch-rate="0">
+				<class name="closest_residues.py" filename="biobb_structure_utils/utils/closest_residues.py" complexity="0" line-rate="0.7976" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -743,24 +742,23 @@
 						<line number="197" hits="1"/>
 						<line number="205" hits="1"/>
 						<line number="208" hits="1"/>
-						<line number="211" hits="1"/>
 						<line number="212" hits="1"/>
 						<line number="214" hits="1"/>
 						<line number="216" hits="1"/>
 						<line number="219" hits="1"/>
 						<line number="228" hits="1"/>
-						<line number="236" hits="1"/>
-						<line number="238" hits="0"/>
-						<line number="242" hits="0"/>
-						<line number="250" hits="0"/>
-						<line number="251" hits="0"/>
-						<line number="257" hits="0"/>
-						<line number="264" hits="0"/>
-						<line number="265" hits="0"/>
+						<line number="238" hits="1"/>
+						<line number="240" hits="0"/>
+						<line number="244" hits="0"/>
+						<line number="252" hits="0"/>
+						<line number="253" hits="0"/>
+						<line number="259" hits="0"/>
 						<line number="266" hits="0"/>
-						<line number="269" hits="0"/>
-						<line number="276" hits="1"/>
-						<line number="277" hits="0"/>
+						<line number="267" hits="0"/>
+						<line number="268" hits="0"/>
+						<line number="271" hits="0"/>
+						<line number="278" hits="1"/>
+						<line number="279" hits="0"/>
 					</lines>
 				</class>
 				<class name="common.py" filename="biobb_structure_utils/utils/common.py" complexity="0" line-rate="0.7986" branch-rate="0">
@@ -912,7 +910,7 @@
 						<line number="255" hits="0"/>
 					</lines>
 				</class>
-				<class name="extract_atoms.py" filename="biobb_structure_utils/utils/extract_atoms.py" complexity="0" line-rate="0.7941" branch-rate="0">
+				<class name="extract_atoms.py" filename="biobb_structure_utils/utils/extract_atoms.py" complexity="0" line-rate="0.791" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -965,27 +963,26 @@
 						<line number="145" hits="0"/>
 						<line number="150" hits="1"/>
 						<line number="154" hits="1"/>
-						<line number="157" hits="1"/>
 						<line number="158" hits="1"/>
 						<line number="160" hits="1"/>
 						<line number="162" hits="1"/>
 						<line number="165" hits="1"/>
 						<line number="174" hits="1"/>
-						<line number="182" hits="1"/>
-						<line number="184" hits="0"/>
-						<line number="188" hits="0"/>
-						<line number="196" hits="0"/>
-						<line number="197" hits="0"/>
-						<line number="200" hits="0"/>
-						<line number="207" hits="0"/>
-						<line number="208" hits="0"/>
+						<line number="184" hits="1"/>
+						<line number="186" hits="0"/>
+						<line number="190" hits="0"/>
+						<line number="198" hits="0"/>
+						<line number="199" hits="0"/>
+						<line number="202" hits="0"/>
 						<line number="209" hits="0"/>
-						<line number="212" hits="0"/>
-						<line number="219" hits="1"/>
-						<line number="220" hits="0"/>
+						<line number="210" hits="0"/>
+						<line number="211" hits="0"/>
+						<line number="214" hits="0"/>
+						<line number="221" hits="1"/>
+						<line number="222" hits="0"/>
 					</lines>
 				</class>
-				<class name="extract_chain.py" filename="biobb_structure_utils/utils/extract_chain.py" complexity="0" line-rate="0.7313" branch-rate="0">
+				<class name="extract_chain.py" filename="biobb_structure_utils/utils/extract_chain.py" complexity="0" line-rate="0.7273" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -1029,7 +1026,6 @@
 						<line number="135" hits="0"/>
 						<line number="148" hits="0"/>
 						<line number="151" hits="1"/>
-						<line number="154" hits="1"/>
 						<line number="155" hits="1"/>
 						<line number="157" hits="1"/>
 						<line number="159" hits="1"/>
@@ -1043,21 +1039,21 @@
 						<line number="175" hits="1"/>
 						<line number="178" hits="1"/>
 						<line number="187" hits="1"/>
-						<line number="195" hits="1"/>
-						<line number="197" hits="0"/>
-						<line number="201" hits="0"/>
-						<line number="209" hits="0"/>
-						<line number="210" hits="0"/>
-						<line number="216" hits="0"/>
-						<line number="223" hits="0"/>
-						<line number="224" hits="0"/>
+						<line number="197" hits="1"/>
+						<line number="199" hits="0"/>
+						<line number="203" hits="0"/>
+						<line number="211" hits="0"/>
+						<line number="212" hits="0"/>
+						<line number="218" hits="0"/>
 						<line number="225" hits="0"/>
-						<line number="228" hits="0"/>
-						<line number="235" hits="1"/>
-						<line number="236" hits="0"/>
+						<line number="226" hits="0"/>
+						<line number="227" hits="0"/>
+						<line number="230" hits="0"/>
+						<line number="237" hits="1"/>
+						<line number="238" hits="0"/>
 					</lines>
 				</class>
-				<class name="extract_heteroatoms.py" filename="biobb_structure_utils/utils/extract_heteroatoms.py" complexity="0" line-rate="0.7536" branch-rate="0">
+				<class name="extract_heteroatoms.py" filename="biobb_structure_utils/utils/extract_heteroatoms.py" complexity="0" line-rate="0.75" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -1111,24 +1107,23 @@
 						<line number="159" hits="1"/>
 						<line number="167" hits="1"/>
 						<line number="170" hits="1"/>
-						<line number="173" hits="1"/>
 						<line number="174" hits="1"/>
 						<line number="176" hits="1"/>
 						<line number="178" hits="1"/>
 						<line number="181" hits="1"/>
 						<line number="190" hits="1"/>
-						<line number="198" hits="1"/>
-						<line number="200" hits="0"/>
-						<line number="204" hits="0"/>
-						<line number="212" hits="0"/>
-						<line number="213" hits="0"/>
-						<line number="219" hits="0"/>
-						<line number="226" hits="0"/>
-						<line number="227" hits="0"/>
+						<line number="200" hits="1"/>
+						<line number="202" hits="0"/>
+						<line number="206" hits="0"/>
+						<line number="214" hits="0"/>
+						<line number="215" hits="0"/>
+						<line number="221" hits="0"/>
 						<line number="228" hits="0"/>
-						<line number="231" hits="0"/>
-						<line number="238" hits="1"/>
-						<line number="239" hits="0"/>
+						<line number="229" hits="0"/>
+						<line number="230" hits="0"/>
+						<line number="233" hits="0"/>
+						<line number="240" hits="1"/>
+						<line number="241" hits="0"/>
 					</lines>
 				</class>
 				<class name="extract_model.py" filename="biobb_structure_utils/utils/extract_model.py" complexity="0" line-rate="0.7671" branch-rate="0">
@@ -1182,31 +1177,31 @@
 						<line number="145" hits="1"/>
 						<line number="148" hits="1"/>
 						<line number="151" hits="1"/>
-						<line number="154" hits="1"/>
-						<line number="156" hits="1"/>
-						<line number="158" hits="1"/>
-						<line number="161" hits="1"/>
-						<line number="163" hits="1"/>
-						<line number="164" hits="0"/>
+						<line number="155" hits="1"/>
+						<line number="157" hits="1"/>
+						<line number="159" hits="1"/>
+						<line number="162" hits="1"/>
+						<line number="164" hits="1"/>
 						<line number="165" hits="0"/>
-						<line number="167" hits="1"/>
-						<line number="168" hits="0"/>
-						<line number="172" hits="0"/>
-						<line number="174" hits="1"/>
-						<line number="177" hits="1"/>
-						<line number="186" hits="1"/>
-						<line number="194" hits="1"/>
-						<line number="196" hits="0"/>
-						<line number="200" hits="0"/>
-						<line number="208" hits="0"/>
-						<line number="209" hits="0"/>
-						<line number="215" hits="0"/>
-						<line number="222" hits="0"/>
-						<line number="223" hits="0"/>
-						<line number="224" hits="0"/>
+						<line number="166" hits="0"/>
+						<line number="168" hits="1"/>
+						<line number="169" hits="0"/>
+						<line number="173" hits="0"/>
+						<line number="175" hits="1"/>
+						<line number="178" hits="1"/>
+						<line number="187" hits="1"/>
+						<line number="197" hits="1"/>
+						<line number="199" hits="0"/>
+						<line number="203" hits="0"/>
+						<line number="211" hits="0"/>
+						<line number="212" hits="0"/>
+						<line number="218" hits="0"/>
+						<line number="225" hits="0"/>
+						<line number="226" hits="0"/>
 						<line number="227" hits="0"/>
-						<line number="234" hits="1"/>
-						<line number="235" hits="0"/>
+						<line number="230" hits="0"/>
+						<line number="237" hits="1"/>
+						<line number="238" hits="0"/>
 					</lines>
 				</class>
 				<class name="extract_molecule.py" filename="biobb_structure_utils/utils/extract_molecule.py" complexity="0" line-rate="0.7667" branch-rate="0">
@@ -1255,26 +1250,26 @@
 						<line number="143" hits="1"/>
 						<line number="146" hits="1"/>
 						<line number="149" hits="1"/>
-						<line number="150" hits="1"/>
-						<line number="152" hits="1"/>
-						<line number="154" hits="1"/>
+						<line number="153" hits="1"/>
+						<line number="155" hits="1"/>
 						<line number="157" hits="1"/>
-						<line number="166" hits="1"/>
-						<line number="174" hits="1"/>
-						<line number="176" hits="0"/>
-						<line number="180" hits="0"/>
-						<line number="188" hits="0"/>
-						<line number="189" hits="0"/>
-						<line number="195" hits="0"/>
-						<line number="202" hits="0"/>
-						<line number="203" hits="0"/>
-						<line number="204" hits="0"/>
+						<line number="160" hits="1"/>
+						<line number="169" hits="1"/>
+						<line number="179" hits="1"/>
+						<line number="181" hits="0"/>
+						<line number="185" hits="0"/>
+						<line number="193" hits="0"/>
+						<line number="194" hits="0"/>
+						<line number="200" hits="0"/>
 						<line number="207" hits="0"/>
-						<line number="214" hits="1"/>
-						<line number="215" hits="0"/>
+						<line number="208" hits="0"/>
+						<line number="209" hits="0"/>
+						<line number="212" hits="0"/>
+						<line number="219" hits="1"/>
+						<line number="220" hits="0"/>
 					</lines>
 				</class>
-				<class name="extract_residues.py" filename="biobb_structure_utils/utils/extract_residues.py" complexity="0" line-rate="0.7812" branch-rate="0">
+				<class name="extract_residues.py" filename="biobb_structure_utils/utils/extract_residues.py" complexity="0" line-rate="0.7778" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -1323,27 +1318,26 @@
 						<line number="146" hits="1"/>
 						<line number="154" hits="1"/>
 						<line number="157" hits="1"/>
-						<line number="160" hits="1"/>
 						<line number="161" hits="1"/>
 						<line number="163" hits="1"/>
 						<line number="165" hits="1"/>
 						<line number="168" hits="1"/>
 						<line number="177" hits="1"/>
-						<line number="185" hits="1"/>
-						<line number="187" hits="0"/>
-						<line number="191" hits="0"/>
-						<line number="199" hits="0"/>
-						<line number="200" hits="0"/>
-						<line number="206" hits="0"/>
-						<line number="213" hits="0"/>
-						<line number="214" hits="0"/>
+						<line number="187" hits="1"/>
+						<line number="189" hits="0"/>
+						<line number="193" hits="0"/>
+						<line number="201" hits="0"/>
+						<line number="202" hits="0"/>
+						<line number="208" hits="0"/>
 						<line number="215" hits="0"/>
-						<line number="218" hits="0"/>
-						<line number="225" hits="1"/>
-						<line number="226" hits="0"/>
+						<line number="216" hits="0"/>
+						<line number="217" hits="0"/>
+						<line number="220" hits="0"/>
+						<line number="227" hits="1"/>
+						<line number="228" hits="0"/>
 					</lines>
 				</class>
-				<class name="remove_ligand.py" filename="biobb_structure_utils/utils/remove_ligand.py" complexity="0" line-rate="0.8" branch-rate="0">
+				<class name="remove_ligand.py" filename="biobb_structure_utils/utils/remove_ligand.py" complexity="0" line-rate="0.7963" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -1383,27 +1377,26 @@
 						<line number="116" hits="1"/>
 						<line number="118" hits="1"/>
 						<line number="122" hits="1"/>
-						<line number="125" hits="1"/>
 						<line number="126" hits="1"/>
 						<line number="128" hits="1"/>
 						<line number="130" hits="1"/>
 						<line number="133" hits="1"/>
 						<line number="142" hits="1"/>
-						<line number="150" hits="1"/>
-						<line number="152" hits="0"/>
-						<line number="156" hits="0"/>
-						<line number="164" hits="0"/>
-						<line number="165" hits="0"/>
-						<line number="168" hits="0"/>
-						<line number="175" hits="0"/>
-						<line number="176" hits="0"/>
+						<line number="152" hits="1"/>
+						<line number="154" hits="0"/>
+						<line number="158" hits="0"/>
+						<line number="166" hits="0"/>
+						<line number="167" hits="0"/>
+						<line number="170" hits="0"/>
 						<line number="177" hits="0"/>
-						<line number="180" hits="0"/>
-						<line number="187" hits="1"/>
-						<line number="188" hits="0"/>
+						<line number="178" hits="0"/>
+						<line number="179" hits="0"/>
+						<line number="182" hits="0"/>
+						<line number="189" hits="1"/>
+						<line number="190" hits="0"/>
 					</lines>
 				</class>
-				<class name="remove_molecules.py" filename="biobb_structure_utils/utils/remove_molecules.py" complexity="0" line-rate="0.791" branch-rate="0">
+				<class name="remove_molecules.py" filename="biobb_structure_utils/utils/remove_molecules.py" complexity="0" line-rate="0.7879" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -1455,27 +1448,26 @@
 						<line number="151" hits="1"/>
 						<line number="159" hits="1"/>
 						<line number="162" hits="1"/>
-						<line number="165" hits="1"/>
 						<line number="166" hits="1"/>
 						<line number="168" hits="1"/>
 						<line number="170" hits="1"/>
 						<line number="173" hits="1"/>
 						<line number="182" hits="1"/>
-						<line number="190" hits="1"/>
-						<line number="192" hits="0"/>
-						<line number="196" hits="0"/>
-						<line number="204" hits="0"/>
-						<line number="205" hits="0"/>
-						<line number="211" hits="0"/>
-						<line number="218" hits="0"/>
-						<line number="219" hits="0"/>
+						<line number="192" hits="1"/>
+						<line number="194" hits="0"/>
+						<line number="198" hits="0"/>
+						<line number="206" hits="0"/>
+						<line number="207" hits="0"/>
+						<line number="213" hits="0"/>
 						<line number="220" hits="0"/>
-						<line number="223" hits="0"/>
-						<line number="230" hits="1"/>
-						<line number="231" hits="0"/>
+						<line number="221" hits="0"/>
+						<line number="222" hits="0"/>
+						<line number="225" hits="0"/>
+						<line number="232" hits="1"/>
+						<line number="233" hits="0"/>
 					</lines>
 				</class>
-				<class name="remove_pdb_water.py" filename="biobb_structure_utils/utils/remove_pdb_water.py" complexity="0" line-rate="0.725" branch-rate="0">
+				<class name="remove_pdb_water.py" filename="biobb_structure_utils/utils/remove_pdb_water.py" complexity="0" line-rate="0.7179" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -1500,27 +1492,26 @@
 						<line number="79" hits="1"/>
 						<line number="92" hits="1"/>
 						<line number="95" hits="1"/>
-						<line number="98" hits="1"/>
 						<line number="99" hits="1"/>
 						<line number="101" hits="1"/>
 						<line number="103" hits="1"/>
 						<line number="106" hits="1"/>
 						<line number="115" hits="1"/>
-						<line number="123" hits="1"/>
-						<line number="125" hits="0"/>
-						<line number="129" hits="0"/>
-						<line number="137" hits="0"/>
-						<line number="138" hits="0"/>
-						<line number="141" hits="0"/>
-						<line number="145" hits="0"/>
-						<line number="146" hits="0"/>
+						<line number="125" hits="1"/>
+						<line number="127" hits="0"/>
+						<line number="131" hits="0"/>
+						<line number="139" hits="0"/>
+						<line number="140" hits="0"/>
+						<line number="143" hits="0"/>
 						<line number="147" hits="0"/>
-						<line number="150" hits="0"/>
-						<line number="157" hits="1"/>
-						<line number="158" hits="0"/>
+						<line number="148" hits="0"/>
+						<line number="149" hits="0"/>
+						<line number="152" hits="0"/>
+						<line number="159" hits="1"/>
+						<line number="160" hits="0"/>
 					</lines>
 				</class>
-				<class name="renumber_structure.py" filename="biobb_structure_utils/utils/renumber_structure.py" complexity="0" line-rate="0.8636" branch-rate="0">
+				<class name="renumber_structure.py" filename="biobb_structure_utils/utils/renumber_structure.py" complexity="0" line-rate="0.8621" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -1592,28 +1583,27 @@
 						<line number="169" hits="1"/>
 						<line number="173" hits="1"/>
 						<line number="177" hits="1"/>
-						<line number="180" hits="1"/>
 						<line number="181" hits="1"/>
 						<line number="183" hits="1"/>
 						<line number="185" hits="1"/>
 						<line number="188" hits="1"/>
 						<line number="198" hits="1"/>
-						<line number="207" hits="1"/>
-						<line number="209" hits="0"/>
-						<line number="213" hits="0"/>
-						<line number="221" hits="0"/>
-						<line number="222" hits="0"/>
-						<line number="225" hits="0"/>
-						<line number="231" hits="0"/>
-						<line number="238" hits="0"/>
-						<line number="239" hits="0"/>
+						<line number="209" hits="1"/>
+						<line number="211" hits="0"/>
+						<line number="215" hits="0"/>
+						<line number="223" hits="0"/>
+						<line number="224" hits="0"/>
+						<line number="227" hits="0"/>
+						<line number="233" hits="0"/>
 						<line number="240" hits="0"/>
-						<line number="243" hits="0"/>
-						<line number="251" hits="1"/>
-						<line number="252" hits="0"/>
+						<line number="241" hits="0"/>
+						<line number="242" hits="0"/>
+						<line number="245" hits="0"/>
+						<line number="253" hits="1"/>
+						<line number="254" hits="0"/>
 					</lines>
 				</class>
-				<class name="sort_gro_residues.py" filename="biobb_structure_utils/utils/sort_gro_residues.py" complexity="0" line-rate="0.7556" branch-rate="0">
+				<class name="sort_gro_residues.py" filename="biobb_structure_utils/utils/sort_gro_residues.py" complexity="0" line-rate="0.75" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -1643,27 +1633,26 @@
 						<line number="89" hits="1"/>
 						<line number="90" hits="1"/>
 						<line number="94" hits="1"/>
-						<line number="97" hits="1"/>
 						<line number="98" hits="1"/>
 						<line number="100" hits="1"/>
 						<line number="102" hits="1"/>
 						<line number="105" hits="1"/>
 						<line number="114" hits="1"/>
-						<line number="122" hits="1"/>
-						<line number="124" hits="0"/>
-						<line number="128" hits="0"/>
-						<line number="136" hits="0"/>
-						<line number="137" hits="0"/>
-						<line number="140" hits="0"/>
-						<line number="144" hits="0"/>
-						<line number="145" hits="0"/>
+						<line number="124" hits="1"/>
+						<line number="126" hits="0"/>
+						<line number="130" hits="0"/>
+						<line number="138" hits="0"/>
+						<line number="139" hits="0"/>
+						<line number="142" hits="0"/>
 						<line number="146" hits="0"/>
-						<line number="149" hits="0"/>
-						<line number="156" hits="1"/>
-						<line number="157" hits="0"/>
+						<line number="147" hits="0"/>
+						<line number="148" hits="0"/>
+						<line number="151" hits="0"/>
+						<line number="158" hits="1"/>
+						<line number="159" hits="0"/>
 					</lines>
 				</class>
-				<class name="str_check_add_hydrogens.py" filename="biobb_structure_utils/utils/str_check_add_hydrogens.py" complexity="0" line-rate="0.7812" branch-rate="0">
+				<class name="str_check_add_hydrogens.py" filename="biobb_structure_utils/utils/str_check_add_hydrogens.py" complexity="0" line-rate="0.7778" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="5" hits="1"/>
@@ -1712,24 +1701,23 @@
 						<line number="140" hits="1"/>
 						<line number="143" hits="1"/>
 						<line number="145" hits="1"/>
-						<line number="148" hits="1"/>
 						<line number="149" hits="1"/>
 						<line number="151" hits="1"/>
 						<line number="153" hits="1"/>
 						<line number="156" hits="1"/>
 						<line number="165" hits="1"/>
-						<line number="173" hits="1"/>
-						<line number="175" hits="0"/>
-						<line number="179" hits="0"/>
-						<line number="187" hits="0"/>
-						<line number="188" hits="0"/>
-						<line number="194" hits="0"/>
-						<line number="201" hits="0"/>
-						<line number="202" hits="0"/>
+						<line number="175" hits="1"/>
+						<line number="177" hits="0"/>
+						<line number="181" hits="0"/>
+						<line number="189" hits="0"/>
+						<line number="190" hits="0"/>
+						<line number="196" hits="0"/>
 						<line number="203" hits="0"/>
-						<line number="206" hits="0"/>
-						<line number="213" hits="1"/>
-						<line number="214" hits="0"/>
+						<line number="204" hits="0"/>
+						<line number="205" hits="0"/>
+						<line number="208" hits="0"/>
+						<line number="215" hits="1"/>
+						<line number="216" hits="0"/>
 					</lines>
 				</class>
 				<class name="structure_check.py" filename="biobb_structure_utils/utils/structure_check.py" complexity="0" line-rate="0.7719" branch-rate="0">
@@ -1775,23 +1763,23 @@
 						<line number="148" hits="1"/>
 						<line number="151" hits="1"/>
 						<line number="154" hits="1"/>
-						<line number="155" hits="1"/>
-						<line number="157" hits="1"/>
-						<line number="159" hits="1"/>
+						<line number="158" hits="1"/>
+						<line number="160" hits="1"/>
 						<line number="162" hits="1"/>
-						<line number="171" hits="1"/>
-						<line number="179" hits="1"/>
-						<line number="181" hits="0"/>
-						<line number="185" hits="0"/>
-						<line number="193" hits="0"/>
-						<line number="194" hits="0"/>
-						<line number="200" hits="0"/>
-						<line number="207" hits="0"/>
-						<line number="208" hits="0"/>
-						<line number="209" hits="0"/>
+						<line number="165" hits="1"/>
+						<line number="174" hits="1"/>
+						<line number="184" hits="1"/>
+						<line number="186" hits="0"/>
+						<line number="190" hits="0"/>
+						<line number="198" hits="0"/>
+						<line number="199" hits="0"/>
+						<line number="205" hits="0"/>
 						<line number="212" hits="0"/>
-						<line number="219" hits="1"/>
-						<line number="220" hits="0"/>
+						<line number="213" hits="0"/>
+						<line number="214" hits="0"/>
+						<line number="217" hits="0"/>
+						<line number="224" hits="1"/>
+						<line number="225" hits="0"/>
 					</lines>
 				</class>
 			</classes>
diff --git a/coverage/coveragebadge.svg b/coverage/coveragebadge.svg
index 6519c40..75b69c4 100644
--- a/coverage/coveragebadge.svg
+++ b/coverage/coveragebadge.svg
@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="116" height="20" role="img" aria-label="Coverage: 81.05%"><title>Coverage: 81.05%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="116" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="63" height="20" fill="#555"/><rect x="63" width="53" height="20" fill="#97ca00"/><rect width="116" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="325" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="530">Coverage</text><text x="325" y="140" transform="scale(.1)" fill="#fff" textLength="530">Coverage</text><text aria-hidden="true" x="885" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">81.05%</text><text x="885" y="140" transform="scale(.1)" fill="#fff" textLength="430">81.05%</text></g></svg>
\ No newline at end of file
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="116" height="20" role="img" aria-label="Coverage: 80.90%"><title>Coverage: 80.90%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="116" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="63" height="20" fill="#555"/><rect x="63" width="53" height="20" fill="#97ca00"/><rect width="116" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="325" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="530">Coverage</text><text x="325" y="140" transform="scale(.1)" fill="#fff" textLength="530">Coverage</text><text aria-hidden="true" x="885" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">80.90%</text><text x="885" y="140" transform="scale(.1)" fill="#fff" textLength="430">80.90%</text></g></svg>
\ No newline at end of file
diff --git a/coverage/function_index.html b/coverage/function_index.html
index 97ea49f..8a769a4 100644
--- a/coverage/function_index.html
+++ b/coverage/function_index.html
@@ -55,7 +55,7 @@ <h2>
         </h2>
         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </header>
@@ -907,10 +907,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html#t81">biobb_structure_utils/utils/cat_pdb.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html#t81"><data value='launch'>CatPDB.launch</data></a></td>
-                <td>27</td>
+                <td>26</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="26 27">96%</td>
+                <td class="right" data-ratio="25 26">96%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html#t142">biobb_structure_utils/utils/cat_pdb.py</a></td>
@@ -921,8 +921,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html#t161">biobb_structure_utils/utils/cat_pdb.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html#t161"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html#t163">biobb_structure_utils/utils/cat_pdb.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html#t163"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -947,10 +947,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html#t98">biobb_structure_utils/utils/closest_residues.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html#t98"><data value='launch'>ClosestResidues.launch</data></a></td>
-                <td>49</td>
+                <td>48</td>
                 <td>7</td>
                 <td>0</td>
-                <td class="right" data-ratio="42 49">86%</td>
+                <td class="right" data-ratio="41 48">85%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html#t219">biobb_structure_utils/utils/closest_residues.py</a></td>
@@ -961,8 +961,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html#t236">biobb_structure_utils/utils/closest_residues.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html#t236"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html#t238">biobb_structure_utils/utils/closest_residues.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html#t238"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1099,10 +1099,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html#t80">biobb_structure_utils/utils/extract_atoms.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html#t80"><data value='launch'>ExtractAtoms.launch</data></a></td>
-                <td>33</td>
+                <td>32</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="29 33">88%</td>
+                <td class="right" data-ratio="28 32">88%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html#t165">biobb_structure_utils/utils/extract_atoms.py</a></td>
@@ -1113,8 +1113,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html#t182">biobb_structure_utils/utils/extract_atoms.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html#t182"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html#t184">biobb_structure_utils/utils/extract_atoms.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html#t184"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1139,10 +1139,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html#t86">biobb_structure_utils/utils/extract_chain.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html#t86"><data value='launch'>ExtractChain.launch</data></a></td>
-                <td>23</td>
+                <td>22</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="19 23">83%</td>
+                <td class="right" data-ratio="18 22">82%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html#t162">biobb_structure_utils/utils/extract_chain.py</a></td>
@@ -1161,8 +1161,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html#t195">biobb_structure_utils/utils/extract_chain.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html#t195"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html#t197">biobb_structure_utils/utils/extract_chain.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html#t197"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1187,10 +1187,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html#t94">biobb_structure_utils/utils/extract_heteroatoms.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html#t94"><data value='launch'>ExtractHeteroAtoms.launch</data></a></td>
-                <td>34</td>
+                <td>33</td>
                 <td>7</td>
                 <td>0</td>
-                <td class="right" data-ratio="27 34">79%</td>
+                <td class="right" data-ratio="26 33">79%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html#t181">biobb_structure_utils/utils/extract_heteroatoms.py</a></td>
@@ -1201,8 +1201,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html#t198">biobb_structure_utils/utils/extract_heteroatoms.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html#t198"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html#t200">biobb_structure_utils/utils/extract_heteroatoms.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html#t200"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1233,24 +1233,24 @@ <h2>
                 <td class="right" data-ratio="27 30">90%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t161">biobb_structure_utils/utils/extract_model.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t161"><data value='check_format_models'>check_format_models</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t162">biobb_structure_utils/utils/extract_model.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t162"><data value='check_format_models'>check_format_models</data></a></td>
                 <td>7</td>
                 <td>4</td>
                 <td>0</td>
                 <td class="right" data-ratio="3 7">43%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t177">biobb_structure_utils/utils/extract_model.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t177"><data value='extract_model'>extract_model</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t178">biobb_structure_utils/utils/extract_model.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t178"><data value='extract_model'>extract_model</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t194">biobb_structure_utils/utils/extract_model.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t194"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t197">biobb_structure_utils/utils/extract_model.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html#t197"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1289,16 +1289,16 @@ <h2>
