Merge branch 'master' of github.com:bioexcel/biobb_structure_utils

bioexcel · May 24, 2024 · 682721e · 682721e
2 parents f8536d1 + 8cba093
commit 682721e
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Showing 17 changed files with 17 additions and 9 deletions.
diff --git a/biobb_structure_utils/json_schemas/cat_pdb.json b/biobb_structure_utils/json_schemas/cat_pdb.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_structure_utils/json_schemas/1.0/cat_pdb",
     "name": "biobb_structure_utils CatPDB",
     "title": "Class to concat two PDB structures in a single PDB file.",
-    "description": null,
+    "description": "Class to concat two PDB structures in a single PDB file.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_structure_utils/json_schemas/extract_atoms.json b/biobb_structure_utils/json_schemas/extract_atoms.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_structure_utils/json_schemas/1.0/extract_atoms",
     "name": "biobb_structure_utils ExtractAtoms",
     "title": "Class to extract atoms from a 3D structure.",
-    "description": null,
+    "description": "Extracts all atoms from a 3D structure that match a regular expression pattern.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_structure_utils/json_schemas/extract_heteroatoms.json b/biobb_structure_utils/json_schemas/extract_heteroatoms.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_structure_utils/json_schemas/1.0/extract_heteroatoms",
     "name": "biobb_structure_utils ExtractHeteroAtoms",
     "title": "Class to extract hetero-atoms from a 3D structure using Biopython.",
-    "description": null,
+    "description": "Extracts a list of heteroatoms from a 3D structure using Biopython.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_structure_utils/json_schemas/extract_residues.json b/biobb_structure_utils/json_schemas/extract_residues.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_structure_utils/json_schemas/1.0/extract_residues",
     "name": "biobb_structure_utils ExtractResidues",
     "title": "Class to extract residues from a 3D structure using Biopython.",
-    "description": null,
+    "description": "Extracts a list of residues from a 3D structure using Biopython.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_structure_utils/json_schemas/remove_ligand.json b/biobb_structure_utils/json_schemas/remove_ligand.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_structure_utils/json_schemas/1.0/remove_ligand",
     "name": "biobb_structure_utils RemoveLigand",
     "title": "Class to remove the selected ligand atoms from a 3D structure.",
-    "description": null,
+    "description": "Remove the selected ligand atoms from a 3D structure.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_structure_utils/json_schemas/remove_molecules.json b/biobb_structure_utils/json_schemas/remove_molecules.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_structure_utils/json_schemas/1.0/remove_molecules",
     "name": "biobb_structure_utils RemoveMolecules",
     "title": "Class to remove molecules from a 3D structure using Biopython.",
-    "description": null,
+    "description": "Remove a list of molecules from a 3D structure using Biopython.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_structure_utils/json_schemas/renumber_structure.json b/biobb_structure_utils/json_schemas/renumber_structure.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_structure_utils/json_schemas/1.0/renumber_structure",
     "name": "biobb_structure_utils RenumberStructure",
     "title": "Class to renumber atomic indexes from a 3D structure.",
-    "description": null,
+    "description": "Renumber atomic indexes from a 3D structure.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_structure_utils/json_schemas/sort_gro_residues.json b/biobb_structure_utils/json_schemas/sort_gro_residues.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_structure_utils/json_schemas/1.0/sort_gro_residues",
     "name": "biobb_structure_utils SortGroResidues",
     "title": "Class to sort the selected residues from a GRO 3D structure.",
-    "description": null,
+    "description": "Sorts the selected residues from a GRO 3D structure.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_structure_utils/test/unitests/test_utils/test_extract_model.py b/biobb_structure_utils/test/unitests/test_utils/test_extract_model.py
@@ -7,7 +7,7 @@ def setup_class(self):
         fx.test_setup(self, 'extract_model')
 
     def teardown_class(self):
-        fx.test_teardown(self)
+        # fx.test_teardown(self)
         pass
 
     def test_launch(self):

diff --git a/biobb_structure_utils/utils/cat_pdb.py b/biobb_structure_utils/utils/cat_pdb.py
@@ -12,6 +12,7 @@ class CatPDB(BiobbObject):
     """
     | biobb_structure_utils CatPDB
     | Class to concat two PDB structures in a single PDB file.
+    | Class to concat two PDB structures in a single PDB file.
 
     Args:
         input_structure1 (str): Input structure 1 file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/cat_protein.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).

diff --git a/biobb_structure_utils/utils/extract_atoms.py b/biobb_structure_utils/utils/extract_atoms.py
@@ -16,6 +16,7 @@ class ExtractAtoms(BiobbObject):
     """
     | biobb_structure_utils ExtractAtoms
     | Class to extract atoms from a 3D structure.
+    | Extracts all atoms from a 3D structure that match a regular expression pattern.