                 <td class="right" data-ratio="14 15">93%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_molecule_py.html#t157">biobb_structure_utils/utils/extract_molecule.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_molecule_py.html#t157"><data value='extract_molecule'>extract_molecule</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_molecule_py.html#t160">biobb_structure_utils/utils/extract_molecule.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_molecule_py.html#t160"><data value='extract_molecule'>extract_molecule</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_molecule_py.html#t174">biobb_structure_utils/utils/extract_molecule.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_molecule_py.html#t174"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_molecule_py.html#t179">biobb_structure_utils/utils/extract_molecule.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_molecule_py.html#t179"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1323,10 +1323,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html#t92">biobb_structure_utils/utils/extract_residues.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html#t92"><data value='launch'>ExtractResidues.launch</data></a></td>
-                <td>30</td>
+                <td>29</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="26 30">87%</td>
+                <td class="right" data-ratio="25 29">86%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html#t168">biobb_structure_utils/utils/extract_residues.py</a></td>
@@ -1337,8 +1337,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html#t185">biobb_structure_utils/utils/extract_residues.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html#t185"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html#t187">biobb_structure_utils/utils/extract_residues.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html#t187"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1363,10 +1363,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html#t76">biobb_structure_utils/utils/remove_ligand.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html#t76"><data value='launch'>RemoveLigand.launch</data></a></td>
-                <td>22</td>
+                <td>21</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="21 22">95%</td>
+                <td class="right" data-ratio="20 21">95%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html#t133">biobb_structure_utils/utils/remove_ligand.py</a></td>
@@ -1377,8 +1377,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html#t150">biobb_structure_utils/utils/remove_ligand.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html#t150"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html#t152">biobb_structure_utils/utils/remove_ligand.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html#t152"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1403,10 +1403,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html#t92">biobb_structure_utils/utils/remove_molecules.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html#t92"><data value='launch'>RemoveMolecules.launch</data></a></td>
-                <td>33</td>
+                <td>32</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="29 33">88%</td>
+                <td class="right" data-ratio="28 32">88%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html#t173">biobb_structure_utils/utils/remove_molecules.py</a></td>
@@ -1417,8 +1417,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html#t190">biobb_structure_utils/utils/remove_molecules.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html#t190"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html#t192">biobb_structure_utils/utils/remove_molecules.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html#t192"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1443,10 +1443,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html#t71">biobb_structure_utils/utils/remove_pdb_water.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html#t71"><data value='launch'>RemovePdbWater.launch</data></a></td>
-                <td>10</td>
+                <td>9</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="9 10">90%</td>
+                <td class="right" data-ratio="8 9">89%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html#t106">biobb_structure_utils/utils/remove_pdb_water.py</a></td>
@@ -1457,8 +1457,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html#t123">biobb_structure_utils/utils/remove_pdb_water.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html#t123"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html#t125">biobb_structure_utils/utils/remove_pdb_water.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html#t125"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1483,10 +1483,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html#t102">biobb_structure_utils/utils/renumber_structure.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html#t102"><data value='launch'>RenumberStructure.launch</data></a></td>
-                <td>44</td>
+                <td>43</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="43 44">98%</td>
+                <td class="right" data-ratio="42 43">98%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html#t188">biobb_structure_utils/utils/renumber_structure.py</a></td>
@@ -1497,8 +1497,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html#t207">biobb_structure_utils/utils/renumber_structure.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html#t207"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html#t209">biobb_structure_utils/utils/renumber_structure.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html#t209"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -1523,10 +1523,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html#t77">biobb_structure_utils/utils/sort_gro_residues.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html#t77"><data value='launch'>SortGroResidues.launch</data></a></td>
-                <td>13</td>
+                <td>12</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="12 13">92%</td>
+                <td class="right" data-ratio="11 12">92%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html#t105">biobb_structure_utils/utils/sort_gro_residues.py</a></td>
@@ -1537,8 +1537,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html#t122">biobb_structure_utils/utils/sort_gro_residues.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html#t122"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html#t124">biobb_structure_utils/utils/sort_gro_residues.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html#t124"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1563,10 +1563,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html#t91">biobb_structure_utils/utils/str_check_add_hydrogens.py</a></td>
                 <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html#t91"><data value='launch'>StrCheckAddHydrogens.launch</data></a></td>
-                <td>27</td>
+                <td>26</td>
                 <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="23 27">85%</td>
+                <td class="right" data-ratio="22 26">85%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html#t156">biobb_structure_utils/utils/str_check_add_hydrogens.py</a></td>
@@ -1577,8 +1577,8 @@ <h2>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html#t173">biobb_structure_utils/utils/str_check_add_hydrogens.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html#t173"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html#t175">biobb_structure_utils/utils/str_check_add_hydrogens.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html#t175"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1609,16 +1609,16 @@ <h2>
                 <td class="right" data-ratio="20 23">87%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_structure_check_py.html#t162">biobb_structure_utils/utils/structure_check.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_structure_check_py.html#t162"><data value='structure_check'>structure_check</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_structure_check_py.html#t165">biobb_structure_utils/utils/structure_check.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_structure_check_py.html#t165"><data value='structure_check'>structure_check</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_cc8067c15db60eec_structure_check_py.html#t179">biobb_structure_utils/utils/structure_check.py</a></td>
-                <td class="name left"><a href="z_cc8067c15db60eec_structure_check_py.html#t179"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_structure_check_py.html#t184">biobb_structure_utils/utils/structure_check.py</a></td>
+                <td class="name left"><a href="z_cc8067c15db60eec_structure_check_py.html#t184"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1637,10 +1637,10 @@ <h2>
             <tr class="total">
                 <td class="name left">Total</td>
                 <td class="name left">&nbsp;</td>
-                <td>1567</td>
+                <td>1555</td>
                 <td>297</td>
                 <td>0</td>
-                <td class="right" data-ratio="1270 1567">81%</td>
+                <td class="right" data-ratio="1258 1555">81%</td>
             </tr>
         </tfoot>
     </table>
@@ -1652,7 +1652,7 @@ <h2>
     <div class="content">
         <p>
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/index.html b/coverage/index.html
index 9bc885c..0d3b8f1 100644
--- a/coverage/index.html
+++ b/coverage/index.html
@@ -54,7 +54,7 @@ <h2>
         </h2>
         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </header>
@@ -247,17 +247,17 @@ <h2>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_cat_pdb_py.html">biobb_structure_utils/utils/cat_pdb.py</a></td>
-                <td>59</td>
+                <td>58</td>
                 <td>12</td>
                 <td>0</td>
-                <td class="right" data-ratio="47 59">80%</td>
+                <td class="right" data-ratio="46 58">79%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_closest_residues_py.html">biobb_structure_utils/utils/closest_residues.py</a></td>
-                <td>85</td>
+                <td>84</td>
                 <td>17</td>
                 <td>0</td>
-                <td class="right" data-ratio="68 85">80%</td>
+                <td class="right" data-ratio="67 84">80%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_common_py.html">biobb_structure_utils/utils/common.py</a></td>
@@ -268,24 +268,24 @@ <h2>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_atoms_py.html">biobb_structure_utils/utils/extract_atoms.py</a></td>
-                <td>68</td>
+                <td>67</td>
                 <td>14</td>
                 <td>0</td>
-                <td class="right" data-ratio="54 68">79%</td>
+                <td class="right" data-ratio="53 67">79%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_chain_py.html">biobb_structure_utils/utils/extract_chain.py</a></td>
-                <td>67</td>
+                <td>66</td>
                 <td>18</td>
                 <td>0</td>
-                <td class="right" data-ratio="49 67">73%</td>
+                <td class="right" data-ratio="48 66">73%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_heteroatoms_py.html">biobb_structure_utils/utils/extract_heteroatoms.py</a></td>
-                <td>69</td>
+                <td>68</td>
                 <td>17</td>
                 <td>0</td>
-                <td class="right" data-ratio="52 69">75%</td>
+                <td class="right" data-ratio="51 68">75%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_model_py.html">biobb_structure_utils/utils/extract_model.py</a></td>
@@ -303,52 +303,52 @@ <h2>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_extract_residues_py.html">biobb_structure_utils/utils/extract_residues.py</a></td>
-                <td>64</td>
+                <td>63</td>
                 <td>14</td>
                 <td>0</td>
-                <td class="right" data-ratio="50 64">78%</td>
+                <td class="right" data-ratio="49 63">78%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_ligand_py.html">biobb_structure_utils/utils/remove_ligand.py</a></td>
-                <td>55</td>
+                <td>54</td>
                 <td>11</td>
                 <td>0</td>
-                <td class="right" data-ratio="44 55">80%</td>
+                <td class="right" data-ratio="43 54">80%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_molecules_py.html">biobb_structure_utils/utils/remove_molecules.py</a></td>
-                <td>67</td>
+                <td>66</td>
                 <td>14</td>
                 <td>0</td>
-                <td class="right" data-ratio="53 67">79%</td>
+                <td class="right" data-ratio="52 66">79%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_remove_pdb_water_py.html">biobb_structure_utils/utils/remove_pdb_water.py</a></td>
-                <td>40</td>
+                <td>39</td>
                 <td>11</td>
                 <td>0</td>
-                <td class="right" data-ratio="29 40">72%</td>
+                <td class="right" data-ratio="28 39">72%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_renumber_structure_py.html">biobb_structure_utils/utils/renumber_structure.py</a></td>
-                <td>88</td>
+                <td>87</td>
                 <td>12</td>
                 <td>0</td>
-                <td class="right" data-ratio="76 88">86%</td>
+                <td class="right" data-ratio="75 87">86%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_sort_gro_residues_py.html">biobb_structure_utils/utils/sort_gro_residues.py</a></td>
-                <td>45</td>
+                <td>44</td>
                 <td>11</td>
                 <td>0</td>
-                <td class="right" data-ratio="34 45">76%</td>
+                <td class="right" data-ratio="33 44">75%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html">biobb_structure_utils/utils/str_check_add_hydrogens.py</a></td>
-                <td>64</td>
+                <td>63</td>
                 <td>14</td>
                 <td>0</td>
-                <td class="right" data-ratio="50 64">78%</td>
+                <td class="right" data-ratio="49 63">78%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_cc8067c15db60eec_structure_check_py.html">biobb_structure_utils/utils/structure_check.py</a></td>
@@ -361,10 +361,10 @@ <h2>
         <tfoot>
             <tr class="total">
                 <td class="name left">Total</td>
-                <td>1567</td>
+                <td>1555</td>
                 <td>297</td>
                 <td>0</td>
-                <td class="right" data-ratio="1270 1567">81%</td>
+                <td class="right" data-ratio="1258 1555">81%</td>
             </tr>
         </tfoot>
     </table>
@@ -376,7 +376,7 @@ <h2>
     <div class="content">
         <p>
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/status.json b/coverage/status.json
index 17199ac..82de230 100644
--- a/coverage/status.json
+++ b/coverage/status.json
@@ -1 +1 @@
-{"note":"This file is an internal implementation detail to speed up HTML report generation. Its format can change at any time. You might be looking for the JSON report: https://coverage.rtfd.io/cmd.html#cmd-json","format":5,"version":"7.6.10","globals":"e77daffb6a1adf4e2a408ba7bbc4078b","files":{"z_d361e47ffa394ddf___init___py":{"hash":"bbb434a53af0936b5519bd8e80739ce4","index":{"url":"z_d361e47ffa394ddf___init___py.html","file":"biobb_structure_utils/__init__.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":4,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_8572508eb5b65ee1___init___py":{"hash":"3c77fc9ef7f887ac2508d4109cf92472","index":{"url":"z_8572508eb5b65ee1___init___py.html","file":"biobb_structure_utils/gro_lib/__init__.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":0,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_8572508eb5b65ee1_gro_py":{"hash":"e64d25d5c4f786ba9fc3151971d1c8a4","index":{"url":"z_8572508eb5b65ee1_gro_py.html","file":"biobb_structure_utils/gro_lib/gro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":210,"n_excluded":0,"n_missing":59,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_7351d3e0b972d178___init___py":{"hash":"3c77fc9ef7f887ac2508d4109cf92472","index":{"url":"z_7351d3e0b972d178___init___py.html","file":"biobb_structure_utils/test/__init__.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":0,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_cat_pdb_py":{"hash":"f6e5e1b9bf7807dca5c8db21d176f251","index":{"url":"z_604d40b87fe2aefd_test_cat_pdb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_closest_residues_py":{"hash":"72d75f5b92868ee20ff5ef58c070ba9b","index":{"url":"z_604d40b87fe2aefd_test_closest_residues_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_atoms_gro_py":{"hash":"24cfe88fe653d9588ccee5e376fae6cd","index":{"url":"z_604d40b87fe2aefd_test_extract_atoms_gro_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_atoms_pdb_py":{"hash":"d8e5800ef6ca912a9a5379971515d455","index":{"url":"z_604d40b87fe2aefd_test_extract_atoms_pdb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_chain_py":{"hash":"18d14d83228c6f29b06db74844c2c820","index":{"url":"z_604d40b87fe2aefd_test_extract_chain_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_heteroatom_py":{"hash":"0f255f73903b6826e278f61d628a940d","index":{"url":"z_604d40b87fe2aefd_test_extract_heteroatom_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_model_py":{"hash":"f68693834fb993e1677c773cf716fd2c","index":{"url":"z_604d40b87fe2aefd_test_extract_model_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_model.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":11,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_molecule_py":{"hash":"9913cc3cb92a75eb7bc3f22870b4fda4","index":{"url":"z_604d40b87fe2aefd_test_extract_molecule_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_residues_py":{"hash":"b787950331d262852b90caa67928d484","index":{"url":"z_604d40b87fe2aefd_test_extract_residues_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_remove_ligand_gro_py":{"hash":"c1fcf506a3b4ec819167a6a12acb2d09","index":{"url":"z_604d40b87fe2aefd_test_remove_ligand_gro_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_remove_ligand_pdb_py":{"hash":"8f0e0700bb0fc2640ceeffcff9d37b37","index":{"url":"z_604d40b87fe2aefd_test_remove_ligand_pdb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_remove_molecules_py":{"hash":"50ffcc2ec232f76db162988d30976f55","index":{"url":"z_604d40b87fe2aefd_test_remove_molecules_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_remove_pdb_water_py":{"hash":"bd685baef096c697999a0fee99fe13f9","index":{"url":"z_604d40b87fe2aefd_test_remove_pdb_water_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_renumber_structure_2vgb_py":{"hash":"b1ce74ebb39495cf2a66fd9e0eb8842d","index":{"url":"z_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":14,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_renumber_structure_gro_py":{"hash":"cd4aa81654cac6bce494afea988dc701","index":{"url":"z_604d40b87fe2aefd_test_renumber_structure_gro_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":14,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_renumber_structure_pdb_py":{"hash":"b795c07101608d0be342460b7f8ee335","index":{"url":"z_604d40b87fe2aefd_test_renumber_structure_pdb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":14,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_renumber_structure_smallgro_py":{"hash":"ceeca096df87221ff57223d12711013b","index":{"url":"z_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":14,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_sort_gro_residues_py":{"hash":"5859875acc97991a4419ed7c9b311d0a","index":{"url":"z_604d40b87fe2aefd_test_sort_gro_residues_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_str_check_add_hydrogens_py":{"hash":"0af9519e96045fd7c2b26dda66880141","index":{"url":"z_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":11,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_structure_check_py":{"hash":"a177b137ed88bdb54a104e9fc4701d96","index":{"url":"z_604d40b87fe2aefd_test_structure_check_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_structure_check.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":11,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec___init___py":{"hash":"59a5b99feea8c100bedf5aebe6e3facf","index":{"url":"z_cc8067c15db60eec___init___py.html","file":"biobb_structure_utils/utils/__init__.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":3,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_cat_pdb_py":{"hash":"c433606dfd73a3ab492aa520ebd52e44","index":{"url":"z_cc8067c15db60eec_cat_pdb_py.html","file":"biobb_structure_utils/utils/cat_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":59,"n_excluded":0,"n_missing":12,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_closest_residues_py":{"hash":"209b86e051f13096ac9745a6c0962a97","index":{"url":"z_cc8067c15db60eec_closest_residues_py.html","file":"biobb_structure_utils/utils/closest_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":85,"n_excluded":0,"n_missing":17,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_common_py":{"hash":"7829216979db7fcf586abe254464009f","index":{"url":"z_cc8067c15db60eec_common_py.html","file":"biobb_structure_utils/utils/common.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":144,"n_excluded":0,"n_missing":29,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_atoms_py":{"hash":"275608a289be6067508bdf9506cd5e03","index":{"url":"z_cc8067c15db60eec_extract_atoms_py.html","file":"biobb_structure_utils/utils/extract_atoms.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":68,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_chain_py":{"hash":"89eeefa137865ee203776afcbefa40d8","index":{"url":"z_cc8067c15db60eec_extract_chain_py.html","file":"biobb_structure_utils/utils/extract_chain.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":67,"n_excluded":0,"n_missing":18,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_heteroatoms_py":{"hash":"b991f99e289f430c171c230a69f71f39","index":{"url":"z_cc8067c15db60eec_extract_heteroatoms_py.html","file":"biobb_structure_utils/utils/extract_heteroatoms.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":69,"n_excluded":0,"n_missing":17,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_model_py":{"hash":"d54b20631322f295b7a045030db1d080","index":{"url":"z_cc8067c15db60eec_extract_model_py.html","file":"biobb_structure_utils/utils/extract_model.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":73,"n_excluded":0,"n_missing":17,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_molecule_py":{"hash":"966a1dbcd39d5eccb2c2aa8cc5a33bef","index":{"url":"z_cc8067c15db60eec_extract_molecule_py.html","file":"biobb_structure_utils/utils/extract_molecule.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":60,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_residues_py":{"hash":"b1638c16a7d94c5614b7a7f6dcaeb0b7","index":{"url":"z_cc8067c15db60eec_extract_residues_py.html","file":"biobb_structure_utils/utils/extract_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":64,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_remove_ligand_py":{"hash":"fdd3ffdf9cd22f47a3558f30e70b9c26","index":{"url":"z_cc8067c15db60eec_remove_ligand_py.html","file":"biobb_structure_utils/utils/remove_ligand.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":55,"n_excluded":0,"n_missing":11,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_remove_molecules_py":{"hash":"39fa089f5dc4fbba79c93eaf3f38fa4c","index":{"url":"z_cc8067c15db60eec_remove_molecules_py.html","file":"biobb_structure_utils/utils/remove_molecules.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":67,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_remove_pdb_water_py":{"hash":"150f9280724fd18380c8a10d47cd58e9","index":{"url":"z_cc8067c15db60eec_remove_pdb_water_py.html","file":"biobb_structure_utils/utils/remove_pdb_water.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":40,"n_excluded":0,"n_missing":11,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_renumber_structure_py":{"hash":"d5755576f6bd06dc9a5f73384bf9045d","index":{"url":"z_cc8067c15db60eec_renumber_structure_py.html","file":"biobb_structure_utils/utils/renumber_structure.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":88,"n_excluded":0,"n_missing":12,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_sort_gro_residues_py":{"hash":"b72a366ec206524a4ee12926dffc1acf","index":{"url":"z_cc8067c15db60eec_sort_gro_residues_py.html","file":"biobb_structure_utils/utils/sort_gro_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":45,"n_excluded":0,"n_missing":11,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_str_check_add_hydrogens_py":{"hash":"78bd7710248f1add39c45de510aa5035","index":{"url":"z_cc8067c15db60eec_str_check_add_hydrogens_py.html","file":"biobb_structure_utils/utils/str_check_add_hydrogens.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":64,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_structure_check_py":{"hash":"f6966ee14c1b712d6438ab967e9ffc0f","index":{"url":"z_cc8067c15db60eec_structure_check_py.html","file":"biobb_structure_utils/utils/structure_check.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":57,"n_excluded":0,"n_missing":13,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}}}}
\ No newline at end of file
+{"note":"This file is an internal implementation detail to speed up HTML report generation. Its format can change at any time. You might be looking for the JSON report: https://coverage.rtfd.io/cmd.html#cmd-json","format":5,"version":"7.6.10","globals":"3a6fa0235d5eb679a9e1fd7b3b9a8538","files":{"z_d361e47ffa394ddf___init___py":{"hash":"bbb434a53af0936b5519bd8e80739ce4","index":{"url":"z_d361e47ffa394ddf___init___py.html","file":"biobb_structure_utils/__init__.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":4,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_8572508eb5b65ee1___init___py":{"hash":"3c77fc9ef7f887ac2508d4109cf92472","index":{"url":"z_8572508eb5b65ee1___init___py.html","file":"biobb_structure_utils/gro_lib/__init__.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":0,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_8572508eb5b65ee1_gro_py":{"hash":"27132cb4255ad4aed746f9fa325746a8","index":{"url":"z_8572508eb5b65ee1_gro_py.html","file":"biobb_structure_utils/gro_lib/gro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":210,"n_excluded":0,"n_missing":59,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_7351d3e0b972d178___init___py":{"hash":"3c77fc9ef7f887ac2508d4109cf92472","index":{"url":"z_7351d3e0b972d178___init___py.html","file":"biobb_structure_utils/test/__init__.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":0,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_cat_pdb_py":{"hash":"f6e5e1b9bf7807dca5c8db21d176f251","index":{"url":"z_604d40b87fe2aefd_test_cat_pdb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_closest_residues_py":{"hash":"72d75f5b92868ee20ff5ef58c070ba9b","index":{"url":"z_604d40b87fe2aefd_test_closest_residues_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_atoms_gro_py":{"hash":"24cfe88fe653d9588ccee5e376fae6cd","index":{"url":"z_604d40b87fe2aefd_test_extract_atoms_gro_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_atoms_pdb_py":{"hash":"d8e5800ef6ca912a9a5379971515d455","index":{"url":"z_604d40b87fe2aefd_test_extract_atoms_pdb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_chain_py":{"hash":"18d14d83228c6f29b06db74844c2c820","index":{"url":"z_604d40b87fe2aefd_test_extract_chain_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_heteroatom_py":{"hash":"0f255f73903b6826e278f61d628a940d","index":{"url":"z_604d40b87fe2aefd_test_extract_heteroatom_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_model_py":{"hash":"f68693834fb993e1677c773cf716fd2c","index":{"url":"z_604d40b87fe2aefd_test_extract_model_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_model.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":11,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_molecule_py":{"hash":"9913cc3cb92a75eb7bc3f22870b4fda4","index":{"url":"z_604d40b87fe2aefd_test_extract_molecule_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_extract_residues_py":{"hash":"b787950331d262852b90caa67928d484","index":{"url":"z_604d40b87fe2aefd_test_extract_residues_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_remove_ligand_gro_py":{"hash":"c1fcf506a3b4ec819167a6a12acb2d09","index":{"url":"z_604d40b87fe2aefd_test_remove_ligand_gro_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_remove_ligand_pdb_py":{"hash":"8f0e0700bb0fc2640ceeffcff9d37b37","index":{"url":"z_604d40b87fe2aefd_test_remove_ligand_pdb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_remove_molecules_py":{"hash":"50ffcc2ec232f76db162988d30976f55","index":{"url":"z_604d40b87fe2aefd_test_remove_molecules_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_remove_pdb_water_py":{"hash":"bd685baef096c697999a0fee99fe13f9","index":{"url":"z_604d40b87fe2aefd_test_remove_pdb_water_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_renumber_structure_2vgb_py":{"hash":"b1ce74ebb39495cf2a66fd9e0eb8842d","index":{"url":"z_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":14,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_renumber_structure_gro_py":{"hash":"cd4aa81654cac6bce494afea988dc701","index":{"url":"z_604d40b87fe2aefd_test_renumber_structure_gro_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":14,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_renumber_structure_pdb_py":{"hash":"b795c07101608d0be342460b7f8ee335","index":{"url":"z_604d40b87fe2aefd_test_renumber_structure_pdb_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":14,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_renumber_structure_smallgro_py":{"hash":"ceeca096df87221ff57223d12711013b","index":{"url":"z_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":14,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_sort_gro_residues_py":{"hash":"5859875acc97991a4419ed7c9b311d0a","index":{"url":"z_604d40b87fe2aefd_test_sort_gro_residues_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":12,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_str_check_add_hydrogens_py":{"hash":"0af9519e96045fd7c2b26dda66880141","index":{"url":"z_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":11,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_604d40b87fe2aefd_test_structure_check_py":{"hash":"a177b137ed88bdb54a104e9fc4701d96","index":{"url":"z_604d40b87fe2aefd_test_structure_check_py.html","file":"biobb_structure_utils/test/unitests/test_utils/test_structure_check.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":11,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec___init___py":{"hash":"59a5b99feea8c100bedf5aebe6e3facf","index":{"url":"z_cc8067c15db60eec___init___py.html","file":"biobb_structure_utils/utils/__init__.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":3,"n_excluded":0,"n_missing":0,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_cat_pdb_py":{"hash":"5355fcfc83fc478e3da9019b2d355e0e","index":{"url":"z_cc8067c15db60eec_cat_pdb_py.html","file":"biobb_structure_utils/utils/cat_pdb.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":58,"n_excluded":0,"n_missing":12,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_closest_residues_py":{"hash":"b6f3a6e1b665ada610e704a4b6a8c0d1","index":{"url":"z_cc8067c15db60eec_closest_residues_py.html","file":"biobb_structure_utils/utils/closest_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":84,"n_excluded":0,"n_missing":17,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_common_py":{"hash":"87652301cde6243bbfed80f95734411f","index":{"url":"z_cc8067c15db60eec_common_py.html","file":"biobb_structure_utils/utils/common.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":144,"n_excluded":0,"n_missing":29,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_atoms_py":{"hash":"fd666b613b299c5d027f26c25d46e258","index":{"url":"z_cc8067c15db60eec_extract_atoms_py.html","file":"biobb_structure_utils/utils/extract_atoms.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":67,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_chain_py":{"hash":"0a86445c0b62e478914db198a022f4d5","index":{"url":"z_cc8067c15db60eec_extract_chain_py.html","file":"biobb_structure_utils/utils/extract_chain.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":66,"n_excluded":0,"n_missing":18,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_heteroatoms_py":{"hash":"702a843bfe1341b14a2768df7cd1212b","index":{"url":"z_cc8067c15db60eec_extract_heteroatoms_py.html","file":"biobb_structure_utils/utils/extract_heteroatoms.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":68,"n_excluded":0,"n_missing":17,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_model_py":{"hash":"f6166b410947370acbbfa51abe29a35c","index":{"url":"z_cc8067c15db60eec_extract_model_py.html","file":"biobb_structure_utils/utils/extract_model.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":73,"n_excluded":0,"n_missing":17,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_molecule_py":{"hash":"64539d799c4375febe256df369a15f2b","index":{"url":"z_cc8067c15db60eec_extract_molecule_py.html","file":"biobb_structure_utils/utils/extract_molecule.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":60,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_extract_residues_py":{"hash":"47e37429168517f845bcb77f750d2d02","index":{"url":"z_cc8067c15db60eec_extract_residues_py.html","file":"biobb_structure_utils/utils/extract_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":63,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_remove_ligand_py":{"hash":"18a286dd251fd3a1e12ea80f6105e6cb","index":{"url":"z_cc8067c15db60eec_remove_ligand_py.html","file":"biobb_structure_utils/utils/remove_ligand.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":54,"n_excluded":0,"n_missing":11,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_remove_molecules_py":{"hash":"282e2afe95fda15444d3e33547d5f47a","index":{"url":"z_cc8067c15db60eec_remove_molecules_py.html","file":"biobb_structure_utils/utils/remove_molecules.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":66,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_remove_pdb_water_py":{"hash":"303adcb3e79f5e9557917b942a0de6c5","index":{"url":"z_cc8067c15db60eec_remove_pdb_water_py.html","file":"biobb_structure_utils/utils/remove_pdb_water.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":39,"n_excluded":0,"n_missing":11,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_renumber_structure_py":{"hash":"2987292bc6fe39e13842bba02e137c83","index":{"url":"z_cc8067c15db60eec_renumber_structure_py.html","file":"biobb_structure_utils/utils/renumber_structure.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":87,"n_excluded":0,"n_missing":12,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_sort_gro_residues_py":{"hash":"d0b87f82282b9e297f1f116bed14f225","index":{"url":"z_cc8067c15db60eec_sort_gro_residues_py.html","file":"biobb_structure_utils/utils/sort_gro_residues.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":44,"n_excluded":0,"n_missing":11,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_str_check_add_hydrogens_py":{"hash":"7ec063ebe6395c907c438378ea50e58d","index":{"url":"z_cc8067c15db60eec_str_check_add_hydrogens_py.html","file":"biobb_structure_utils/utils/str_check_add_hydrogens.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":63,"n_excluded":0,"n_missing":14,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}},"z_cc8067c15db60eec_structure_check_py":{"hash":"c265bab819a266a39bec0880eea726cc","index":{"url":"z_cc8067c15db60eec_structure_check_py.html","file":"biobb_structure_utils/utils/structure_check.py","description":"","nums":{"precision":0,"n_files":1,"n_statements":57,"n_excluded":0,"n_missing":13,"n_branches":0,"n_partial_branches":0,"n_missing_branches":0}}}}}
\ No newline at end of file
diff --git a/coverage/z_604d40b87fe2aefd_test_cat_pdb_py.html b/coverage/z_604d40b87fe2aefd_test_cat_pdb_py.html
index d98ad0e..d3643c9 100644
--- a/coverage/z_604d40b87fe2aefd_test_cat_pdb_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_cat_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_closest_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_closest_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_closest_residues_py.html b/coverage/z_604d40b87fe2aefd_test_closest_residues_py.html
index 326f2f6..0227d88 100644
--- a/coverage/z_604d40b87fe2aefd_test_closest_residues_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_closest_residues_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_extract_atoms_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_extract_atoms_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_extract_atoms_gro_py.html b/coverage/z_604d40b87fe2aefd_test_extract_atoms_gro_py.html
index 66e7dc1..388d6cc 100644
--- a/coverage/z_604d40b87fe2aefd_test_extract_atoms_gro_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_extract_atoms_gro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_extract_atoms_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_extract_atoms_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_extract_atoms_pdb_py.html b/coverage/z_604d40b87fe2aefd_test_extract_atoms_pdb_py.html
index 4872f07..0943805 100644
--- a/coverage/z_604d40b87fe2aefd_test_extract_atoms_pdb_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_extract_atoms_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_extract_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_extract_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_extract_chain_py.html b/coverage/z_604d40b87fe2aefd_test_extract_chain_py.html
index 9537050..a704e7e 100644
--- a/coverage/z_604d40b87fe2aefd_test_extract_chain_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_extract_chain_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_extract_heteroatom_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_extract_heteroatom_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_extract_heteroatom_py.html b/coverage/z_604d40b87fe2aefd_test_extract_heteroatom_py.html
index c525936..efd674d 100644
--- a/coverage/z_604d40b87fe2aefd_test_extract_heteroatom_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_extract_heteroatom_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_extract_model_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_extract_model_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_extract_model_py.html b/coverage/z_604d40b87fe2aefd_test_extract_model_py.html
index 3926bc1..3ecf54c 100644
--- a/coverage/z_604d40b87fe2aefd_test_extract_model_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_extract_model_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_extract_molecule_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_extract_molecule_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_extract_molecule_py.html b/coverage/z_604d40b87fe2aefd_test_extract_molecule_py.html
index c3a96a7..6f66cfb 100644
--- a/coverage/z_604d40b87fe2aefd_test_extract_molecule_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_extract_molecule_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_extract_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_extract_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_extract_residues_py.html b/coverage/z_604d40b87fe2aefd_test_extract_residues_py.html
index 627c6d3..ab9894a 100644
--- a/coverage/z_604d40b87fe2aefd_test_extract_residues_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_extract_residues_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_remove_ligand_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_remove_ligand_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_remove_ligand_gro_py.html b/coverage/z_604d40b87fe2aefd_test_remove_ligand_gro_py.html
index 0eafd74..19c49e1 100644
--- a/coverage/z_604d40b87fe2aefd_test_remove_ligand_gro_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_remove_ligand_gro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_remove_ligand_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_remove_ligand_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_remove_ligand_pdb_py.html b/coverage/z_604d40b87fe2aefd_test_remove_ligand_pdb_py.html
index 3c67139..4c6b642 100644
--- a/coverage/z_604d40b87fe2aefd_test_remove_ligand_pdb_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_remove_ligand_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_remove_molecules_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_remove_molecules_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_remove_molecules_py.html b/coverage/z_604d40b87fe2aefd_test_remove_molecules_py.html
index 43a7f24..a273ee4 100644
--- a/coverage/z_604d40b87fe2aefd_test_remove_molecules_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_remove_molecules_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_remove_pdb_water_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_remove_pdb_water_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_remove_pdb_water_py.html b/coverage/z_604d40b87fe2aefd_test_remove_pdb_water_py.html
index 4fd3ff5..a76a4c7 100644
--- a/coverage/z_604d40b87fe2aefd_test_remove_pdb_water_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_remove_pdb_water_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html b/coverage/z_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html
index f987e5a..202a6c8 100644
--- a/coverage/z_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_renumber_structure_2vgb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_renumber_structure_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -108,7 +108,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_renumber_structure_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_renumber_structure_gro_py.html b/coverage/z_604d40b87fe2aefd_test_renumber_structure_gro_py.html
index 2bc4d53..3b1d735 100644
--- a/coverage/z_604d40b87fe2aefd_test_renumber_structure_gro_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_renumber_structure_gro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_renumber_structure_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -108,7 +108,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_renumber_structure_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_renumber_structure_pdb_py.html b/coverage/z_604d40b87fe2aefd_test_renumber_structure_pdb_py.html
index f8a0ffe..dfc40e0 100644
--- a/coverage/z_604d40b87fe2aefd_test_renumber_structure_pdb_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_renumber_structure_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -108,7 +108,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html b/coverage/z_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html
index fbccfa5..9f206dd 100644
--- a/coverage/z_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_renumber_structure_smallgro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_sort_gro_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -108,7 +108,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_sort_gro_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_sort_gro_residues_py.html b/coverage/z_604d40b87fe2aefd_test_sort_gro_residues_py.html
index 66d60d3..edb0b94 100644
--- a/coverage/z_604d40b87fe2aefd_test_sort_gro_residues_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_sort_gro_residues_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html b/coverage/z_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html
index 05fe8d8..c04811e 100644
--- a/coverage/z_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_str_check_add_hydrogens_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_structure_check_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_structure_check_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_604d40b87fe2aefd_test_structure_check_py.html b/coverage/z_604d40b87fe2aefd_test_structure_check_py.html
index ffbc6e5..f2ab912 100644
--- a/coverage/z_604d40b87fe2aefd_test_structure_check_py.html
+++ b/coverage/z_604d40b87fe2aefd_test_structure_check_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -105,7 +105,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_7351d3e0b972d178___init___py.html b/coverage/z_7351d3e0b972d178___init___py.html
index b8d6a5a..fb02a43 100644
--- a/coverage/z_7351d3e0b972d178___init___py.html
+++ b/coverage/z_7351d3e0b972d178___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_604d40b87fe2aefd_test_cat_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -89,7 +89,7 @@ <h2>
             <a class="nav" href="z_604d40b87fe2aefd_test_cat_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8572508eb5b65ee1___init___py.html b/coverage/z_8572508eb5b65ee1___init___py.html
index 130a2ea..3fef604 100644
--- a/coverage/z_8572508eb5b65ee1___init___py.html
+++ b/coverage/z_8572508eb5b65ee1___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8572508eb5b65ee1_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -89,7 +89,7 @@ <h2>
             <a class="nav" href="z_8572508eb5b65ee1_gro_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8572508eb5b65ee1_gro_py.html b/coverage/z_8572508eb5b65ee1_gro_py.html
index 8d5537d..0473c90 100644
--- a/coverage/z_8572508eb5b65ee1_gro_py.html
+++ b/coverage/z_8572508eb5b65ee1_gro_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_7351d3e0b972d178___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -488,7 +488,7 @@ <h2>
             <a class="nav" href="z_7351d3e0b972d178___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec___init___py.html b/coverage/z_cc8067c15db60eec___init___py.html
index 012acf9..7153161 100644
--- a/coverage/z_cc8067c15db60eec___init___py.html
+++ b/coverage/z_cc8067c15db60eec___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_cat_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -125,7 +125,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_cat_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_cat_pdb_py.html b/coverage/z_cc8067c15db60eec_cat_pdb_py.html
index a7625ef..1aef4d4 100644
--- a/coverage/z_cc8067c15db60eec_cat_pdb_py.html
+++ b/coverage/z_cc8067c15db60eec_cat_pdb_py.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-    <title>Coverage for biobb_structure_utils/utils/cat_pdb.py: 80%</title>
+    <title>Coverage for biobb_structure_utils/utils/cat_pdb.py: 79%</title>
     <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
     <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
     <script src="coverage_html_cb_6fb7b396.js" defer></script>
@@ -12,7 +12,7 @@
     <div class="content">
         <h1>
             <span class="text">Coverage for </span><b>biobb_structure_utils/utils/cat_pdb.py</b>:
-            <span class="pc_cov">80%</span>
+            <span class="pc_cov">79%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">59 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">47<span class="text"> run</span></button>
+            <span class="text">58 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">46<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">12<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_closest_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -213,7 +213,7 @@ <h2>
     <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -239,56 +239,58 @@ <h2>
     <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Concat two PDB structures in a single PDB file."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="str">"-i1"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="str">"--input_structure1"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure 1 file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="str">"-i2"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="str">"--input_structure2"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure 2 file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">cat_pdb</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">input_structure1</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">input_structure2</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure2</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">    <span class="nam">cat_pdb</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">CatPDB</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Concat two PDB structures in a single PDB file."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="str">"-i1"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="str">"--input_structure1"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure 1 file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="str">"-i2"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="str">"--input_structure2"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure 2 file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">cat_pdb</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">input_structure1</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">input_structure2</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure2</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -298,7 +300,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_closest_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_closest_residues_py.html b/coverage/z_cc8067c15db60eec_closest_residues_py.html
index 3787dd6..450f1c6 100644
--- a/coverage/z_cc8067c15db60eec_closest_residues_py.html
+++ b/coverage/z_cc8067c15db60eec_closest_residues_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">85 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">68<span class="text"> run</span></button>
+            <span class="text">84 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">67<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">17<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -290,7 +290,7 @@ <h2>
     <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -314,49 +314,51 @@ <h2>
     <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Search closest residues to a list of given residues."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="str">"--output_residues_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output residues file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">    <span class="nam">closest_residues</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">output_residues_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_residues_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="nam">closest_residues</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">ClosestResidues</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Search closest residues to a list of given residues."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="str">"--output_residues_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output residues file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">    <span class="nam">closest_residues</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">output_residues_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_residues_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -366,7 +368,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_common_py.html b/coverage/z_cc8067c15db60eec_common_py.html
index 629e360..76cbf5b 100644
--- a/coverage/z_cc8067c15db60eec_common_py.html
+++ b/coverage/z_cc8067c15db60eec_common_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_extract_atoms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -344,7 +344,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_extract_atoms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_extract_atoms_py.html b/coverage/z_cc8067c15db60eec_extract_atoms_py.html
index cab69cf..0ecd5f6 100644
--- a/coverage/z_cc8067c15db60eec_extract_atoms_py.html
+++ b/coverage/z_cc8067c15db60eec_extract_atoms_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">68 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">54<span class="text"> run</span></button>
+            <span class="text">67 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">53<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">14<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_extract_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -236,7 +236,7 @@ <h2>
     <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -260,46 +260,48 @@ <h2>
     <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Remove the selected ligand atoms from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_structure_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file name"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file name"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="nam">extract_atoms</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="nam">extract_atoms</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">ExtractAtoms</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Remove the selected ligand atoms from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_structure_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file name"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file name"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="nam">extract_atoms</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -309,7 +311,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_extract_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_extract_chain_py.html b/coverage/z_cc8067c15db60eec_extract_chain_py.html
index 704434e..6b5bfda 100644
--- a/coverage/z_cc8067c15db60eec_extract_chain_py.html
+++ b/coverage/z_cc8067c15db60eec_extract_chain_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">67 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">49<span class="text"> run</span></button>
+            <span class="text">66 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">48<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">18<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_extract_heteroatoms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -233,7 +233,7 @@ <h2>
     <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -273,49 +273,51 @@ <h2>
     <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a chain from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">extract_chain</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">    <span class="nam">extract_chain</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">ExtractChain</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a chain from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="nam">extract_chain</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -325,7 +327,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_extract_heteroatoms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_extract_heteroatoms_py.html b/coverage/z_cc8067c15db60eec_extract_heteroatoms_py.html
index f5f03a4..8964251 100644
--- a/coverage/z_cc8067c15db60eec_extract_heteroatoms_py.html
+++ b/coverage/z_cc8067c15db60eec_extract_heteroatoms_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">69 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">52<span class="text"> run</span></button>
+            <span class="text">68 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">51<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">17<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_extract_model_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -252,7 +252,7 @@ <h2>
     <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -276,49 +276,51 @@ <h2>
     <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a list of heteroatoms from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="str">"--output_heteroatom_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output heteroatom file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="nam">extract_heteroatoms</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">output_heteroatom_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_heteroatom_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="nam">extract_heteroatoms</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">ExtractHeteroAtoms</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a list of heteroatoms from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="str">"--output_heteroatom_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output heteroatom file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="nam">extract_heteroatoms</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">output_heteroatom_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_heteroatom_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -328,7 +330,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_extract_model_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_extract_model_py.html b/coverage/z_cc8067c15db60eec_extract_model_py.html
index bfae8fa..9293b47 100644
--- a/coverage/z_cc8067c15db60eec_extract_model_py.html
+++ b/coverage/z_cc8067c15db60eec_extract_model_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_extract_molecule_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -230,91 +230,94 @@ <h2>
     <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">                <span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">,</span> <span class="nam">tmp_folder</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">                <span class="com"># self.stage_io_dict.get("unique_dir", ""),</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t"><span class="key">def</span> <span class="nam">check_format_models</span><span class="op">(</span><span class="nam">models</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">    <span class="str">"""Check format of models list"""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">    <span class="key">if</span> <span class="key">not</span> <span class="nam">models</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">"Empty models parameter, all models will be returned."</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="key">return</span> <span class="str">"All"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">    <span class="key">if</span> <span class="key">not</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">models</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="str">"Incorrect format of models parameter, all models will be returned."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">out_log</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="key">return</span> <span class="str">"All"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">    <span class="key">return</span> <span class="nam">models</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t"><span class="key">def</span> <span class="nam">check_format_models</span><span class="op">(</span><span class="nam">models</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">    <span class="str">"""Check format of models list"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">    <span class="key">if</span> <span class="key">not</span> <span class="nam">models</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">"Empty models parameter, all models will be returned."</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="key">return</span> <span class="str">"All"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">    <span class="key">if</span> <span class="key">not</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">models</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="str">"Incorrect format of models parameter, all models will be returned."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">out_log</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="key">return</span> <span class="str">"All"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">    <span class="key">return</span> <span class="nam">models</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t"><span class="key">def</span> <span class="nam">extract_model</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">    <span class="nam">input_structure_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="nam">output_structure_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t"><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">    <span class="str">"""Execute the :class:`ExtractModel &lt;utils.extract_model.ExtractModel>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;utils.extract_model.ExtractModel.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="key">return</span> <span class="nam">ExtractModel</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t"><span class="key">def</span> <span class="nam">extract_model</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="nam">input_structure_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">    <span class="nam">output_structure_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t"><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="str">"""Execute the :class:`ExtractModel &lt;utils.extract_model.ExtractModel>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;utils.extract_model.ExtractModel.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="key">return</span> <span class="nam">ExtractModel</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a model from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">extract_model</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">    <span class="nam">extract_model</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">ExtractModel</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a model from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="nam">extract_model</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -324,7 +327,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_extract_molecule_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_extract_molecule_py.html b/coverage/z_cc8067c15db60eec_extract_molecule_py.html
index 4c47f95..811a09c 100644
--- a/coverage/z_cc8067c15db60eec_extract_molecule_py.html
+++ b/coverage/z_cc8067c15db60eec_extract_molecule_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_extract_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -228,73 +228,78 @@ <h2>
     <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">,</span> <span class="nam">tmp_folder</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="com"># tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t"><span class="key">def</span> <span class="nam">extract_molecule</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">    <span class="nam">input_structure_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">    <span class="nam">output_molecule_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t"><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">    <span class="str">"""Execute the :class:`ExtractMolecule &lt;utils.extract_molecule.ExtractMolecule>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;utils.extract_molecule.ExtractMolecule.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">    <span class="key">return</span> <span class="nam">ExtractMolecule</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">output_molecule_path</span><span class="op">=</span><span class="nam">output_molecule_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a molecule from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="str">"--output_molecule_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output heteroatom file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="nam">extract_molecule</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">output_molecule_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_molecule_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t"><span class="key">def</span> <span class="nam">extract_molecule</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">    <span class="nam">input_structure_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">    <span class="nam">output_molecule_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t"><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">    <span class="str">"""Execute the :class:`ExtractMolecule &lt;utils.extract_molecule.ExtractMolecule>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;utils.extract_molecule.ExtractMolecule.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">    <span class="key">return</span> <span class="nam">ExtractMolecule</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">output_molecule_path</span><span class="op">=</span><span class="nam">output_molecule_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">    <span class="nam">extract_molecule</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">ExtractMolecule</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a molecule from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="str">"--output_molecule_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output heteroatom file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="nam">extract_molecule</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">output_molecule_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_molecule_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -304,7 +309,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_extract_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_extract_residues_py.html b/coverage/z_cc8067c15db60eec_extract_residues_py.html
index 69f0b2f..e2944d0 100644
--- a/coverage/z_cc8067c15db60eec_extract_residues_py.html
+++ b/coverage/z_cc8067c15db60eec_extract_residues_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">64 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">50<span class="text"> run</span></button>
+            <span class="text">63 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">49<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">14<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_remove_ligand_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -239,7 +239,7 @@ <h2>
     <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -263,49 +263,51 @@ <h2>
     <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a list of residues from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="str">"--output_residues_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output residues file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="nam">extract_residues</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">output_residues_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_residues_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="nam">extract_residues</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">ExtractResidues</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Extract a list of residues from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="str">"--output_residues_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output residues file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">extract_residues</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">output_residues_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_residues_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -315,7 +317,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_remove_ligand_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_remove_ligand_py.html b/coverage/z_cc8067c15db60eec_remove_ligand_py.html
index c3a527f..88e3c9d 100644
--- a/coverage/z_cc8067c15db60eec_remove_ligand_py.html
+++ b/coverage/z_cc8067c15db60eec_remove_ligand_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">55 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">44<span class="text"> run</span></button>
+            <span class="text">54 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">43<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">11<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_remove_molecules_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -204,7 +204,7 @@ <h2>
     <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -228,46 +228,48 @@ <h2>
     <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Remove the selected ligand atoms from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_structure_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file name"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file name"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">    <span class="nam">remove_ligand</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">    <span class="nam">remove_ligand</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">RemoveLigand</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Remove the selected ligand atoms from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_structure_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file name"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file name"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">    <span class="nam">remove_ligand</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -277,7 +279,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_remove_molecules_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_remove_molecules_py.html b/coverage/z_cc8067c15db60eec_remove_molecules_py.html
index ea9b62f..32644a0 100644
--- a/coverage/z_cc8067c15db60eec_remove_molecules_py.html
+++ b/coverage/z_cc8067c15db60eec_remove_molecules_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">67 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">53<span class="text"> run</span></button>
+            <span class="text">66 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">52<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">14<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_remove_pdb_water_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -244,7 +244,7 @@ <h2>
     <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -268,49 +268,51 @@ <h2>
     <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Removes a list of molecules from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="str">"--output_molecules_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output molecules file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">remove_molecules</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">output_molecules_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_molecules_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="nam">remove_molecules</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">RemoveMolecules</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Removes a list of molecules from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="str">"--output_molecules_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output molecules file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">remove_molecules</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="nam">output_molecules_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_molecules_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -320,7 +322,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_remove_pdb_water_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_remove_pdb_water_py.html b/coverage/z_cc8067c15db60eec_remove_pdb_water_py.html
index 59ac081..5ba11e5 100644
--- a/coverage/z_cc8067c15db60eec_remove_pdb_water_py.html
+++ b/coverage/z_cc8067c15db60eec_remove_pdb_water_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">40 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">29<span class="text"> run</span></button>
+            <span class="text">39 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">28<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">11<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_renumber_structure_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -177,7 +177,7 @@ <h2>
     <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -201,43 +201,45 @@ <h2>
     <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Remove the water molecules from a PDB 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_pdb_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input pdb file name"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span> <span class="str">"--output_pdb_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Output pdb file name"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">    <span class="nam">remove_pdb_water</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">input_pdb_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">output_pdb_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_pdb_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">    <span class="nam">remove_pdb_water</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">RemovePdbWater</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Remove the water molecules from a PDB 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_pdb_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input pdb file name"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span> <span class="str">"--output_pdb_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Output pdb file name"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">    <span class="nam">remove_pdb_water</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">input_pdb_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">output_pdb_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_pdb_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -247,7 +249,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_renumber_structure_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_renumber_structure_py.html b/coverage/z_cc8067c15db60eec_renumber_structure_py.html
index ddeefd2..f3ecf89 100644
--- a/coverage/z_cc8067c15db60eec_renumber_structure_py.html
+++ b/coverage/z_cc8067c15db60eec_renumber_structure_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">88 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">76<span class="text"> run</span></button>
+            <span class="text">87 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">75<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">12<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_sort_gro_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -259,7 +259,7 @@ <h2>
     <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -285,53 +285,55 @@ <h2>
     <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Renumber atoms and residues from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_structure_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file name"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file name"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="str">"-j"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="str">"--output_mapping_json_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output mapping json file name"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">    <span class="nam">renumber_structure</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">output_mapping_json_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_mapping_json_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="nam">renumber_structure</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">RenumberStructure</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Renumber atoms and residues from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_structure_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file name"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file name"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="str">"-j"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="str">"--output_mapping_json_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output mapping json file name"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">    <span class="nam">renumber_structure</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">output_mapping_json_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_mapping_json_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -341,7 +343,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_sort_gro_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_sort_gro_residues_py.html b/coverage/z_cc8067c15db60eec_sort_gro_residues_py.html
index 1413cf6..9d9e106 100644
--- a/coverage/z_cc8067c15db60eec_sort_gro_residues_py.html
+++ b/coverage/z_cc8067c15db60eec_sort_gro_residues_py.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-    <title>Coverage for biobb_structure_utils/utils/sort_gro_residues.py: 76%</title>
+    <title>Coverage for biobb_structure_utils/utils/sort_gro_residues.py: 75%</title>
     <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
     <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
     <script src="coverage_html_cb_6fb7b396.js" defer></script>
@@ -12,7 +12,7 @@
     <div class="content">
         <h1>
             <span class="text">Coverage for </span><b>biobb_structure_utils/utils/sort_gro_residues.py</b>:
-            <span class="pc_cov">76%</span>
+            <span class="pc_cov">75%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">45 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">34<span class="text"> run</span></button>
+            <span class="text">44 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">33<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">11<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -176,7 +176,7 @@ <h2>
     <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -200,43 +200,45 @@ <h2>
     <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Renumber atoms and residues from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_gro_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input GRO file name"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span> <span class="str">"--output_gro_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Output sorted GRO file name"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">    <span class="nam">sort_gro_residues</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">input_gro_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_gro_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">output_gro_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_gro_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">    <span class="nam">sort_gro_residues</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">SortGroResidues</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Renumber atoms and residues from a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span> <span class="str">"--input_gro_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Input GRO file name"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span> <span class="str">"--output_gro_path"</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">"Output sorted GRO file name"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">    <span class="nam">sort_gro_residues</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">input_gro_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_gro_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">output_gro_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_gro_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -246,7 +248,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_str_check_add_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_str_check_add_hydrogens_py.html b/coverage/z_cc8067c15db60eec_str_check_add_hydrogens_py.html
index 13eb4aa..060fc3c 100644
--- a/coverage/z_cc8067c15db60eec_str_check_add_hydrogens_py.html
+++ b/coverage/z_cc8067c15db60eec_str_check_add_hydrogens_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">64 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">50<span class="text"> run</span></button>
+            <span class="text">63 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">49<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">14<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cc8067c15db60eec_structure_check_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -227,7 +227,7 @@ <h2>
     <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">check_output_end</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_structure_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -251,49 +251,51 @@ <h2>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Class to add hydrogens to a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file path. Accepted formats: pdb, pdbqt."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="nam">str_check_add_hydrogens</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">    <span class="nam">str_check_add_hydrogens</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">StrCheckAddHydrogens</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"Class to add hydrogens to a 3D structure."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="str">"--output_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output structure file path. Accepted formats: pdb, pdbqt."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="nam">str_check_add_hydrogens</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">output_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -303,7 +305,7 @@ <h2>
             <a class="nav" href="z_cc8067c15db60eec_structure_check_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cc8067c15db60eec_structure_check_py.html b/coverage/z_cc8067c15db60eec_structure_check_py.html
index 25ac728..1fe977d 100644
--- a/coverage/z_cc8067c15db60eec_structure_check_py.html
+++ b/coverage/z_cc8067c15db60eec_structure_check_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -233,73 +233,78 @@ <h2>
     <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># Remove temporal files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">,</span> <span class="nam">tmp_folder</span><span class="op">]</span><span class="op">)</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="com"># self.stage_io_dict.get("unique_dir", ""),</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t"><span class="key">def</span> <span class="nam">structure_check</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">    <span class="nam">input_structure_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">    <span class="nam">output_summary_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t"><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">    <span class="str">"""Execute the :class:`StructureCheck &lt;utils.structure_check.StructureCheck>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;utils.structure_check.StructureCheck.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">    <span class="key">return</span> <span class="nam">StructureCheck</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">output_summary_path</span><span class="op">=</span><span class="nam">output_summary_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="str">"--output_summary_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output summary checking results. Accepted formats: json."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="nam">structure_check</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">output_summary_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_summary_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t"><span class="key">def</span> <span class="nam">structure_check</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">    <span class="nam">input_structure_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">    <span class="nam">output_summary_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t"><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">    <span class="str">"""Execute the :class:`StructureCheck &lt;utils.structure_check.StructureCheck>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;utils.structure_check.StructureCheck.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">    <span class="key">return</span> <span class="nam">StructureCheck</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">output_summary_path</span><span class="op">=</span><span class="nam">output_summary_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="nam">structure_check</span><span class="op">.</span><span class="nam">__doc__</span> <span class="op">=</span> <span class="nam">StructureCheck</span><span class="op">.</span><span class="nam">__doc__</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">description</span><span class="op">=</span><span class="str">"This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="str">"-c"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="str">"--config"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"This file can be a YAML file, JSON file or JSON string"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">"required arguments"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="str">"-i"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="str">"--input_structure_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Input structure file path. Accepted formats: pdb."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="str">"-o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="str">"--output_summary_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">help</span><span class="op">=</span><span class="str">"Output summary checking results. Accepted formats: json."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">if</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">else</span> <span class="key">None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="nam">structure_check</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">input_structure_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_structure_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">output_summary_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_summary_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">"__main__"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -309,7 +314,7 @@ <h2>
             <a class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_d361e47ffa394ddf___init___py.html b/coverage/z_d361e47ffa394ddf___init___py.html
index 44152c0..dbdc219 100644
--- a/coverage/z_d361e47ffa394ddf___init___py.html
+++ b/coverage/z_d361e47ffa394ddf___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8572508eb5b65ee1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -94,7 +94,7 @@ <h2>
             <a class="nav" href="z_8572508eb5b65ee1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-21 17:25 +0000
+            created at 2025-01-28 11:50 +0000
         </p>
     </div>
 </footer>
diff --git a/flake8/index.html b/flake8/index.html
index 2edad09..24785f9 100644
--- a/flake8/index.html
+++ b/flake8/index.html
@@ -9,7 +9,7 @@
       <div id="masthead" class="sev-4"></div>
       <div id="page">
           <h1>flake8 violations</h1>
-         <p id="versions">Generated on 2025-01-21 17:24
+         <p id="versions">Generated on 2025-01-28 11:49
             with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.12.1, pyflakes: 3.2.0
          </p>
          <ul id="index">
diff --git a/junit/junit.xml b/junit/junit.xml
index b29151c..73e68ba 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="20" time="81.302" timestamp="2025-01-21T17:24:33.907076+00:00" hostname="github-actions.vm.mmb.pcb.ub.es"><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_cat_pdb.TestCatPDB" name="test_launch" time="0.343" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_closest_residues.TestClosestResidues" name="test_launch" time="5.808" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_atoms_gro.TestExtractAtomsGRO" name="test_launch" time="10.653" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_atoms_pdb.TestExtractAtomsPDB" name="test_launch" time="0.196" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_chain.TestExtractChain" name="test_launch" time="1.109" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_heteroatom.TestExtractHeteroAtoms" name="test_launch" time="2.897" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_model.TestExtractModel" name="test_launch" time="8.450" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_molecule.TestExtractMolecule" name="test_launch" time="1.896" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_residues.TestExtractResidues" name="test_launch" time="1.560" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_ligand_gro.TestRemoveLigandGro" name="test_launch" time="1.189" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_ligand_pdb.TestRemoveLigandPDB" name="test_launch" time="7.371" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_molecules.TestRemoveMolecules" name="test_launch" time="16.990" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_pdb_water.TestRemovePDBWater" name="test_launch" time="2.244" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_2vgb.TestRenumberStructure2VGB" name="test_launch" time="2.249" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_gro.TestRenumberStructureGRO" name="test_launch" time="0.378" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_pdb.TestRenumberStructurePDB" name="test_launch" time="0.088" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_smallgro.TestRenumberStructureSMALLGRO" name="test_launch" time="0.084" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_sort_gro_residues.TestSortGroResidues" name="test_launch" time="10.248" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_str_check_add_hydrogens.TestStrCheckAddHydrogens" name="test_str_check_add_hydrogens" time="2.747" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_structure_check.TestStructureCheck" name="test_launch" time="3.134" /></testsuite></testsuites>
\ No newline at end of file
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="20" time="33.392" timestamp="2025-01-28T11:50:03.012834+00:00" hostname="biobb-runners"><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_cat_pdb.TestCatPDB" name="test_launch" time="0.246" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_closest_residues.TestClosestResidues" name="test_launch" time="2.070" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_atoms_gro.TestExtractAtomsGRO" name="test_launch" time="5.074" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_atoms_pdb.TestExtractAtomsPDB" name="test_launch" time="0.077" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_chain.TestExtractChain" name="test_launch" time="0.423" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_heteroatom.TestExtractHeteroAtoms" name="test_launch" time="1.106" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_model.TestExtractModel" name="test_launch" time="3.274" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_molecule.TestExtractMolecule" name="test_launch" time="0.866" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_extract_residues.TestExtractResidues" name="test_launch" time="0.659" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_ligand_gro.TestRemoveLigandGro" name="test_launch" time="0.497" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_ligand_pdb.TestRemoveLigandPDB" name="test_launch" time="2.674" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_molecules.TestRemoveMolecules" name="test_launch" time="6.450" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_remove_pdb_water.TestRemovePDBWater" name="test_launch" time="0.888" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_2vgb.TestRenumberStructure2VGB" name="test_launch" time="0.919" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_gro.TestRenumberStructureGRO" name="test_launch" time="0.172" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_pdb.TestRenumberStructurePDB" name="test_launch" time="0.038" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_renumber_structure_smallgro.TestRenumberStructureSMALLGRO" name="test_launch" time="0.038" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_sort_gro_residues.TestSortGroResidues" name="test_launch" time="4.837" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_str_check_add_hydrogens.TestStrCheckAddHydrogens" name="test_str_check_add_hydrogens" time="1.105" /><testcase classname="biobb_structure_utils.test.unitests.test_utils.test_structure_check.TestStructureCheck" name="test_launch" time="1.250" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index 4b47779..3ac65b8 100644
--- a/junit/report.html
+++ b/junit/report.html
@@ -7,7 +7,7 @@
   </head>
   <body>
     <h1 id="title">report.html</h1>
-    <p>Report generated on 21-Jan-2025 at 17:25:55 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 28-Jan-2025 at 11:50:36 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
         v4.1.1</p>
     <div id="environment-header">
       <h2>Environment</h2>
@@ -61,7 +61,7 @@ <h2>Environment</h2>
         <h2>Summary</h2>
         <div class="additional-summary prefix">
         </div>
-        <p class="run-count">20 tests took 00:01:20.</p>
+        <p class="run-count">20 tests took 00:00:33.</p>
         <p class="filter">(Un)check the boxes to filter the results.</p>
         <div class="summary__reload">
           <div class="summary__reload__button hidden" onclick="location.reload()">
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.9.21&#34;, &#34;Platform&#34;: &#34;Linux-5.15.0-125-generic-x86_64-with-glibc2.35&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.4&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;html&#34;: &#34;4.1.1&#34;, &#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&#34;, &#34;duration&#34;: &#34;343 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;343 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:24:34,921 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.cat_pdb Version: 5.0.0\n2025-01-21 17:24:34,922 [MainThread  ] [INFO ]  /tmp/biobb/unitests_45/cat_pdb/sandbox_36c2170a-4514-443c-b9c2-3ef67dc8ba06 directory successfully created\n2025-01-21 17:24:34,924 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_protein.pdb to /tmp/biobb/unitests_45/cat_pdb/sandbox_36c2170a-4514-443c-b9c2-3ef67dc8ba06\n2025-01-21 17:24:34,924 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_ligand.pdb to /tmp/biobb/unitests_45/cat_pdb/sandbox_36c2170a-4514-443c-b9c2-3ef67dc8ba06\n2025-01-21 17:24:34,929 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_45/cat_pdb/sandbox_36c2170a-4514-443c-b9c2-3ef67dc8ba06&amp;#x27;]\n2025-01-21 17:24:34,930 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_45/cat_pdb/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_45/cat_pdb/output_structure_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2058\n     Atoms ALIGNED in PDB_B: 2058\n     RMS: 8.794008030148362e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_45/cat_pdb/cat_pdb_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.cat_pdb Version: 5.0.0\nINFO     /tmp/biobb/unitests_45/cat_pdb/cat_pdb_log.out:file_utils.py:82 /tmp/biobb/unitests_45/cat_pdb/sandbox_36c2170a-4514-443c-b9c2-3ef67dc8ba06 directory successfully created\nINFO     /tmp/biobb/unitests_45/cat_pdb/cat_pdb_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_protein.pdb to /tmp/biobb/unitests_45/cat_pdb/sandbox_36c2170a-4514-443c-b9c2-3ef67dc8ba06\nINFO     /tmp/biobb/unitests_45/cat_pdb/cat_pdb_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_ligand.pdb to /tmp/biobb/unitests_45/cat_pdb/sandbox_36c2170a-4514-443c-b9c2-3ef67dc8ba06\nINFO     /tmp/biobb/unitests_45/cat_pdb/cat_pdb_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_45/cat_pdb/sandbox_36c2170a-4514-443c-b9c2-3ef67dc8ba06&amp;#x27;]\nINFO     /tmp/biobb/unitests_45/cat_pdb/cat_pdb_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_45\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&#34;, &#34;duration&#34;: &#34;00:00:06&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:06&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:24:35,294 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.closest_residues Version: 5.0.0\n2025-01-21 17:24:35,294 [MainThread  ] [INFO ]  /tmp/biobb/unitests_45/closest_residues/sandbox_79c4c9cc-e7c7-4308-a3b4-6594975e7a1d directory successfully created\n2025-01-21 17:24:35,298 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_45/closest_residues/sandbox_79c4c9cc-e7c7-4308-a3b4-6594975e7a1d\n2025-01-21 17:24:36,348 [MainThread  ] [INFO ]  Found 548 nearby residues\n2025-01-21 17:24:40,494 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_45/closest_residues/sandbox_79c4c9cc-e7c7-4308-a3b4-6594975e7a1d/output_residues_path.pdb\n2025-01-21 17:24:40,500 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_45/closest_residues/sandbox_79c4c9cc-e7c7-4308-a3b4-6594975e7a1d&amp;#x27;]\n2025-01-21 17:24:40,501 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_45/closest_residues/output_residues_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_45/closest_residues/output_residues_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_closest_residues.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 4251\n     Atoms ALIGNED in PDB_B: 4251\n     RMS: 2.381398461260282e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_45/closest_residues/closest_residues_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.closest_residues Version: 5.0.0\nINFO     /tmp/biobb/unitests_45/closest_residues/closest_residues_log.out:file_utils.py:82 /tmp/biobb/unitests_45/closest_residues/sandbox_79c4c9cc-e7c7-4308-a3b4-6594975e7a1d directory successfully created\nINFO     /tmp/biobb/unitests_45/closest_residues/closest_residues_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_45/closest_residues/sandbox_79c4c9cc-e7c7-4308-a3b4-6594975e7a1d\nINFO     /tmp/biobb/unitests_45/closest_residues/closest_residues_log.out:file_utils.py:409 Found 548 nearby residues\nINFO     /tmp/biobb/unitests_45/closest_residues/closest_residues_log.out:file_utils.py:409 Writting pdb to: /tmp/biobb/unitests_45/closest_residues/sandbox_79c4c9cc-e7c7-4308-a3b4-6594975e7a1d/output_residues_path.pdb\nINFO     /tmp/biobb/unitests_45/closest_residues/closest_residues_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_45/closest_residues/sandbox_79c4c9cc-e7c7-4308-a3b4-6594975e7a1d&amp;#x27;]\nINFO     /tmp/biobb/unitests_45/closest_residues/closest_residues_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_45\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&#34;, &#34;duration&#34;: &#34;00:00:11&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:11&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:24:41,108 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_atoms Version: 5.0.0\n2025-01-21 17:24:41,109 [MainThread  ] [INFO ]  /tmp/biobb/unitests_45/extract_atoms_gro/sandbox_e5fd234a-437d-4272-9a5c-4cd4bfe17986 directory successfully created\n2025-01-21 17:24:41,119 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/G2S_stateA_frame92.sorted.gro to /tmp/biobb/unitests_45/extract_atoms_gro/sandbox_e5fd234a-437d-4272-9a5c-4cd4bfe17986\n2025-01-21 17:24:41,119 [MainThread  ] [INFO ]  GRO format detected, extracting all atoms matching ^D\n2025-01-21 17:24:51,629 [MainThread  ] [INFO ]  4 atoms found writting GRO file\n2025-01-21 17:24:51,679 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_atoms_gro/sandbox_e5fd234a-437d-4272-9a5c-4cd4bfe17986&amp;#x27;]\n2025-01-21 17:24:51,680 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_45/extract_atoms_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_45/extract_atoms_gro/output_structure_path.gro\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/dummy_atoms.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_45/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_atoms Version: 5.0.0\nINFO     /tmp/biobb/unitests_45/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:82 /tmp/biobb/unitests_45/extract_atoms_gro/sandbox_e5fd234a-437d-4272-9a5c-4cd4bfe17986 directory successfully created\nINFO     /tmp/biobb/unitests_45/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/G2S_stateA_frame92.sorted.gro to /tmp/biobb/unitests_45/extract_atoms_gro/sandbox_e5fd234a-437d-4272-9a5c-4cd4bfe17986\nINFO     /tmp/biobb/unitests_45/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 GRO format detected, extracting all atoms matching ^D\nINFO     /tmp/biobb/unitests_45/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 4 atoms found writting GRO file\nINFO     /tmp/biobb/unitests_45/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_atoms_gro/sandbox_e5fd234a-437d-4272-9a5c-4cd4bfe17986&amp;#x27;]\nINFO     /tmp/biobb/unitests_45/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_45\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&#34;, &#34;duration&#34;: &#34;196 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;196 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:24:51,763 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_atoms Version: 5.0.0\n2025-01-21 17:24:51,764 [MainThread  ] [INFO ]  /tmp/biobb/unitests_45/extract_atoms/sandbox_12f06c46-1f3f-4c82-a14a-39a1ad1bb07c directory successfully created\n2025-01-21 17:24:51,767 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_45/extract_atoms/sandbox_12f06c46-1f3f-4c82-a14a-39a1ad1bb07c\n2025-01-21 17:24:51,768 [MainThread  ] [INFO ]  PDB format detected, extracting all atoms matching OE2\n2025-01-21 17:24:51,854 [MainThread  ] [INFO ]  141 atoms found writting PDB file\n2025-01-21 17:24:51,855 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_atoms/sandbox_12f06c46-1f3f-4c82-a14a-39a1ad1bb07c&amp;#x27;]\n2025-01-21 17:24:51,856 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_45/extract_atoms/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_45/extract_atoms/output_structure_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/OE2_atoms.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 141\n     Atoms ALIGNED in PDB_B: 141\n     RMS: 1.4208176252736295e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_45/extract_atoms/extract_atoms_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_atoms Version: 5.0.0\nINFO     /tmp/biobb/unitests_45/extract_atoms/extract_atoms_log.out:file_utils.py:82 /tmp/biobb/unitests_45/extract_atoms/sandbox_12f06c46-1f3f-4c82-a14a-39a1ad1bb07c directory successfully created\nINFO     /tmp/biobb/unitests_45/extract_atoms/extract_atoms_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_45/extract_atoms/sandbox_12f06c46-1f3f-4c82-a14a-39a1ad1bb07c\nINFO     /tmp/biobb/unitests_45/extract_atoms/extract_atoms_log.out:file_utils.py:409 PDB format detected, extracting all atoms matching OE2\nINFO     /tmp/biobb/unitests_45/extract_atoms/extract_atoms_log.out:file_utils.py:409 141 atoms found writting PDB file\nINFO     /tmp/biobb/unitests_45/extract_atoms/extract_atoms_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_atoms/sandbox_12f06c46-1f3f-4c82-a14a-39a1ad1bb07c&amp;#x27;]\nINFO     /tmp/biobb/unitests_45/extract_atoms/extract_atoms_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_45\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:24:51,963 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_chain Version: 5.0.0\n2025-01-21 17:24:51,964 [MainThread  ] [INFO ]  /tmp/biobb/unitests_45/extract_chain/sandbox_f681d849-a3f5-4691-93e7-0285262a77db directory successfully created\n2025-01-21 17:24:51,967 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_chain.pdb to /tmp/biobb/unitests_45/extract_chain/sandbox_f681d849-a3f5-4691-93e7-0285262a77db\n2025-01-21 17:24:51,967 [MainThread  ] [INFO ]  Selected Chains: B,C\n2025-01-21 17:24:51,968 [MainThread  ] [INFO ]  Warning: Use permissive=True is a risky option use it under your own responsability\n2025-01-21 17:24:52,007 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_chain/sandbox_f681d849-a3f5-4691-93e7-0285262a77db&amp;#x27;]\n2025-01-21 17:24:52,008 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_45/extract_chain/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_45/extract_chain/output_structure_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_chain.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 7893\n     Atoms ALIGNED in PDB_B: 7893\n     RMS: 1.7903585739260547e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_45/extract_chain/extract_chain_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_chain Version: 5.0.0\nINFO     /tmp/biobb/unitests_45/extract_chain/extract_chain_log.out:file_utils.py:82 /tmp/biobb/unitests_45/extract_chain/sandbox_f681d849-a3f5-4691-93e7-0285262a77db directory successfully created\nINFO     /tmp/biobb/unitests_45/extract_chain/extract_chain_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_chain.pdb to /tmp/biobb/unitests_45/extract_chain/sandbox_f681d849-a3f5-4691-93e7-0285262a77db\nINFO     /tmp/biobb/unitests_45/extract_chain/extract_chain_log.out:file_utils.py:409 Selected Chains: B,C\nINFO     /tmp/biobb/unitests_45/extract_chain/extract_chain_log.out:file_utils.py:409 Warning: Use permissive=True is a risky option use it under your own responsability\nINFO     /tmp/biobb/unitests_45/extract_chain/extract_chain_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_chain/sandbox_f681d849-a3f5-4691-93e7-0285262a77db&amp;#x27;]\nINFO     /tmp/biobb/unitests_45/extract_chain/extract_chain_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_45\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:24:53,119 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_heteroatoms Version: 5.0.0\n2025-01-21 17:24:53,120 [MainThread  ] [INFO ]  /tmp/biobb/unitests_45/extract_heteroatoms/sandbox_91a9b6dd-ce85-4965-815f-eb40a244715c directory successfully created\n2025-01-21 17:24:53,129 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb to /tmp/biobb/unitests_45/extract_heteroatoms/sandbox_91a9b6dd-ce85-4965-815f-eb40a244715c\n2025-01-21 17:24:55,887 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_45/extract_heteroatoms/sandbox_91a9b6dd-ce85-4965-815f-eb40a244715c/output_heteroatom_path.pdb\n2025-01-21 17:24:55,890 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_heteroatoms/sandbox_91a9b6dd-ce85-4965-815f-eb40a244715c&amp;#x27;]\n2025-01-21 17:24:55,891 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_45/extract_heteroatoms/output_heteroatom_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_45/extract_heteroatoms/output_heteroatom_path.pdb\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_heteroatom.pdb\n        File_A hash: b&amp;#x27;\\x1e\\x83\\x13\\xbd\\xed\\xd0\\xcb0J\\xed\\x0eCp\\xe8\\xe2\\x91\\xf0w~x\\xd5\\x95\\xfc^9\\x83J\\x00\\x0f!^\\x04&amp;#x27;\n        File_B hash: b&amp;#x27;\\x1e\\x83\\x13\\xbd\\xed\\xd0\\xcb0J\\xed\\x0eCp\\xe8\\xe2\\x91\\xf0w~x\\xd5\\x95\\xfc^9\\x83J\\x00\\x0f!^\\x04&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_45/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_heteroatoms Version: 5.0.0\nINFO     /tmp/biobb/unitests_45/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:82 /tmp/biobb/unitests_45/extract_heteroatoms/sandbox_91a9b6dd-ce85-4965-815f-eb40a244715c directory successfully created\nINFO     /tmp/biobb/unitests_45/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb to /tmp/biobb/unitests_45/extract_heteroatoms/sandbox_91a9b6dd-ce85-4965-815f-eb40a244715c\nINFO     /tmp/biobb/unitests_45/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409 Writting pdb to: /tmp/biobb/unitests_45/extract_heteroatoms/sandbox_91a9b6dd-ce85-4965-815f-eb40a244715c/output_heteroatom_path.pdb\nINFO     /tmp/biobb/unitests_45/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_heteroatoms/sandbox_91a9b6dd-ce85-4965-815f-eb40a244715c&amp;#x27;]\nINFO     /tmp/biobb/unitests_45/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_45\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&#34;, &#34;duration&#34;: &#34;00:00:08&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:08&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:24:55,975 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_model Version: 5.0.0\n2025-01-21 17:24:55,975 [MainThread  ] [INFO ]  /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e directory successfully created\n2025-01-21 17:24:55,981 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_model.pdb to /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e\n2025-01-21 17:24:55,981 [MainThread  ] [INFO ]  Creating d9f1181a-38ca-4dd7-8e4f-a717d8a295f5 temporary folder\n2025-01-21 17:24:55,982 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e/extract_model.pdb -o d9f1181a-38ca-4dd7-8e4f-a717d8a295f5/model1.pdb --force_save models --select 1\n\n2025-01-21 17:25:00,094 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f...\n2025-01-21 17:25:00,095 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 17:25:00,096 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 1\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 1\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on d9f1181a-38ca-4dd7-8e4f-a717d8a295f5/model1.pdb\n\n2025-01-21 17:25:00,096 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e/extract_model.pdb -o d9f1181a-38ca-4dd7-8e4f-a717d8a295f5/model4.pdb --force_save models --select 4\n\n2025-01-21 17:25:04,062 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f...\n2025-01-21 17:25:04,063 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 17:25:04,063 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 4\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 4\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on d9f1181a-38ca-4dd7-8e4f-a717d8a295f5/model4.pdb\n\n2025-01-21 17:25:04,071 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e&amp;#x27;, &amp;#x27;d9f1181a-38ca-4dd7-8e4f-a717d8a295f5&amp;#x27;]\n2025-01-21 17:25:04,072 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_45/extract_model/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_45/extract_model/output_structure_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_model.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 636\n     Atoms ALIGNED in PDB_B: 636\n     RMS: 6.0667406824158584e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_model Version: 5.0.0\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:file_utils.py:82 /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e directory successfully created\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_model.pdb to /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:file_utils.py:409 Creating d9f1181a-38ca-4dd7-8e4f-a717d8a295f5 temporary folder\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e/extract_model.pdb -o d9f1181a-38ca-4dd7-8e4f-a717d8a295f5/model1.pdb --force_save models --select 1\n\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f...\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 1\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 1\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on d9f1181a-38ca-4dd7-8e4f-a717d8a295f5/model1.pdb\n\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e/extract_model.pdb -o d9f1181a-38ca-4dd7-8e4f-a717d8a295f5/model4.pdb --force_save models --select 4\n\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f...\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 4\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 4\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on d9f1181a-38ca-4dd7-8e4f-a717d8a295f5/model4.pdb\n\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_45/extract_model/sandbox_927e24ab-317b-4f98-97cc-88b1bcfc457e&amp;#x27;, &amp;#x27;d9f1181a-38ca-4dd7-8e4f-a717d8a295f5&amp;#x27;]\nINFO     /tmp/biobb/unitests_45/extract_model/extract_model_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:04,432 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_molecule Version: 5.0.0\n2025-01-21 17:25:04,433 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/extract_molecule/sandbox_c77c63a6-8644-4a0d-8baf-98e41b6ca17c directory successfully created\n2025-01-21 17:25:04,434 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb to /tmp/biobb/unitests_46/extract_molecule/sandbox_c77c63a6-8644-4a0d-8baf-98e41b6ca17c\n2025-01-21 17:25:04,435 [MainThread  ] [INFO ]  Creating cbc11212-7051-49d1-a67a-d50532dde1df temporary folder\n2025-01-21 17:25:04,435 [MainThread  ] [INFO ]  check_structure -i /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb -o /tmp/biobb/unitests_46/extract_molecule/output_molecule_path.pdb --force_save --non_interactive command_list --list cbc11212-7051-49d1-a67a-d50532dde1df/extract_prot.lst\n\n2025-01-21 17:25:05,992 [MainThread  ] [INFO ]  Executing: check_structure -i /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_...\n2025-01-21 17:25:05,993 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 17:25:05,993 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb loaded\n PDB id: 1G54 \n Title: carbonic anhydrase ii complexed with 4-(aminosulfonyl)-n-[(2,3,4,5,6- pentafluorophenyl)methyl]-benzamide\n Experimental method: x-ray diffraction\n Keywords: carbonic anhydrase ii, 4-(aminosulfonyl)-n-[(2, 3, 4, 5, 6- pentafluorophenyl)methyl]-benzamide, lyase\n Resolution (A): 1.86\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  332\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  74\n Num. ligands or modified residues:  3\n Num. water mol.:  71\n Num. atoms:  2156\nMetal/Ion residues found\n ZN A262\n HG A263\nSmall mol ligands found\nFFB A555\n\nStep 1: ligands --remove All\n\nRunning ligands. Options: --remove All\nDetected 3 Ligands\n  ZN A262\n  HG A263\n FFB A555\nLigands removed All (3)\n\nStep 2: water --remove Yes\n\nRunning water. Options: --remove Yes\nDetected 71 Water molecules\nRemoved 71 Water molecules\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  258\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  2058\nStructure saved on /tmp/biobb/unitests_46/extract_molecule/output_molecule_path.pdb\n\n2025-01-21 17:25:05,995 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/extract_molecule/sandbox_c77c63a6-8644-4a0d-8baf-98e41b6ca17c&amp;#x27;, &amp;#x27;cbc11212-7051-49d1-a67a-d50532dde1df&amp;#x27;]\n2025-01-21 17:25:05,996 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/extract_molecule/output_molecule_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_46/extract_molecule/output_molecule_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_molecule.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2058\n     Atoms ALIGNED in PDB_B: 2058\n     RMS: 8.794008030148362e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_molecule Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:file_utils.py:82 /tmp/biobb/unitests_46/extract_molecule/sandbox_c77c63a6-8644-4a0d-8baf-98e41b6ca17c directory successfully created\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb to /tmp/biobb/unitests_46/extract_molecule/sandbox_c77c63a6-8644-4a0d-8baf-98e41b6ca17c\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:file_utils.py:409 Creating cbc11212-7051-49d1-a67a-d50532dde1df temporary folder\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:63 check_structure -i /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb -o /tmp/biobb/unitests_46/extract_molecule/output_molecule_path.pdb --force_save --non_interactive command_list --list cbc11212-7051-49d1-a67a-d50532dde1df/extract_prot.lst\n\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:36 Executing: check_structure -i /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_...\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb loaded\n PDB id: 1G54 \n Title: carbonic anhydrase ii complexed with 4-(aminosulfonyl)-n-[(2,3,4,5,6- pentafluorophenyl)methyl]-benzamide\n Experimental method: x-ray diffraction\n Keywords: carbonic anhydrase ii, 4-(aminosulfonyl)-n-[(2, 3, 4, 5, 6- pentafluorophenyl)methyl]-benzamide, lyase\n Resolution (A): 1.86\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  332\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  74\n Num. ligands or modified residues:  3\n Num. water mol.:  71\n Num. atoms:  2156\nMetal/Ion residues found\n ZN A262\n HG A263\nSmall mol ligands found\nFFB A555\n\nStep 1: ligands --remove All\n\nRunning ligands. Options: --remove All\nDetected 3 Ligands\n  ZN A262\n  HG A263\n FFB A555\nLigands removed All (3)\n\nStep 2: water --remove Yes\n\nRunning water. Options: --remove Yes\nDetected 71 Water molecules\nRemoved 71 Water molecules\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  258\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  2058\nStructure saved on /tmp/biobb/unitests_46/extract_molecule/output_molecule_path.pdb\n\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/extract_molecule/sandbox_c77c63a6-8644-4a0d-8baf-98e41b6ca17c&amp;#x27;, &amp;#x27;cbc11212-7051-49d1-a67a-d50532dde1df&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/extract_molecule/extract_molecule_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:06,333 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_residues Version: 5.0.0\n2025-01-21 17:25:06,333 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/extract_residues/sandbox_334bca3e-aafc-48f9-9b6a-06bf28f6cb4d directory successfully created\n2025-01-21 17:25:06,336 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_46/extract_residues/sandbox_334bca3e-aafc-48f9-9b6a-06bf28f6cb4d\n2025-01-21 17:25:07,807 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_46/extract_residues/sandbox_334bca3e-aafc-48f9-9b6a-06bf28f6cb4d/output_residues_path.pdb\n2025-01-21 17:25:07,809 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/extract_residues/sandbox_334bca3e-aafc-48f9-9b6a-06bf28f6cb4d&amp;#x27;]\n2025-01-21 17:25:07,810 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/extract_residues/output_residues_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_46/extract_residues/output_residues_path.pdb\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_residues.pdb\n        File_A hash: b&amp;#x27;\\xf0\\x84\\xb8D\\x90whe\\xc3T\\xe2\\xf3\\\\\\xd72\\xfaT\\x9d\\x19\\x88\\xab\\x03\\xbe\\xf6\\x9a\\x81\\xec\\x15tx`D&amp;#x27;\n        File_B hash: b&amp;#x27;\\xf0\\x84\\xb8D\\x90whe\\xc3T\\xe2\\xf3\\\\\\xd72\\xfaT\\x9d\\x19\\x88\\xab\\x03\\xbe\\xf6\\x9a\\x81\\xec\\x15tx`D&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/extract_residues/extract_residues_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_residues Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/extract_residues/extract_residues_log.out:file_utils.py:82 /tmp/biobb/unitests_46/extract_residues/sandbox_334bca3e-aafc-48f9-9b6a-06bf28f6cb4d directory successfully created\nINFO     /tmp/biobb/unitests_46/extract_residues/extract_residues_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_46/extract_residues/sandbox_334bca3e-aafc-48f9-9b6a-06bf28f6cb4d\nINFO     /tmp/biobb/unitests_46/extract_residues/extract_residues_log.out:file_utils.py:409 Writting pdb to: /tmp/biobb/unitests_46/extract_residues/sandbox_334bca3e-aafc-48f9-9b6a-06bf28f6cb4d/output_residues_path.pdb\nINFO     /tmp/biobb/unitests_46/extract_residues/extract_residues_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/extract_residues/sandbox_334bca3e-aafc-48f9-9b6a-06bf28f6cb4d&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/extract_residues/extract_residues_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:07,893 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.remove_ligand Version: 5.0.0\n2025-01-21 17:25:07,894 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/remove_ligand_gro/sandbox_953de3fc-2f39-4086-8b06-2d21f5bb7ca9 directory successfully created\n2025-01-21 17:25:07,903 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_46/remove_ligand_gro/sandbox_953de3fc-2f39-4086-8b06-2d21f5bb7ca9\n2025-01-21 17:25:07,904 [MainThread  ] [INFO ]  GRO format detected, removing all atoms from residues named AQ4\n2025-01-21 17:25:08,912 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/remove_ligand_gro/sandbox_953de3fc-2f39-4086-8b06-2d21f5bb7ca9&amp;#x27;]\n2025-01-21 17:25:08,912 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/remove_ligand_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_46/remove_ligand_gro/output_structure_path.gro\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_md_1.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.remove_ligand Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:82 /tmp/biobb/unitests_46/remove_ligand_gro/sandbox_953de3fc-2f39-4086-8b06-2d21f5bb7ca9 directory successfully created\nINFO     /tmp/biobb/unitests_46/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_46/remove_ligand_gro/sandbox_953de3fc-2f39-4086-8b06-2d21f5bb7ca9\nINFO     /tmp/biobb/unitests_46/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409 GRO format detected, removing all atoms from residues named AQ4\nINFO     /tmp/biobb/unitests_46/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/remove_ligand_gro/sandbox_953de3fc-2f39-4086-8b06-2d21f5bb7ca9&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:09,085 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.remove_ligand Version: 5.0.0\n2025-01-21 17:25:09,086 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/remove_ligand/sandbox_f7e70bd7-f5e6-4f1f-8d57-e9a4dcc1605b directory successfully created\n2025-01-21 17:25:09,096 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.pdb to /tmp/biobb/unitests_46/remove_ligand/sandbox_f7e70bd7-f5e6-4f1f-8d57-e9a4dcc1605b\n2025-01-21 17:25:09,097 [MainThread  ] [INFO ]  PDB format detected, removing all atoms from residues named AQ4\n2025-01-21 17:25:09,229 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/remove_ligand/sandbox_f7e70bd7-f5e6-4f1f-8d57-e9a4dcc1605b&amp;#x27;]\n2025-01-21 17:25:09,229 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/remove_ligand/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_46/remove_ligand/output_structure_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_md_1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 12872\n     Atoms ALIGNED in PDB_B: 12872\n     RMS: 1.3713554610601623e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/remove_ligand/remove_ligand_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.remove_ligand Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/remove_ligand/remove_ligand_log.out:file_utils.py:82 /tmp/biobb/unitests_46/remove_ligand/sandbox_f7e70bd7-f5e6-4f1f-8d57-e9a4dcc1605b directory successfully created\nINFO     /tmp/biobb/unitests_46/remove_ligand/remove_ligand_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.pdb to /tmp/biobb/unitests_46/remove_ligand/sandbox_f7e70bd7-f5e6-4f1f-8d57-e9a4dcc1605b\nINFO     /tmp/biobb/unitests_46/remove_ligand/remove_ligand_log.out:file_utils.py:409 PDB format detected, removing all atoms from residues named AQ4\nINFO     /tmp/biobb/unitests_46/remove_ligand/remove_ligand_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/remove_ligand/sandbox_f7e70bd7-f5e6-4f1f-8d57-e9a4dcc1605b&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/remove_ligand/remove_ligand_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&#34;, &#34;duration&#34;: &#34;00:00:17&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:17&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:16,459 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.remove_molecules Version: 5.0.0\n2025-01-21 17:25:16,459 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/remove_molecules/sandbox_0ffc9f7d-6b40-4fff-a0ea-a96bc52e50da directory successfully created\n2025-01-21 17:25:16,462 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_46/remove_molecules/sandbox_0ffc9f7d-6b40-4fff-a0ea-a96bc52e50da\n2025-01-21 17:25:33,335 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_46/remove_molecules/sandbox_0ffc9f7d-6b40-4fff-a0ea-a96bc52e50da/output_molecules_path.pdb\n2025-01-21 17:25:33,352 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/remove_molecules/sandbox_0ffc9f7d-6b40-4fff-a0ea-a96bc52e50da&amp;#x27;]\n2025-01-21 17:25:33,353 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/remove_molecules/output_molecules_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_46/remove_molecules/output_molecules_path.pdb\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_remove_molecules.pdb\n        File_A hash: b&amp;#x27;q$\\x11\\xa5u\\xca5\\xc0\\x90\\xd8\\x1bB&amp;amp;{\\xfcNm\\x85\\xb5(\\x8f\\x13\\xf0\\xef,\\xe6\\x8c\\x0ftV}\\x1d&amp;#x27;\n        File_B hash: b&amp;#x27;q$\\x11\\xa5u\\xca5\\xc0\\x90\\xd8\\x1bB&amp;amp;{\\xfcNm\\x85\\xb5(\\x8f\\x13\\xf0\\xef,\\xe6\\x8c\\x0ftV}\\x1d&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/remove_molecules/remove_molecules_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.remove_molecules Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/remove_molecules/remove_molecules_log.out:file_utils.py:82 /tmp/biobb/unitests_46/remove_molecules/sandbox_0ffc9f7d-6b40-4fff-a0ea-a96bc52e50da directory successfully created\nINFO     /tmp/biobb/unitests_46/remove_molecules/remove_molecules_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_46/remove_molecules/sandbox_0ffc9f7d-6b40-4fff-a0ea-a96bc52e50da\nINFO     /tmp/biobb/unitests_46/remove_molecules/remove_molecules_log.out:file_utils.py:409 Writting pdb to: /tmp/biobb/unitests_46/remove_molecules/sandbox_0ffc9f7d-6b40-4fff-a0ea-a96bc52e50da/output_molecules_path.pdb\nINFO     /tmp/biobb/unitests_46/remove_molecules/remove_molecules_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/remove_molecules/sandbox_0ffc9f7d-6b40-4fff-a0ea-a96bc52e50da&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/remove_molecules/remove_molecules_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:33,450 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.remove_pdb_water Version: 5.0.0\n2025-01-21 17:25:33,451 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af directory successfully created\n2025-01-21 17:25:33,453 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_WAT.pdb to /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af\n2025-01-21 17:25:33,453 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af/WT_aq4_md_WAT.pdb -o /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af/output_pdb_path.pdb --force_save water --remove yes\n\n2025-01-21 17:25:34,994 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2...\n2025-01-21 17:25:34,995 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 17:25:34,995 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af/WT_aq4_md_WAT.pdb loaded\n PDB id:  \n Title: protein in water\n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\n Num. residues:  397\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 294 (total 2404 H atoms)\n Num. HETATM residues:  2\n Num. ligands or modified residues:  0\n Num. water mol.:  2\n Num. atoms:  4858\nRunning water. Options: --remove yes\nDetected 2 Water molecules\nRemoved 2 Water molecules\nFinal Num. models: 1\nFinal Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\nFinal Num. residues:  395\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 292 (total 2401 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  4853\nStructure saved on /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af/output_pdb_path.pdb\n\n2025-01-21 17:25:34,998 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af&amp;#x27;]\n2025-01-21 17:25:34,998 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/remove_pdb_water/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_46/remove_pdb_water/output_pdb_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_no_wat.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3004\n     Atoms ALIGNED in PDB_B: 3004\n     RMS: 1.562368088062136e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.remove_pdb_water Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:82 /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af directory successfully created\nINFO     /tmp/biobb/unitests_46/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_WAT.pdb to /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af\nINFO     /tmp/biobb/unitests_46/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af/WT_aq4_md_WAT.pdb -o /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af/output_pdb_path.pdb --force_save water --remove yes\n\nINFO     /tmp/biobb/unitests_46/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2...\nINFO     /tmp/biobb/unitests_46/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_46/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af/WT_aq4_md_WAT.pdb loaded\n PDB id:  \n Title: protein in water\n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\n Num. residues:  397\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 294 (total 2404 H atoms)\n Num. HETATM residues:  2\n Num. ligands or modified residues:  0\n Num. water mol.:  2\n Num. atoms:  4858\nRunning water. Options: --remove yes\nDetected 2 Water molecules\nRemoved 2 Water molecules\nFinal Num. models: 1\nFinal Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\nFinal Num. residues:  395\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 292 (total 2401 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  4853\nStructure saved on /tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_46/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/remove_pdb_water/sandbox_d8f3f840-95c2-48e4-b8ca-b19a9db5d7af&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:35,700 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\n2025-01-21 17:25:35,701 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/renumber_structure_2vgb/sandbox_4c725fd3-b92a-41bb-bb7f-88145d954e59 directory successfully created\n2025-01-21 17:25:35,704 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_46/renumber_structure_2vgb/sandbox_4c725fd3-b92a-41bb-bb7f-88145d954e59\n2025-01-21 17:25:35,705 [MainThread  ] [INFO ]  PDB format detected, reenumerating atoms\n2025-01-21 17:25:35,898 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/renumber_structure_2vgb/sandbox_4c725fd3-b92a-41bb-bb7f-88145d954e59&amp;#x27;]\n2025-01-21 17:25:35,898 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/renumber_structure_2vgb/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_46/renumber_structure_2vgb/output_structure_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_2vgb.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 15488\n     Atoms ALIGNED in PDB_B: 15488\n     RMS: 1.1140374429086235e-14\n     RMS_CUTOFF: 1\nChecking if empty file: /tmp/biobb/unitests_46/renumber_structure_2vgb/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_46/renumber_structure_2vgb/output_mapping_json_path.json\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/2vgb_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;F\\xbe!`V\\xdb.\\x99\\xfb\\xda\\x94\\xb1\\xa8\\xdf6\\xbcJ\\\\\\\\\\xc7k\\xb6\\xe9\\xc1I\\nm\\xc1\\xe4:v\\x15&amp;#x27;\n        File_B hash: b&amp;#x27;F\\xbe!`V\\xdb.\\x99\\xfb\\xda\\x94\\xb1\\xa8\\xdf6\\xbcJ\\\\\\\\\\xc7k\\xb6\\xe9\\xc1I\\nm\\xc1\\xe4:v\\x15&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:82 /tmp/biobb/unitests_46/renumber_structure_2vgb/sandbox_4c725fd3-b92a-41bb-bb7f-88145d954e59 directory successfully created\nINFO     /tmp/biobb/unitests_46/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_46/renumber_structure_2vgb/sandbox_4c725fd3-b92a-41bb-bb7f-88145d954e59\nINFO     /tmp/biobb/unitests_46/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409 PDB format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_46/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/renumber_structure_2vgb/sandbox_4c725fd3-b92a-41bb-bb7f-88145d954e59&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&#34;, &#34;duration&#34;: &#34;378 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;378 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:37,951 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\n2025-01-21 17:25:37,952 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/renumber_structure_gro/sandbox_4bf2dc61-5e6f-4d34-9c4a-68c8515da92b directory successfully created\n2025-01-21 17:25:37,954 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/pyruvate.gro to /tmp/biobb/unitests_46/renumber_structure_gro/sandbox_4bf2dc61-5e6f-4d34-9c4a-68c8515da92b\n2025-01-21 17:25:37,954 [MainThread  ] [INFO ]  GRO format detected, reenumerating atoms\n2025-01-21 17:25:38,231 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/renumber_structure_gro/sandbox_4bf2dc61-5e6f-4d34-9c4a-68c8515da92b&amp;#x27;]\n2025-01-21 17:25:38,232 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/renumber_structure_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_46/renumber_structure_gro/output_structure_path.gro\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_pyruvate.gro\nChecking if empty file: /tmp/biobb/unitests_46/renumber_structure_gro/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_46/renumber_structure_gro/output_mapping_json_path.json\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/pyruvate_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;/\\xa1\\xe9\\x19X\\xe3\\xb5\\x15R \\x81\\x02\\xc4PX\\x11h\\x08\\x83\\xdb\\r\\xf9j\\xebP\\xe9\\\\\\x1eT#A\\r&amp;#x27;\n        File_B hash: b&amp;#x27;/\\xa1\\xe9\\x19X\\xe3\\xb5\\x15R \\x81\\x02\\xc4PX\\x11h\\x08\\x83\\xdb\\r\\xf9j\\xebP\\xe9\\\\\\x1eT#A\\r&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:82 /tmp/biobb/unitests_46/renumber_structure_gro/sandbox_4bf2dc61-5e6f-4d34-9c4a-68c8515da92b directory successfully created\nINFO     /tmp/biobb/unitests_46/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/pyruvate.gro to /tmp/biobb/unitests_46/renumber_structure_gro/sandbox_4bf2dc61-5e6f-4d34-9c4a-68c8515da92b\nINFO     /tmp/biobb/unitests_46/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409 GRO format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_46/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/renumber_structure_gro/sandbox_4bf2dc61-5e6f-4d34-9c4a-68c8515da92b&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&#34;, &#34;duration&#34;: &#34;88 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;88 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:38,331 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\n2025-01-21 17:25:38,331 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/renumber_structure/sandbox_ae5a71ff-1964-4817-9316-ffc4b06b31b6 directory successfully created\n2025-01-21 17:25:38,332 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cl3.noH.pdb to /tmp/biobb/unitests_46/renumber_structure/sandbox_ae5a71ff-1964-4817-9316-ffc4b06b31b6\n2025-01-21 17:25:38,333 [MainThread  ] [INFO ]  PDB format detected, reenumerating atoms\n2025-01-21 17:25:38,335 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/renumber_structure/sandbox_ae5a71ff-1964-4817-9316-ffc4b06b31b6&amp;#x27;]\n2025-01-21 17:25:38,336 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/renumber_structure/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_46/renumber_structure/output_structure_path.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_cl3_noH.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 28\n     Atoms ALIGNED in PDB_B: 28\n     RMS: 2.6855991067210084e-15\n     RMS_CUTOFF: 1\nChecking if empty file: /tmp/biobb/unitests_46/renumber_structure/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_46/renumber_structure/output_mapping_json_path.json\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/cl3_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;\\xe5\\xbc\\xaf\\xec\\xc4\\x1a\\x14\\x1d&amp;gt;\\x1f\\xe1\\x1a\\xbe_\\xd5g\\xb6\\xac\\xeb\\xce\\x9a\\xa4\\x9f\\xa7\\xf9\\x98\\xc7\\x00\\xaa\\xa2\\t\\x13&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe5\\xbc\\xaf\\xec\\xc4\\x1a\\x14\\x1d&amp;gt;\\x1f\\xe1\\x1a\\xbe_\\xd5g\\xb6\\xac\\xeb\\xce\\x9a\\xa4\\x9f\\xa7\\xf9\\x98\\xc7\\x00\\xaa\\xa2\\t\\x13&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/renumber_structure/renumber_structure_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/renumber_structure/renumber_structure_log.out:file_utils.py:82 /tmp/biobb/unitests_46/renumber_structure/sandbox_ae5a71ff-1964-4817-9316-ffc4b06b31b6 directory successfully created\nINFO     /tmp/biobb/unitests_46/renumber_structure/renumber_structure_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cl3.noH.pdb to /tmp/biobb/unitests_46/renumber_structure/sandbox_ae5a71ff-1964-4817-9316-ffc4b06b31b6\nINFO     /tmp/biobb/unitests_46/renumber_structure/renumber_structure_log.out:file_utils.py:409 PDB format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_46/renumber_structure/renumber_structure_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/renumber_structure/sandbox_ae5a71ff-1964-4817-9316-ffc4b06b31b6&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/renumber_structure/renumber_structure_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&#34;, &#34;duration&#34;: &#34;84 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;84 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:38,421 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\n2025-01-21 17:25:38,422 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/renumber_structure_smallgro/sandbox_ce6ed40d-7b90-4c44-8d76-a02f2049fe8c directory successfully created\n2025-01-21 17:25:38,423 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/smallgro.gro to /tmp/biobb/unitests_46/renumber_structure_smallgro/sandbox_ce6ed40d-7b90-4c44-8d76-a02f2049fe8c\n2025-01-21 17:25:38,423 [MainThread  ] [INFO ]  GRO format detected, reenumerating atoms\n2025-01-21 17:25:38,426 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/renumber_structure_smallgro/sandbox_ce6ed40d-7b90-4c44-8d76-a02f2049fe8c&amp;#x27;]\n2025-01-21 17:25:38,427 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/renumber_structure_smallgro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_46/renumber_structure_smallgro/output_structure_path.gro\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_smallgro.gro\nChecking if empty file: /tmp/biobb/unitests_46/renumber_structure_smallgro/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_46/renumber_structure_smallgro/output_mapping_json_path.json\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/smallgro_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;\\x8a\\t\\xfd\\xe8\\x8f@K\\xafz\\xd2\\x8dO\\xed[\\xe0\\xcchg\\xda\\xd7\\x13\\xb4\\x0c\\xcf3\\rNRg,\\xaf\\xf4&amp;#x27;\n        File_B hash: b&amp;#x27;\\x8a\\t\\xfd\\xe8\\x8f@K\\xafz\\xd2\\x8dO\\xed[\\xe0\\xcchg\\xda\\xd7\\x13\\xb4\\x0c\\xcf3\\rNRg,\\xaf\\xf4&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:82 /tmp/biobb/unitests_46/renumber_structure_smallgro/sandbox_ce6ed40d-7b90-4c44-8d76-a02f2049fe8c directory successfully created\nINFO     /tmp/biobb/unitests_46/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/smallgro.gro to /tmp/biobb/unitests_46/renumber_structure_smallgro/sandbox_ce6ed40d-7b90-4c44-8d76-a02f2049fe8c\nINFO     /tmp/biobb/unitests_46/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409 GRO format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_46/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/renumber_structure_smallgro/sandbox_ce6ed40d-7b90-4c44-8d76-a02f2049fe8c&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&#34;, &#34;duration&#34;: &#34;00:00:10&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:10&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:38,508 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.sort_gro_residues Version: 5.0.0\n2025-01-21 17:25:38,509 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/sort_gro_residues/sandbox_e266e03c-54e9-49e0-a62d-827d6b438dbe directory successfully created\n2025-01-21 17:25:38,515 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_46/sort_gro_residues/sandbox_e266e03c-54e9-49e0-a62d-827d6b438dbe\n2025-01-21 17:25:48,596 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/sort_gro_residues/sandbox_e266e03c-54e9-49e0-a62d-827d6b438dbe&amp;#x27;]\n2025-01-21 17:25:48,597 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/sort_gro_residues/output_gro_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_46/sort_gro_residues/output_gro_path.gro\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_aq4_md_sorted.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.sort_gro_residues Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:82 /tmp/biobb/unitests_46/sort_gro_residues/sandbox_e266e03c-54e9-49e0-a62d-827d6b438dbe directory successfully created\nINFO     /tmp/biobb/unitests_46/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_46/sort_gro_residues/sandbox_e266e03c-54e9-49e0-a62d-827d6b438dbe\nINFO     /tmp/biobb/unitests_46/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/sort_gro_residues/sandbox_e266e03c-54e9-49e0-a62d-827d6b438dbe&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:48,760 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.str_check_add_hydrogens Version: 5.0.0\n2025-01-21 17:25:48,761 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9 directory successfully created\n2025-01-21 17:25:48,762 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/str_no_H.pdb to /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9\n2025-01-21 17:25:48,763 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9/str_no_H.pdb -o /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9/output_structure_path.pdbqt --non_interactive --force_save --keep_canonical_resnames command_list --list &amp;#x27;add_hydrogen --add_charges ADT --add_mode auto &amp;#x27;\n\n2025-01-21 17:25:51,402 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c0...\n2025-01-21 17:25:51,403 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 17:25:51,404 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9/str_no_H.pdb loaded\n PDB id:  \n Title: \n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  532\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  15\n Num. ligands or modified residues:  3\n Num. water mol.:  12\n Num. atoms:  3946\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\n\nStep 1: add_hydrogen --add_charges ADT --add_mode auto \nRunning add_hydrogen. Options: --add_charges ADT --add_mode auto\nFound 143 Residues requiring selection on adding H atoms\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A72 by HIE\nReplacing HIS A121 by HIE\nReplacing HIS A124 by HIE\nReplacing HIS A127 by HIE\nReplacing HIS A278 by HIE\nReplacing HIS A306 by HIE\nReplacing HIS A317 by HIE\nReplacing HIS A422 by HIE\nReplacing HIS A434 by HIE\nReplacing HIS A507 by HIE\nUpdating partial charges and atom types\nWarning: OXT atom missing in CILE A573. Run backbone --fix_atoms first\nWarning: FBP not found in residue library atom, charges set to 0.\nWarning: K not found in residue library atom, charges set to 0.\nWarning: MN not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nTotal assigned charge:      -1.25\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  532\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 517 (total 3995 H atoms)\nFinal Num. HETATM residues:  15\nFinal Num. ligands or modified residues:  3\nFinal Num. water mol.:  12\nFinal Num. atoms:  7941\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\nWarning: reverting residue names to canonical on output\nStructure saved on /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9/output_structure_path.pdbqt\n\n2025-01-21 17:25:51,414 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/str_check_add_hydrogens/output_structure_path.pdbqt file ends with END, cleaning\n2025-01-21 17:25:51,423 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9&amp;#x27;]\n2025-01-21 17:25:51,424 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/str_check_add_hydrogens/output_structure_path.pdbqt\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.str_check_add_hydrogens Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9 directory successfully created\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/str_no_H.pdb to /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9/str_no_H.pdb -o /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9/output_structure_path.pdbqt --non_interactive --force_save --keep_canonical_resnames command_list --list &amp;#x27;add_hydrogen --add_charges ADT --add_mode auto &amp;#x27;\n\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c0...\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9/str_no_H.pdb loaded\n PDB id:  \n Title: \n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  532\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  15\n Num. ligands or modified residues:  3\n Num. water mol.:  12\n Num. atoms:  3946\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\n\nStep 1: add_hydrogen --add_charges ADT --add_mode auto \nRunning add_hydrogen. Options: --add_charges ADT --add_mode auto\nFound 143 Residues requiring selection on adding H atoms\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A72 by HIE\nReplacing HIS A121 by HIE\nReplacing HIS A124 by HIE\nReplacing HIS A127 by HIE\nReplacing HIS A278 by HIE\nReplacing HIS A306 by HIE\nReplacing HIS A317 by HIE\nReplacing HIS A422 by HIE\nReplacing HIS A434 by HIE\nReplacing HIS A507 by HIE\nUpdating partial charges and atom types\nWarning: OXT atom missing in CILE A573. Run backbone --fix_atoms first\nWarning: FBP not found in residue library atom, charges set to 0.\nWarning: K not found in residue library atom, charges set to 0.\nWarning: MN not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nTotal assigned charge:      -1.25\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  532\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 517 (total 3995 H atoms)\nFinal Num. HETATM residues:  15\nFinal Num. ligands or modified residues:  3\nFinal Num. water mol.:  12\nFinal Num. atoms:  7941\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\nWarning: reverting residue names to canonical on output\nStructure saved on /tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9/output_structure_path.pdbqt\n\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409 /tmp/biobb/unitests_46/str_check_add_hydrogens/output_structure_path.pdbqt file ends with END, cleaning\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/str_check_add_hydrogens/sandbox_10a2c034-5e27-4f3d-af42-503c962d3fc9&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-21 17:25:51,516 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.structure_check Version: 5.0.0\n2025-01-21 17:25:51,516 [MainThread  ] [INFO ]  /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60 directory successfully created\n2025-01-21 17:25:51,519 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60\n2025-01-21 17:25:51,520 [MainThread  ] [INFO ]  Computing features: chains, models\n2025-01-21 17:25:51,520 [MainThread  ] [INFO ]  Creating a1891291-3ff5-432c-a151-7bd7d4eb7ecc temporary folder\n2025-01-21 17:25:51,521 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60/2vgb.pdb --json /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60/output_summary_path.json --check_only --non_interactive command_list --list a1891291-3ff5-432c-a151-7bd7d4eb7ecc/command_list.lst\n\n2025-01-21 17:25:54,561 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-...\n2025-01-21 17:25:54,562 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-21 17:25:54,563 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60/2vgb.pdb loaded\n PDB id: 2VGB \n Title: human erythrocyte pyruvate kinase\n Experimental method: x-ray diffraction\n Keywords: metal-binding, phosphorylation, pyruvate kinase in the active r- state, kinase, pyruvate, magnesium, glycolysis, transferase, disease mutation\n Resolution (A): 2.73\n\n Num. models: 1\n Num. chains: 4 (A: Protein, B: Protein, C: Protein, D: Protein)\n Num. residues:  2118\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  81\n Num. ligands or modified residues:  16\n Num. water mol.:  65\n Num. atoms:  15612\nMetal/Ion residues found\n  K A582\n MN A583\n  K B586\n MN B587\n  K C590\n MN C591\n  K D594\n MN D595\nSmall mol ligands found\nFBP A580\nPGA A581\nFBP B580\nPGA B581\nFBP C580\nPGA C581\nFBP D580\nPGA D581\n\nStep 1: chains\n\nRunning chains.\nDetected 4 Chain(s)\n A: Protein\n B: Protein\n C: Protein\n D: Protein\n\nStep 2: models\n\nRunning models.\nDetected 1 Model(s)\nFound Single model\nCommand list completed\nSummary data saved on /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60/output_summary_path.json\n\n2025-01-21 17:25:54,565 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60&amp;#x27;, &amp;#x27;a1891291-3ff5-432c-a151-7bd7d4eb7ecc&amp;#x27;]\n2025-01-21 17:25:54,566 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_46/structure_check/output_summary_path.json\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.structure_check Version: 5.0.0\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:file_utils.py:82 /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60 directory successfully created\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:file_utils.py:409 Computing features: chains, models\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:file_utils.py:409 Creating a1891291-3ff5-432c-a151-7bd7d4eb7ecc temporary folder\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60/2vgb.pdb --json /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60/output_summary_path.json --check_only --non_interactive command_list --list a1891291-3ff5-432c-a151-7bd7d4eb7ecc/command_list.lst\n\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-...\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60/2vgb.pdb loaded\n PDB id: 2VGB \n Title: human erythrocyte pyruvate kinase\n Experimental method: x-ray diffraction\n Keywords: metal-binding, phosphorylation, pyruvate kinase in the active r- state, kinase, pyruvate, magnesium, glycolysis, transferase, disease mutation\n Resolution (A): 2.73\n\n Num. models: 1\n Num. chains: 4 (A: Protein, B: Protein, C: Protein, D: Protein)\n Num. residues:  2118\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  81\n Num. ligands or modified residues:  16\n Num. water mol.:  65\n Num. atoms:  15612\nMetal/Ion residues found\n  K A582\n MN A583\n  K B586\n MN B587\n  K C590\n MN C591\n  K D594\n MN D595\nSmall mol ligands found\nFBP A580\nPGA A581\nFBP B580\nPGA B581\nFBP C580\nPGA C581\nFBP D580\nPGA D581\n\nStep 1: chains\n\nRunning chains.\nDetected 4 Chain(s)\n A: Protein\n B: Protein\n C: Protein\n D: Protein\n\nStep 2: models\n\nRunning models.\nDetected 1 Model(s)\nFound Single model\nCommand list completed\nSummary data saved on /tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60/output_summary_path.json\n\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_46/structure_check/sandbox_e129035c-c120-442e-94a8-52b5c6676d60&amp;#x27;, &amp;#x27;a1891291-3ff5-432c-a151-7bd7d4eb7ecc&amp;#x27;]\nINFO     /tmp/biobb/unitests_46/structure_check/structure_check_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_46\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.10.16&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-204-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.4&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&#34;, &#34;duration&#34;: &#34;246 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py::TestCatPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;246 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:03,482 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.cat_pdb Version: 5.0.0\n2025-01-28 11:50:03,482 [MainThread  ] [INFO ]  /tmp/biobb/unitests_47/cat_pdb/sandbox_a735e0d1-4a6c-4f72-8b48-c3172f7ccccd directory successfully created\n2025-01-28 11:50:03,483 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_protein.pdb to /tmp/biobb/unitests_47/cat_pdb/sandbox_a735e0d1-4a6c-4f72-8b48-c3172f7ccccd\n2025-01-28 11:50:03,483 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_ligand.pdb to /tmp/biobb/unitests_47/cat_pdb/sandbox_a735e0d1-4a6c-4f72-8b48-c3172f7ccccd\n2025-01-28 11:50:03,485 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_47/cat_pdb/sandbox_a735e0d1-4a6c-4f72-8b48-c3172f7ccccd&amp;#x27;]\n2025-01-28 11:50:03,485 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_47/cat_pdb/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_47/cat_pdb/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2058\n     Atoms ALIGNED in PDB_B: 2058\n     RMS: 6.579094722437545e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_47/cat_pdb/cat_pdb_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.cat_pdb Version: 5.0.0\nINFO     /tmp/biobb/unitests_47/cat_pdb/cat_pdb_log.out:file_utils.py:82 /tmp/biobb/unitests_47/cat_pdb/sandbox_a735e0d1-4a6c-4f72-8b48-c3172f7ccccd directory successfully created\nINFO     /tmp/biobb/unitests_47/cat_pdb/cat_pdb_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_protein.pdb to /tmp/biobb/unitests_47/cat_pdb/sandbox_a735e0d1-4a6c-4f72-8b48-c3172f7ccccd\nINFO     /tmp/biobb/unitests_47/cat_pdb/cat_pdb_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cat_ligand.pdb to /tmp/biobb/unitests_47/cat_pdb/sandbox_a735e0d1-4a6c-4f72-8b48-c3172f7ccccd\nINFO     /tmp/biobb/unitests_47/cat_pdb/cat_pdb_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_47/cat_pdb/sandbox_a735e0d1-4a6c-4f72-8b48-c3172f7ccccd&amp;#x27;]\nINFO     /tmp/biobb/unitests_47/cat_pdb/cat_pdb_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_47\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py::TestClosestResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:03,741 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.closest_residues Version: 5.0.0\n2025-01-28 11:50:03,741 [MainThread  ] [INFO ]  /tmp/biobb/unitests_47/closest_residues/sandbox_06b6b817-49e3-409b-8137-11c9501c4e31 directory successfully created\n2025-01-28 11:50:03,742 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_47/closest_residues/sandbox_06b6b817-49e3-409b-8137-11c9501c4e31\n2025-01-28 11:50:04,149 [MainThread  ] [INFO ]  Found 548 nearby residues\n2025-01-28 11:50:05,592 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_47/closest_residues/sandbox_06b6b817-49e3-409b-8137-11c9501c4e31/output_residues_path.pdb\n2025-01-28 11:50:05,594 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_47/closest_residues/sandbox_06b6b817-49e3-409b-8137-11c9501c4e31&amp;#x27;]\n2025-01-28 11:50:05,595 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_47/closest_residues/output_residues_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_47/closest_residues/output_residues_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_closest_residues.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 4251\n     Atoms ALIGNED in PDB_B: 4251\n     RMS: 1.931680690520553e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_47/closest_residues/closest_residues_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.closest_residues Version: 5.0.0\nINFO     /tmp/biobb/unitests_47/closest_residues/closest_residues_log.out:file_utils.py:82 /tmp/biobb/unitests_47/closest_residues/sandbox_06b6b817-49e3-409b-8137-11c9501c4e31 directory successfully created\nINFO     /tmp/biobb/unitests_47/closest_residues/closest_residues_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_47/closest_residues/sandbox_06b6b817-49e3-409b-8137-11c9501c4e31\nINFO     /tmp/biobb/unitests_47/closest_residues/closest_residues_log.out:file_utils.py:409 Found 548 nearby residues\nINFO     /tmp/biobb/unitests_47/closest_residues/closest_residues_log.out:file_utils.py:409 Writting pdb to: /tmp/biobb/unitests_47/closest_residues/sandbox_06b6b817-49e3-409b-8137-11c9501c4e31/output_residues_path.pdb\nINFO     /tmp/biobb/unitests_47/closest_residues/closest_residues_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_47/closest_residues/sandbox_06b6b817-49e3-409b-8137-11c9501c4e31&amp;#x27;]\nINFO     /tmp/biobb/unitests_47/closest_residues/closest_residues_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_47\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py::TestExtractAtomsGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:05,811 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_atoms Version: 5.0.0\n2025-01-28 11:50:05,812 [MainThread  ] [INFO ]  /tmp/biobb/unitests_47/extract_atoms_gro/sandbox_baec0480-a877-48a5-9074-b03bbeafbfce directory successfully created\n2025-01-28 11:50:05,815 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/G2S_stateA_frame92.sorted.gro to /tmp/biobb/unitests_47/extract_atoms_gro/sandbox_baec0480-a877-48a5-9074-b03bbeafbfce\n2025-01-28 11:50:05,815 [MainThread  ] [INFO ]  GRO format detected, extracting all atoms matching ^D\n2025-01-28 11:50:10,848 [MainThread  ] [INFO ]  4 atoms found writting GRO file\n2025-01-28 11:50:10,850 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_atoms_gro/sandbox_baec0480-a877-48a5-9074-b03bbeafbfce&amp;#x27;]\n2025-01-28 11:50:10,850 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_47/extract_atoms_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_47/extract_atoms_gro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/dummy_atoms.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_47/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_atoms Version: 5.0.0\nINFO     /tmp/biobb/unitests_47/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:82 /tmp/biobb/unitests_47/extract_atoms_gro/sandbox_baec0480-a877-48a5-9074-b03bbeafbfce directory successfully created\nINFO     /tmp/biobb/unitests_47/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/G2S_stateA_frame92.sorted.gro to /tmp/biobb/unitests_47/extract_atoms_gro/sandbox_baec0480-a877-48a5-9074-b03bbeafbfce\nINFO     /tmp/biobb/unitests_47/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 GRO format detected, extracting all atoms matching ^D\nINFO     /tmp/biobb/unitests_47/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 4 atoms found writting GRO file\nINFO     /tmp/biobb/unitests_47/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_atoms_gro/sandbox_baec0480-a877-48a5-9074-b03bbeafbfce&amp;#x27;]\nINFO     /tmp/biobb/unitests_47/extract_atoms_gro/extract_atoms_gro_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_47\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&#34;, &#34;duration&#34;: &#34;77 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py::TestExtractAtomsPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;77 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:10,886 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_atoms Version: 5.0.0\n2025-01-28 11:50:10,887 [MainThread  ] [INFO ]  /tmp/biobb/unitests_47/extract_atoms/sandbox_afd6001a-cd31-4430-ae11-2a46791f599b directory successfully created\n2025-01-28 11:50:10,888 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_47/extract_atoms/sandbox_afd6001a-cd31-4430-ae11-2a46791f599b\n2025-01-28 11:50:10,888 [MainThread  ] [INFO ]  PDB format detected, extracting all atoms matching OE2\n2025-01-28 11:50:10,919 [MainThread  ] [INFO ]  141 atoms found writting PDB file\n2025-01-28 11:50:10,920 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_atoms/sandbox_afd6001a-cd31-4430-ae11-2a46791f599b&amp;#x27;]\n2025-01-28 11:50:10,920 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_47/extract_atoms/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_47/extract_atoms/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/OE2_atoms.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 141\n     Atoms ALIGNED in PDB_B: 141\n     RMS: 1.3133613935773403e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_47/extract_atoms/extract_atoms_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_atoms Version: 5.0.0\nINFO     /tmp/biobb/unitests_47/extract_atoms/extract_atoms_log.out:file_utils.py:82 /tmp/biobb/unitests_47/extract_atoms/sandbox_afd6001a-cd31-4430-ae11-2a46791f599b directory successfully created\nINFO     /tmp/biobb/unitests_47/extract_atoms/extract_atoms_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_47/extract_atoms/sandbox_afd6001a-cd31-4430-ae11-2a46791f599b\nINFO     /tmp/biobb/unitests_47/extract_atoms/extract_atoms_log.out:file_utils.py:409 PDB format detected, extracting all atoms matching OE2\nINFO     /tmp/biobb/unitests_47/extract_atoms/extract_atoms_log.out:file_utils.py:409 141 atoms found writting PDB file\nINFO     /tmp/biobb/unitests_47/extract_atoms/extract_atoms_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_atoms/sandbox_afd6001a-cd31-4430-ae11-2a46791f599b&amp;#x27;]\nINFO     /tmp/biobb/unitests_47/extract_atoms/extract_atoms_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_47\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&#34;, &#34;duration&#34;: &#34;423 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py::TestExtractChain::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;423 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:10,965 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_chain Version: 5.0.0\n2025-01-28 11:50:10,965 [MainThread  ] [INFO ]  /tmp/biobb/unitests_47/extract_chain/sandbox_702b38b4-f59f-439a-b6aa-797a6863c5cc directory successfully created\n2025-01-28 11:50:10,966 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_chain.pdb to /tmp/biobb/unitests_47/extract_chain/sandbox_702b38b4-f59f-439a-b6aa-797a6863c5cc\n2025-01-28 11:50:10,966 [MainThread  ] [INFO ]  Selected Chains: B,C\n2025-01-28 11:50:10,966 [MainThread  ] [INFO ]  Warning: Use permissive=True is a risky option use it under your own responsability\n2025-01-28 11:50:10,981 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_chain/sandbox_702b38b4-f59f-439a-b6aa-797a6863c5cc&amp;#x27;]\n2025-01-28 11:50:10,982 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_47/extract_chain/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_47/extract_chain/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_chain.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 7893\n     Atoms ALIGNED in PDB_B: 7893\n     RMS: 1.6129351886983116e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_47/extract_chain/extract_chain_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_chain Version: 5.0.0\nINFO     /tmp/biobb/unitests_47/extract_chain/extract_chain_log.out:file_utils.py:82 /tmp/biobb/unitests_47/extract_chain/sandbox_702b38b4-f59f-439a-b6aa-797a6863c5cc directory successfully created\nINFO     /tmp/biobb/unitests_47/extract_chain/extract_chain_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_chain.pdb to /tmp/biobb/unitests_47/extract_chain/sandbox_702b38b4-f59f-439a-b6aa-797a6863c5cc\nINFO     /tmp/biobb/unitests_47/extract_chain/extract_chain_log.out:file_utils.py:409 Selected Chains: B,C\nINFO     /tmp/biobb/unitests_47/extract_chain/extract_chain_log.out:file_utils.py:409 Warning: Use permissive=True is a risky option use it under your own responsability\nINFO     /tmp/biobb/unitests_47/extract_chain/extract_chain_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_chain/sandbox_702b38b4-f59f-439a-b6aa-797a6863c5cc&amp;#x27;]\nINFO     /tmp/biobb/unitests_47/extract_chain/extract_chain_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_47\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py::TestExtractHeteroAtoms::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:11,393 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_heteroatoms Version: 5.0.0\n2025-01-28 11:50:11,393 [MainThread  ] [INFO ]  /tmp/biobb/unitests_47/extract_heteroatoms/sandbox_f4455103-9d0b-4349-8e59-a29b61a33db6 directory successfully created\n2025-01-28 11:50:11,396 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb to /tmp/biobb/unitests_47/extract_heteroatoms/sandbox_f4455103-9d0b-4349-8e59-a29b61a33db6\n2025-01-28 11:50:12,459 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_47/extract_heteroatoms/sandbox_f4455103-9d0b-4349-8e59-a29b61a33db6/output_heteroatom_path.pdb\n2025-01-28 11:50:12,460 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_heteroatoms/sandbox_f4455103-9d0b-4349-8e59-a29b61a33db6&amp;#x27;]\n2025-01-28 11:50:12,460 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_47/extract_heteroatoms/output_heteroatom_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_47/extract_heteroatoms/output_heteroatom_path.pdb\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_heteroatom.pdb\n        File_A hash: b&amp;#x27;\\x1e\\x83\\x13\\xbd\\xed\\xd0\\xcb0J\\xed\\x0eCp\\xe8\\xe2\\x91\\xf0w~x\\xd5\\x95\\xfc^9\\x83J\\x00\\x0f!^\\x04&amp;#x27;\n        File_B hash: b&amp;#x27;\\x1e\\x83\\x13\\xbd\\xed\\xd0\\xcb0J\\xed\\x0eCp\\xe8\\xe2\\x91\\xf0w~x\\xd5\\x95\\xfc^9\\x83J\\x00\\x0f!^\\x04&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_47/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_heteroatoms Version: 5.0.0\nINFO     /tmp/biobb/unitests_47/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:82 /tmp/biobb/unitests_47/extract_heteroatoms/sandbox_f4455103-9d0b-4349-8e59-a29b61a33db6 directory successfully created\nINFO     /tmp/biobb/unitests_47/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb to /tmp/biobb/unitests_47/extract_heteroatoms/sandbox_f4455103-9d0b-4349-8e59-a29b61a33db6\nINFO     /tmp/biobb/unitests_47/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409 Writting pdb to: /tmp/biobb/unitests_47/extract_heteroatoms/sandbox_f4455103-9d0b-4349-8e59-a29b61a33db6/output_heteroatom_path.pdb\nINFO     /tmp/biobb/unitests_47/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_heteroatoms/sandbox_f4455103-9d0b-4349-8e59-a29b61a33db6&amp;#x27;]\nINFO     /tmp/biobb/unitests_47/extract_heteroatoms/extract_heteroatoms_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_47\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_model.py::TestExtractModel::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:12,498 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_model Version: 5.0.0\n2025-01-28 11:50:12,498 [MainThread  ] [INFO ]  /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6 directory successfully created\n2025-01-28 11:50:12,500 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_model.pdb to /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6\n2025-01-28 11:50:12,500 [MainThread  ] [INFO ]  Creating a1f421b9-3a6e-4782-a190-9b7707b30a7e temporary folder\n2025-01-28 11:50:12,500 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6/extract_model.pdb -o a1f421b9-3a6e-4782-a190-9b7707b30a7e/model1.pdb --force_save models --select 1\n\n2025-01-28 11:50:14,041 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-42...\n2025-01-28 11:50:14,041 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-28 11:50:14,041 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 1\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 1\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on a1f421b9-3a6e-4782-a190-9b7707b30a7e/model1.pdb\n\n2025-01-28 11:50:14,041 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6/extract_model.pdb -o a1f421b9-3a6e-4782-a190-9b7707b30a7e/model4.pdb --force_save models --select 4\n\n2025-01-28 11:50:15,639 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-42...\n2025-01-28 11:50:15,639 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-28 11:50:15,639 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 4\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 4\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on a1f421b9-3a6e-4782-a190-9b7707b30a7e/model4.pdb\n\n2025-01-28 11:50:15,642 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6&amp;#x27;, &amp;#x27;a1f421b9-3a6e-4782-a190-9b7707b30a7e&amp;#x27;]\n2025-01-28 11:50:15,642 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_47/extract_model/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_47/extract_model/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_model.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 636\n     Atoms ALIGNED in PDB_B: 636\n     RMS: 5.262008214811879e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_model Version: 5.0.0\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:file_utils.py:82 /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6 directory successfully created\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_model.pdb to /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:file_utils.py:409 Creating a1f421b9-3a6e-4782-a190-9b7707b30a7e temporary folder\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6/extract_model.pdb -o a1f421b9-3a6e-4782-a190-9b7707b30a7e/model1.pdb --force_save models --select 1\n\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-42...\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 1\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 1\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on a1f421b9-3a6e-4782-a190-9b7707b30a7e/model1.pdb\n\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6/extract_model.pdb -o a1f421b9-3a6e-4782-a190-9b7707b30a7e/model4.pdb --force_save models --select 4\n\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-42...\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6/extract_model.pdb loaded\n PDB id: 1NMR \n Title: solution structure of c-terminal domain from trypanosoma cruzi poly(a)-binding protein\n Experimental method: solution nmr\n Keywords: all helical domain, peptide binding protein\n Resolution (A): N.A.\n\n Num. models: 20 (type: Ensembl/NMR,    6.831 A)\n Num. chains: 20 (A/0: Protein|A/1: Protein|A/2: Protein|A/3: Protein|A/4: Protein|A/5: Protein|A/6: Protein|A/7: Protein|A/8: Protein|A/9: Protein|A/10: Protein|A/11: Protein|A/12: Protein|A/13: Protein|A/14: Protein|A/15: Protein|A/16: Protein|A/17: Protein|A/18: Protein|A/19: Protein)\n Num. residues:  1700\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 1700 (total 13080 H atoms)\n Num. HETATM residues:  0\n Num. ligands or modified residues:  0\n Num. water mol.:  0\n Num. atoms:  25800\nRunning models. Options: --select 4\nDetected 20 Model(s)\nModels  superimpose, RMSd:    6.831 A, guessed as Ensembl/NMR \nSelecting model num. 4\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  85\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 85 (total 654 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1290\nStructure saved on a1f421b9-3a6e-4782-a190-9b7707b30a7e/model4.pdb\n\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_47/extract_model/sandbox_af014458-a201-4207-9802-0a322dca72e6&amp;#x27;, &amp;#x27;a1f421b9-3a6e-4782-a190-9b7707b30a7e&amp;#x27;]\nINFO     /tmp/biobb/unitests_47/extract_model/extract_model_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&#34;, &#34;duration&#34;: &#34;866 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py::TestExtractMolecule::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;866 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:15,775 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_molecule Version: 5.0.0\n2025-01-28 11:50:15,775 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/extract_molecule/sandbox_87d0349b-6ae1-40fc-8aac-9123e3ea8587 directory successfully created\n2025-01-28 11:50:15,776 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb to /tmp/biobb/unitests_48/extract_molecule/sandbox_87d0349b-6ae1-40fc-8aac-9123e3ea8587\n2025-01-28 11:50:15,776 [MainThread  ] [INFO ]  Creating aa65e45d-8c97-4a07-a47d-538d8e4c3aeb temporary folder\n2025-01-28 11:50:15,776 [MainThread  ] [INFO ]  check_structure -i /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb -o /tmp/biobb/unitests_48/extract_molecule/output_molecule_path.pdb --force_save --non_interactive command_list --list aa65e45d-8c97-4a07-a47d-538d8e4c3aeb/extract_prot.lst\n\n2025-01-28 11:50:16,518 [MainThread  ] [INFO ]  Executing: check_structure -i /home/user/actions-runner/_work/biobb_structure_utils/biobb_s...\n2025-01-28 11:50:16,518 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-28 11:50:16,518 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb loaded\n PDB id: 1G54 \n Title: carbonic anhydrase ii complexed with 4-(aminosulfonyl)-n-[(2,3,4,5,6- pentafluorophenyl)methyl]-benzamide\n Experimental method: x-ray diffraction\n Keywords: carbonic anhydrase ii, 4-(aminosulfonyl)-n-[(2, 3, 4, 5, 6- pentafluorophenyl)methyl]-benzamide, lyase\n Resolution (A): 1.86\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  332\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  74\n Num. ligands or modified residues:  3\n Num. water mol.:  71\n Num. atoms:  2156\nMetal/Ion residues found\n ZN A262\n HG A263\nSmall mol ligands found\nFFB A555\n\nStep 1: ligands --remove All\n\nRunning ligands. Options: --remove All\nDetected 3 Ligands\n  ZN A262\n  HG A263\n FFB A555\nLigands removed All (3)\n\nStep 2: water --remove Yes\n\nRunning water. Options: --remove Yes\nDetected 71 Water molecules\nRemoved 71 Water molecules\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  258\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  2058\nStructure saved on /tmp/biobb/unitests_48/extract_molecule/output_molecule_path.pdb\n\n2025-01-28 11:50:16,519 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/extract_molecule/sandbox_87d0349b-6ae1-40fc-8aac-9123e3ea8587&amp;#x27;]\n2025-01-28 11:50:16,519 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/extract_molecule/output_molecule_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_48/extract_molecule/output_molecule_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_molecule.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2058\n     Atoms ALIGNED in PDB_B: 2058\n     RMS: 6.579094722437545e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_molecule Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:file_utils.py:82 /tmp/biobb/unitests_48/extract_molecule/sandbox_87d0349b-6ae1-40fc-8aac-9123e3ea8587 directory successfully created\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb to /tmp/biobb/unitests_48/extract_molecule/sandbox_87d0349b-6ae1-40fc-8aac-9123e3ea8587\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:file_utils.py:409 Creating aa65e45d-8c97-4a07-a47d-538d8e4c3aeb temporary folder\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:63 check_structure -i /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb -o /tmp/biobb/unitests_48/extract_molecule/output_molecule_path.pdb --force_save --non_interactive command_list --list aa65e45d-8c97-4a07-a47d-538d8e4c3aeb/extract_prot.lst\n\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:36 Executing: check_structure -i /home/user/actions-runner/_work/biobb_structure_utils/biobb_s...\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/extract_molecule.pdb loaded\n PDB id: 1G54 \n Title: carbonic anhydrase ii complexed with 4-(aminosulfonyl)-n-[(2,3,4,5,6- pentafluorophenyl)methyl]-benzamide\n Experimental method: x-ray diffraction\n Keywords: carbonic anhydrase ii, 4-(aminosulfonyl)-n-[(2, 3, 4, 5, 6- pentafluorophenyl)methyl]-benzamide, lyase\n Resolution (A): 1.86\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  332\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  74\n Num. ligands or modified residues:  3\n Num. water mol.:  71\n Num. atoms:  2156\nMetal/Ion residues found\n ZN A262\n HG A263\nSmall mol ligands found\nFFB A555\n\nStep 1: ligands --remove All\n\nRunning ligands. Options: --remove All\nDetected 3 Ligands\n  ZN A262\n  HG A263\n FFB A555\nLigands removed All (3)\n\nStep 2: water --remove Yes\n\nRunning water. Options: --remove Yes\nDetected 71 Water molecules\nRemoved 71 Water molecules\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  258\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  2058\nStructure saved on /tmp/biobb/unitests_48/extract_molecule/output_molecule_path.pdb\n\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/extract_molecule/sandbox_87d0349b-6ae1-40fc-8aac-9123e3ea8587&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/extract_molecule/extract_molecule_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&#34;, &#34;duration&#34;: &#34;659 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py::TestExtractResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;659 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:16,641 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.extract_residues Version: 5.0.0\n2025-01-28 11:50:16,641 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/extract_residues/sandbox_00cd3ddb-92c3-4387-9d7c-6c5dd5eaef0f directory successfully created\n2025-01-28 11:50:16,643 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_48/extract_residues/sandbox_00cd3ddb-92c3-4387-9d7c-6c5dd5eaef0f\n2025-01-28 11:50:17,263 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_48/extract_residues/sandbox_00cd3ddb-92c3-4387-9d7c-6c5dd5eaef0f/output_residues_path.pdb\n2025-01-28 11:50:17,264 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/extract_residues/sandbox_00cd3ddb-92c3-4387-9d7c-6c5dd5eaef0f&amp;#x27;]\n2025-01-28 11:50:17,264 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/extract_residues/output_residues_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_48/extract_residues/output_residues_path.pdb\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_extract_residues.pdb\n        File_A hash: b&amp;#x27;\\xf0\\x84\\xb8D\\x90whe\\xc3T\\xe2\\xf3\\\\\\xd72\\xfaT\\x9d\\x19\\x88\\xab\\x03\\xbe\\xf6\\x9a\\x81\\xec\\x15tx`D&amp;#x27;\n        File_B hash: b&amp;#x27;\\xf0\\x84\\xb8D\\x90whe\\xc3T\\xe2\\xf3\\\\\\xd72\\xfaT\\x9d\\x19\\x88\\xab\\x03\\xbe\\xf6\\x9a\\x81\\xec\\x15tx`D&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/extract_residues/extract_residues_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.extract_residues Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/extract_residues/extract_residues_log.out:file_utils.py:82 /tmp/biobb/unitests_48/extract_residues/sandbox_00cd3ddb-92c3-4387-9d7c-6c5dd5eaef0f directory successfully created\nINFO     /tmp/biobb/unitests_48/extract_residues/extract_residues_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_48/extract_residues/sandbox_00cd3ddb-92c3-4387-9d7c-6c5dd5eaef0f\nINFO     /tmp/biobb/unitests_48/extract_residues/extract_residues_log.out:file_utils.py:409 Writting pdb to: /tmp/biobb/unitests_48/extract_residues/sandbox_00cd3ddb-92c3-4387-9d7c-6c5dd5eaef0f/output_residues_path.pdb\nINFO     /tmp/biobb/unitests_48/extract_residues/extract_residues_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/extract_residues/sandbox_00cd3ddb-92c3-4387-9d7c-6c5dd5eaef0f&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/extract_residues/extract_residues_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&#34;, &#34;duration&#34;: &#34;497 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py::TestRemoveLigandGro::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;497 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:17,302 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.remove_ligand Version: 5.0.0\n2025-01-28 11:50:17,302 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/remove_ligand_gro/sandbox_e0647391-f262-4c68-a033-057d4a746887 directory successfully created\n2025-01-28 11:50:17,305 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_48/remove_ligand_gro/sandbox_e0647391-f262-4c68-a033-057d4a746887\n2025-01-28 11:50:17,305 [MainThread  ] [INFO ]  GRO format detected, removing all atoms from residues named AQ4\n2025-01-28 11:50:17,726 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/remove_ligand_gro/sandbox_e0647391-f262-4c68-a033-057d4a746887&amp;#x27;]\n2025-01-28 11:50:17,728 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/remove_ligand_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_48/remove_ligand_gro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_md_1.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.remove_ligand Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:82 /tmp/biobb/unitests_48/remove_ligand_gro/sandbox_e0647391-f262-4c68-a033-057d4a746887 directory successfully created\nINFO     /tmp/biobb/unitests_48/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_48/remove_ligand_gro/sandbox_e0647391-f262-4c68-a033-057d4a746887\nINFO     /tmp/biobb/unitests_48/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409 GRO format detected, removing all atoms from residues named AQ4\nINFO     /tmp/biobb/unitests_48/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/remove_ligand_gro/sandbox_e0647391-f262-4c68-a033-057d4a746887&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/remove_ligand_gro/remove_ligand_gro_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py::TestRemoveLigandPDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:17,800 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.remove_ligand Version: 5.0.0\n2025-01-28 11:50:17,800 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/remove_ligand/sandbox_b4969f91-8005-40e9-8f0f-168b26c13893 directory successfully created\n2025-01-28 11:50:17,803 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.pdb to /tmp/biobb/unitests_48/remove_ligand/sandbox_b4969f91-8005-40e9-8f0f-168b26c13893\n2025-01-28 11:50:17,803 [MainThread  ] [INFO ]  PDB format detected, removing all atoms from residues named AQ4\n2025-01-28 11:50:17,852 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/remove_ligand/sandbox_b4969f91-8005-40e9-8f0f-168b26c13893&amp;#x27;]\n2025-01-28 11:50:17,852 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/remove_ligand/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_48/remove_ligand/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_md_1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 12872\n     Atoms ALIGNED in PDB_B: 12872\n     RMS: 1.549802168438611e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/remove_ligand/remove_ligand_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.remove_ligand Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/remove_ligand/remove_ligand_log.out:file_utils.py:82 /tmp/biobb/unitests_48/remove_ligand/sandbox_b4969f91-8005-40e9-8f0f-168b26c13893 directory successfully created\nINFO     /tmp/biobb/unitests_48/remove_ligand/remove_ligand_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.pdb to /tmp/biobb/unitests_48/remove_ligand/sandbox_b4969f91-8005-40e9-8f0f-168b26c13893\nINFO     /tmp/biobb/unitests_48/remove_ligand/remove_ligand_log.out:file_utils.py:409 PDB format detected, removing all atoms from residues named AQ4\nINFO     /tmp/biobb/unitests_48/remove_ligand/remove_ligand_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/remove_ligand/sandbox_b4969f91-8005-40e9-8f0f-168b26c13893&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/remove_ligand/remove_ligand_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&#34;, &#34;duration&#34;: &#34;00:00:06&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py::TestRemoveMolecules::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:06&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:20,479 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.remove_molecules Version: 5.0.0\n2025-01-28 11:50:20,479 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/remove_molecules/sandbox_b8f1790d-3d12-49d7-be5d-a1bd64345ced directory successfully created\n2025-01-28 11:50:20,481 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_48/remove_molecules/sandbox_b8f1790d-3d12-49d7-be5d-a1bd64345ced\n2025-01-28 11:50:26,789 [MainThread  ] [INFO ]  Writting pdb to: /tmp/biobb/unitests_48/remove_molecules/sandbox_b8f1790d-3d12-49d7-be5d-a1bd64345ced/output_molecules_path.pdb\n2025-01-28 11:50:26,885 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/remove_molecules/sandbox_b8f1790d-3d12-49d7-be5d-a1bd64345ced&amp;#x27;]\n2025-01-28 11:50:26,885 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/remove_molecules/output_molecules_path.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_48/remove_molecules/output_molecules_path.pdb\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_remove_molecules.pdb\n        File_A hash: b&amp;#x27;q$\\x11\\xa5u\\xca5\\xc0\\x90\\xd8\\x1bB&amp;amp;{\\xfcNm\\x85\\xb5(\\x8f\\x13\\xf0\\xef,\\xe6\\x8c\\x0ftV}\\x1d&amp;#x27;\n        File_B hash: b&amp;#x27;q$\\x11\\xa5u\\xca5\\xc0\\x90\\xd8\\x1bB&amp;amp;{\\xfcNm\\x85\\xb5(\\x8f\\x13\\xf0\\xef,\\xe6\\x8c\\x0ftV}\\x1d&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/remove_molecules/remove_molecules_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.remove_molecules Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/remove_molecules/remove_molecules_log.out:file_utils.py:82 /tmp/biobb/unitests_48/remove_molecules/sandbox_b8f1790d-3d12-49d7-be5d-a1bd64345ced directory successfully created\nINFO     /tmp/biobb/unitests_48/remove_molecules/remove_molecules_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_48/remove_molecules/sandbox_b8f1790d-3d12-49d7-be5d-a1bd64345ced\nINFO     /tmp/biobb/unitests_48/remove_molecules/remove_molecules_log.out:file_utils.py:409 Writting pdb to: /tmp/biobb/unitests_48/remove_molecules/sandbox_b8f1790d-3d12-49d7-be5d-a1bd64345ced/output_molecules_path.pdb\nINFO     /tmp/biobb/unitests_48/remove_molecules/remove_molecules_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/remove_molecules/sandbox_b8f1790d-3d12-49d7-be5d-a1bd64345ced&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/remove_molecules/remove_molecules_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&#34;, &#34;duration&#34;: &#34;888 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py::TestRemovePDBWater::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;888 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:26,936 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.remove_pdb_water Version: 5.0.0\n2025-01-28 11:50:26,936 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae directory successfully created\n2025-01-28 11:50:26,937 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_WAT.pdb to /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae\n2025-01-28 11:50:26,937 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae/WT_aq4_md_WAT.pdb -o /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae/output_pdb_path.pdb --force_save water --remove yes\n\n2025-01-28 11:50:27,599 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37...\n2025-01-28 11:50:27,600 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-28 11:50:27,600 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae/WT_aq4_md_WAT.pdb loaded\n PDB id:  \n Title: protein in water\n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\n Num. residues:  397\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 294 (total 2404 H atoms)\n Num. HETATM residues:  2\n Num. ligands or modified residues:  0\n Num. water mol.:  2\n Num. atoms:  4858\nRunning water. Options: --remove yes\nDetected 2 Water molecules\nRemoved 2 Water molecules\nFinal Num. models: 1\nFinal Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\nFinal Num. residues:  395\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 292 (total 2401 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  4853\nStructure saved on /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae/output_pdb_path.pdb\n\n2025-01-28 11:50:27,601 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae&amp;#x27;]\n2025-01-28 11:50:27,601 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/remove_pdb_water/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_48/remove_pdb_water/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_apo_no_wat.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3004\n     Atoms ALIGNED in PDB_B: 3004\n     RMS: 1.3997192439430224e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.remove_pdb_water Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:82 /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae directory successfully created\nINFO     /tmp/biobb/unitests_48/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_WAT.pdb to /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae\nINFO     /tmp/biobb/unitests_48/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae/WT_aq4_md_WAT.pdb -o /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae/output_pdb_path.pdb --force_save water --remove yes\n\nINFO     /tmp/biobb/unitests_48/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37...\nINFO     /tmp/biobb/unitests_48/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_48/remove_pdb_water/remove_pdb_water_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae/WT_aq4_md_WAT.pdb loaded\n PDB id:  \n Title: protein in water\n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\n Num. residues:  397\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 294 (total 2404 H atoms)\n Num. HETATM residues:  2\n Num. ligands or modified residues:  0\n Num. water mol.:  2\n Num. atoms:  4858\nRunning water. Options: --remove yes\nDetected 2 Water molecules\nRemoved 2 Water molecules\nFinal Num. models: 1\nFinal Num. chains: 3 ( : Unknown, A: Protein, B: Unknown)\nFinal Num. residues:  395\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 292 (total 2401 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  4853\nStructure saved on /tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_48/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/remove_pdb_water/sandbox_c2a5eafc-db37-4fc4-99c9-0698e708ddae&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/remove_pdb_water/remove_pdb_water_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&#34;, &#34;duration&#34;: &#34;919 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py::TestRenumberStructure2VGB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;919 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:27,824 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\n2025-01-28 11:50:27,824 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/renumber_structure_2vgb/sandbox_d83a5dde-0a3d-402a-901c-4dd08984252c directory successfully created\n2025-01-28 11:50:27,826 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_48/renumber_structure_2vgb/sandbox_d83a5dde-0a3d-402a-901c-4dd08984252c\n2025-01-28 11:50:27,826 [MainThread  ] [INFO ]  PDB format detected, reenumerating atoms\n2025-01-28 11:50:27,947 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/renumber_structure_2vgb/sandbox_d83a5dde-0a3d-402a-901c-4dd08984252c&amp;#x27;]\n2025-01-28 11:50:27,947 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/renumber_structure_2vgb/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_48/renumber_structure_2vgb/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/ref_2vgb.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 15488\n     Atoms ALIGNED in PDB_B: 15488\n     RMS: 1.871093208699659e-14\n     RMS_CUTOFF: 1\nChecking if empty file: /tmp/biobb/unitests_48/renumber_structure_2vgb/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_48/renumber_structure_2vgb/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/2vgb_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;F\\xbe!`V\\xdb.\\x99\\xfb\\xda\\x94\\xb1\\xa8\\xdf6\\xbcJ\\\\\\\\\\xc7k\\xb6\\xe9\\xc1I\\nm\\xc1\\xe4:v\\x15&amp;#x27;\n        File_B hash: b&amp;#x27;F\\xbe!`V\\xdb.\\x99\\xfb\\xda\\x94\\xb1\\xa8\\xdf6\\xbcJ\\\\\\\\\\xc7k\\xb6\\xe9\\xc1I\\nm\\xc1\\xe4:v\\x15&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:82 /tmp/biobb/unitests_48/renumber_structure_2vgb/sandbox_d83a5dde-0a3d-402a-901c-4dd08984252c directory successfully created\nINFO     /tmp/biobb/unitests_48/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_48/renumber_structure_2vgb/sandbox_d83a5dde-0a3d-402a-901c-4dd08984252c\nINFO     /tmp/biobb/unitests_48/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409 PDB format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_48/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/renumber_structure_2vgb/sandbox_d83a5dde-0a3d-402a-901c-4dd08984252c&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/renumber_structure_2vgb/renumber_structure_2vgb_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&#34;, &#34;duration&#34;: &#34;172 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py::TestRenumberStructureGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;172 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:28,744 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\n2025-01-28 11:50:28,744 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/renumber_structure_gro/sandbox_8539438e-df7f-46cb-a9b8-75d245cc6e71 directory successfully created\n2025-01-28 11:50:28,745 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/pyruvate.gro to /tmp/biobb/unitests_48/renumber_structure_gro/sandbox_8539438e-df7f-46cb-a9b8-75d245cc6e71\n2025-01-28 11:50:28,745 [MainThread  ] [INFO ]  GRO format detected, reenumerating atoms\n2025-01-28 11:50:28,871 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/renumber_structure_gro/sandbox_8539438e-df7f-46cb-a9b8-75d245cc6e71&amp;#x27;]\n2025-01-28 11:50:28,871 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/renumber_structure_gro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_48/renumber_structure_gro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_pyruvate.gro\nChecking if empty file: /tmp/biobb/unitests_48/renumber_structure_gro/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_48/renumber_structure_gro/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/pyruvate_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;/\\xa1\\xe9\\x19X\\xe3\\xb5\\x15R \\x81\\x02\\xc4PX\\x11h\\x08\\x83\\xdb\\r\\xf9j\\xebP\\xe9\\\\\\x1eT#A\\r&amp;#x27;\n        File_B hash: b&amp;#x27;/\\xa1\\xe9\\x19X\\xe3\\xb5\\x15R \\x81\\x02\\xc4PX\\x11h\\x08\\x83\\xdb\\r\\xf9j\\xebP\\xe9\\\\\\x1eT#A\\r&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:82 /tmp/biobb/unitests_48/renumber_structure_gro/sandbox_8539438e-df7f-46cb-a9b8-75d245cc6e71 directory successfully created\nINFO     /tmp/biobb/unitests_48/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/pyruvate.gro to /tmp/biobb/unitests_48/renumber_structure_gro/sandbox_8539438e-df7f-46cb-a9b8-75d245cc6e71\nINFO     /tmp/biobb/unitests_48/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409 GRO format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_48/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/renumber_structure_gro/sandbox_8539438e-df7f-46cb-a9b8-75d245cc6e71&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/renumber_structure_gro/renumber_structure_gro_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&#34;, &#34;duration&#34;: &#34;38 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py::TestRenumberStructurePDB::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;38 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:28,916 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\n2025-01-28 11:50:28,916 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/renumber_structure/sandbox_191b6ded-9e70-48a2-8270-f79520c8706b directory successfully created\n2025-01-28 11:50:28,916 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cl3.noH.pdb to /tmp/biobb/unitests_48/renumber_structure/sandbox_191b6ded-9e70-48a2-8270-f79520c8706b\n2025-01-28 11:50:28,916 [MainThread  ] [INFO ]  PDB format detected, reenumerating atoms\n2025-01-28 11:50:28,917 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/renumber_structure/sandbox_191b6ded-9e70-48a2-8270-f79520c8706b&amp;#x27;]\n2025-01-28 11:50:28,917 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/renumber_structure/output_structure_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_48/renumber_structure/output_structure_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_cl3_noH.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 28\n     Atoms ALIGNED in PDB_B: 28\n     RMS: 1.89900533991096e-15\n     RMS_CUTOFF: 1\nChecking if empty file: /tmp/biobb/unitests_48/renumber_structure/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_48/renumber_structure/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/cl3_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;\\xe5\\xbc\\xaf\\xec\\xc4\\x1a\\x14\\x1d&amp;gt;\\x1f\\xe1\\x1a\\xbe_\\xd5g\\xb6\\xac\\xeb\\xce\\x9a\\xa4\\x9f\\xa7\\xf9\\x98\\xc7\\x00\\xaa\\xa2\\t\\x13&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe5\\xbc\\xaf\\xec\\xc4\\x1a\\x14\\x1d&amp;gt;\\x1f\\xe1\\x1a\\xbe_\\xd5g\\xb6\\xac\\xeb\\xce\\x9a\\xa4\\x9f\\xa7\\xf9\\x98\\xc7\\x00\\xaa\\xa2\\t\\x13&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/renumber_structure/renumber_structure_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/renumber_structure/renumber_structure_log.out:file_utils.py:82 /tmp/biobb/unitests_48/renumber_structure/sandbox_191b6ded-9e70-48a2-8270-f79520c8706b directory successfully created\nINFO     /tmp/biobb/unitests_48/renumber_structure/renumber_structure_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/cl3.noH.pdb to /tmp/biobb/unitests_48/renumber_structure/sandbox_191b6ded-9e70-48a2-8270-f79520c8706b\nINFO     /tmp/biobb/unitests_48/renumber_structure/renumber_structure_log.out:file_utils.py:409 PDB format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_48/renumber_structure/renumber_structure_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/renumber_structure/sandbox_191b6ded-9e70-48a2-8270-f79520c8706b&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/renumber_structure/renumber_structure_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&#34;, &#34;duration&#34;: &#34;38 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py::TestRenumberStructureSMALLGRO::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;38 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:28,956 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\n2025-01-28 11:50:28,957 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/renumber_structure_smallgro/sandbox_1410f379-e42b-4efb-a23d-0e8a770ac093 directory successfully created\n2025-01-28 11:50:28,957 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/smallgro.gro to /tmp/biobb/unitests_48/renumber_structure_smallgro/sandbox_1410f379-e42b-4efb-a23d-0e8a770ac093\n2025-01-28 11:50:28,957 [MainThread  ] [INFO ]  GRO format detected, reenumerating atoms\n2025-01-28 11:50:28,958 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/renumber_structure_smallgro/sandbox_1410f379-e42b-4efb-a23d-0e8a770ac093&amp;#x27;]\n2025-01-28 11:50:28,958 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/renumber_structure_smallgro/output_structure_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_48/renumber_structure_smallgro/output_structure_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/renum_smallgro.gro\nChecking if empty file: /tmp/biobb/unitests_48/renumber_structure_smallgro/output_mapping_json_path.json\nComparing: \n        File_A: /tmp/biobb/unitests_48/renumber_structure_smallgro/output_mapping_json_path.json\n        File_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/smallgro_output_mapping_json_path.json\n        File_A hash: b&amp;#x27;\\x8a\\t\\xfd\\xe8\\x8f@K\\xafz\\xd2\\x8dO\\xed[\\xe0\\xcchg\\xda\\xd7\\x13\\xb4\\x0c\\xcf3\\rNRg,\\xaf\\xf4&amp;#x27;\n        File_B hash: b&amp;#x27;\\x8a\\t\\xfd\\xe8\\x8f@K\\xafz\\xd2\\x8dO\\xed[\\xe0\\xcchg\\xda\\xd7\\x13\\xb4\\x0c\\xcf3\\rNRg,\\xaf\\xf4&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.renumber_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:82 /tmp/biobb/unitests_48/renumber_structure_smallgro/sandbox_1410f379-e42b-4efb-a23d-0e8a770ac093 directory successfully created\nINFO     /tmp/biobb/unitests_48/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/smallgro.gro to /tmp/biobb/unitests_48/renumber_structure_smallgro/sandbox_1410f379-e42b-4efb-a23d-0e8a770ac093\nINFO     /tmp/biobb/unitests_48/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409 GRO format detected, reenumerating atoms\nINFO     /tmp/biobb/unitests_48/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/renumber_structure_smallgro/sandbox_1410f379-e42b-4efb-a23d-0e8a770ac093&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/renumber_structure_smallgro/renumber_structure_smallgro_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py::TestSortGroResidues::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:28,997 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.sort_gro_residues Version: 5.0.0\n2025-01-28 11:50:28,997 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/sort_gro_residues/sandbox_17613e1a-dc1a-4a37-ac0f-e1c4e05164c8 directory successfully created\n2025-01-28 11:50:28,999 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_48/sort_gro_residues/sandbox_17613e1a-dc1a-4a37-ac0f-e1c4e05164c8\n2025-01-28 11:50:33,761 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/sort_gro_residues/sandbox_17613e1a-dc1a-4a37-ac0f-e1c4e05164c8&amp;#x27;]\n2025-01-28 11:50:33,761 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/sort_gro_residues/output_gro_path.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_48/sort_gro_residues/output_gro_path.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/reference/utils/WT_aq4_md_sorted.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.sort_gro_residues Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:82 /tmp/biobb/unitests_48/sort_gro_residues/sandbox_17613e1a-dc1a-4a37-ac0f-e1c4e05164c8 directory successfully created\nINFO     /tmp/biobb/unitests_48/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro to /tmp/biobb/unitests_48/sort_gro_residues/sandbox_17613e1a-dc1a-4a37-ac0f-e1c4e05164c8\nINFO     /tmp/biobb/unitests_48/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/sort_gro_residues/sandbox_17613e1a-dc1a-4a37-ac0f-e1c4e05164c8&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/sort_gro_residues/sort_gro_residues_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py::TestStrCheckAddHydrogens::test_str_check_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:33,839 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.str_check_add_hydrogens Version: 5.0.0\n2025-01-28 11:50:33,839 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1 directory successfully created\n2025-01-28 11:50:33,840 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/str_no_H.pdb to /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1\n2025-01-28 11:50:33,840 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1/str_no_H.pdb -o /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1/output_structure_path.pdbqt --non_interactive --force_save --keep_canonical_resnames command_list --list &amp;#x27;add_hydrogen --add_charges ADT --add_mode auto &amp;#x27;\n\n2025-01-28 11:50:34,842 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f0...\n2025-01-28 11:50:34,843 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-28 11:50:34,843 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1/str_no_H.pdb loaded\n PDB id:  \n Title: \n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  532\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  15\n Num. ligands or modified residues:  3\n Num. water mol.:  12\n Num. atoms:  3946\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\n\nStep 1: add_hydrogen --add_charges ADT --add_mode auto \nRunning add_hydrogen. Options: --add_charges ADT --add_mode auto\nFound 143 Residues requiring selection on adding H atoms\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A72 by HIE\nReplacing HIS A121 by HIE\nReplacing HIS A124 by HIE\nReplacing HIS A127 by HIE\nReplacing HIS A278 by HIE\nReplacing HIS A306 by HIE\nReplacing HIS A317 by HIE\nReplacing HIS A422 by HIE\nReplacing HIS A434 by HIE\nReplacing HIS A507 by HIE\nUpdating partial charges and atom types\nWarning: OXT atom missing in CILE A573. Run backbone --fix_atoms first\nWarning: FBP not found in residue library atom, charges set to 0.\nWarning: K not found in residue library atom, charges set to 0.\nWarning: MN not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nTotal assigned charge:      -1.25\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  532\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 517 (total 3995 H atoms)\nFinal Num. HETATM residues:  15\nFinal Num. ligands or modified residues:  3\nFinal Num. water mol.:  12\nFinal Num. atoms:  7941\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\nWarning: reverting residue names to canonical on output\nStructure saved on /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1/output_structure_path.pdbqt\n\n2025-01-28 11:50:34,847 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/str_check_add_hydrogens/output_structure_path.pdbqt file ends with END, cleaning\n2025-01-28 11:50:34,851 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1&amp;#x27;]\n2025-01-28 11:50:34,851 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/str_check_add_hydrogens/output_structure_path.pdbqt\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.str_check_add_hydrogens Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1 directory successfully created\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/str_no_H.pdb to /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1/str_no_H.pdb -o /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1/output_structure_path.pdbqt --non_interactive --force_save --keep_canonical_resnames command_list --list &amp;#x27;add_hydrogen --add_charges ADT --add_mode auto &amp;#x27;\n\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f0...\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1/str_no_H.pdb loaded\n PDB id:  \n Title: \n Experimental method: unknown\n Resolution (A): N.A.\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  532\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  15\n Num. ligands or modified residues:  3\n Num. water mol.:  12\n Num. atoms:  3946\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\n\nStep 1: add_hydrogen --add_charges ADT --add_mode auto \nRunning add_hydrogen. Options: --add_charges ADT --add_mode auto\nFound 143 Residues requiring selection on adding H atoms\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A72 by HIE\nReplacing HIS A121 by HIE\nReplacing HIS A124 by HIE\nReplacing HIS A127 by HIE\nReplacing HIS A278 by HIE\nReplacing HIS A306 by HIE\nReplacing HIS A317 by HIE\nReplacing HIS A422 by HIE\nReplacing HIS A434 by HIE\nReplacing HIS A507 by HIE\nUpdating partial charges and atom types\nWarning: OXT atom missing in CILE A573. Run backbone --fix_atoms first\nWarning: FBP not found in residue library atom, charges set to 0.\nWarning: K not found in residue library atom, charges set to 0.\nWarning: MN not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nWarning: HOH not found in residue library atom, charges set to 0.\nTotal assigned charge:      -1.25\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  532\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 517 (total 3995 H atoms)\nFinal Num. HETATM residues:  15\nFinal Num. ligands or modified residues:  3\nFinal Num. water mol.:  12\nFinal Num. atoms:  7941\nMetal/Ion residues found\n  K A582\n MN A583\nSmall mol ligands found\nFBP A580\nWarning: reverting residue names to canonical on output\nStructure saved on /tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1/output_structure_path.pdbqt\n\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409 /tmp/biobb/unitests_48/str_check_add_hydrogens/output_structure_path.pdbqt file ends with END, cleaning\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/str_check_add_hydrogens/sandbox_bdb9f027-5d69-40f4-a368-ad595d5827c1&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/str_check_add_hydrogens/str_check_add_hydrogens_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}], &#34;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_structure_utils/test/unitests/test_utils/test_structure_check.py::TestStructureCheck::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-28 11:50:34,943 [MainThread  ] [INFO ]  Module: biobb_structure_utils.utils.structure_check Version: 5.0.0\n2025-01-28 11:50:34,943 [MainThread  ] [INFO ]  /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568 directory successfully created\n2025-01-28 11:50:34,944 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568\n2025-01-28 11:50:34,944 [MainThread  ] [INFO ]  Computing features: chains, models\n2025-01-28 11:50:34,945 [MainThread  ] [INFO ]  Creating 4a59764c-b1cf-4501-ae8f-b30e6b08b422 temporary folder\n2025-01-28 11:50:34,945 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568/2vgb.pdb --json /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568/output_summary_path.json --check_only --non_interactive command_list --list 4a59764c-b1cf-4501-ae8f-b30e6b08b422/command_list.lst\n\n2025-01-28 11:50:36,156 [MainThread  ] [INFO ]  Executing: check_structure -i /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-...\n2025-01-28 11:50:36,157 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-28 11:50:36,157 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568/2vgb.pdb loaded\n PDB id: 2VGB \n Title: human erythrocyte pyruvate kinase\n Experimental method: x-ray diffraction\n Keywords: metal-binding, phosphorylation, pyruvate kinase in the active r- state, kinase, pyruvate, magnesium, glycolysis, transferase, disease mutation\n Resolution (A): 2.73\n\n Num. models: 1\n Num. chains: 4 (A: Protein, B: Protein, C: Protein, D: Protein)\n Num. residues:  2118\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  81\n Num. ligands or modified residues:  16\n Num. water mol.:  65\n Num. atoms:  15612\nMetal/Ion residues found\n  K A582\n MN A583\n  K B586\n MN B587\n  K C590\n MN C591\n  K D594\n MN D595\nSmall mol ligands found\nFBP A580\nPGA A581\nFBP B580\nPGA B581\nFBP C580\nPGA C581\nFBP D580\nPGA D581\n\nStep 1: chains\n\nRunning chains.\nDetected 4 Chain(s)\n A: Protein\n B: Protein\n C: Protein\n D: Protein\n\nStep 2: models\n\nRunning models.\nDetected 1 Model(s)\nFound Single model\nCommand list completed\nSummary data saved on /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568/output_summary_path.json\n\n2025-01-28 11:50:36,157 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568&amp;#x27;, &amp;#x27;4a59764c-b1cf-4501-ae8f-b30e6b08b422&amp;#x27;]\n2025-01-28 11:50:36,158 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_48/structure_check/output_summary_path.json\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:file_utils.py:409 Module: biobb_structure_utils.utils.structure_check Version: 5.0.0\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:file_utils.py:82 /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568 directory successfully created\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_structure_utils/biobb_structure_utils/biobb_structure_utils/test/data/utils/2vgb.pdb to /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:file_utils.py:409 Computing features: chains, models\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:file_utils.py:409 Creating 4a59764c-b1cf-4501-ae8f-b30e6b08b422 temporary folder\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:cmd_wrapper.py:63 check_structure -i /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568/2vgb.pdb --json /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568/output_summary_path.json --check_only --non_interactive command_list --list 4a59764c-b1cf-4501-ae8f-b30e6b08b422/command_list.lst\n\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:cmd_wrapper.py:36 Executing: check_structure -i /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-...\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568/2vgb.pdb loaded\n PDB id: 2VGB \n Title: human erythrocyte pyruvate kinase\n Experimental method: x-ray diffraction\n Keywords: metal-binding, phosphorylation, pyruvate kinase in the active r- state, kinase, pyruvate, magnesium, glycolysis, transferase, disease mutation\n Resolution (A): 2.73\n\n Num. models: 1\n Num. chains: 4 (A: Protein, B: Protein, C: Protein, D: Protein)\n Num. residues:  2118\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  81\n Num. ligands or modified residues:  16\n Num. water mol.:  65\n Num. atoms:  15612\nMetal/Ion residues found\n  K A582\n MN A583\n  K B586\n MN B587\n  K C590\n MN C591\n  K D594\n MN D595\nSmall mol ligands found\nFBP A580\nPGA A581\nFBP B580\nPGA B581\nFBP C580\nPGA C581\nFBP D580\nPGA D581\n\nStep 1: chains\n\nRunning chains.\nDetected 4 Chain(s)\n A: Protein\n B: Protein\n C: Protein\n D: Protein\n\nStep 2: models\n\nRunning models.\nDetected 1 Model(s)\nFound Single model\nCommand list completed\nSummary data saved on /tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568/output_summary_path.json\n\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_48/structure_check/sandbox_46d8f3a1-4186-4928-b85b-06332c81b568&amp;#x27;, &amp;#x27;4a59764c-b1cf-4501-ae8f-b30e6b08b422&amp;#x27;]\nINFO     /tmp/biobb/unitests_48/structure_check/structure_check_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_48\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
     <script>
       (function(){function r(e,n,t){function o(i,f){if(!n[i]){if(!e[i]){var c="function"==typeof require&&require;if(!f&&c)return c(i,!0);if(u)return u(i,!0);var a=new Error("Cannot find module '"+i+"'");throw a.code="MODULE_NOT_FOUND",a}var p=n[i]={exports:{}};e[i][0].call(p.exports,function(r){var n=e[i][1][r];return o(n||r)},p,p.exports,r,e,n,t)}return n[i].exports}for(var u="function"==typeof require&&require,i=0;i<t.length;i++)o(t[i]);return o}return r})()({1:[function(require,module,exports){
 const { getCollapsedCategory, setCollapsedIds } = require('./storage.js')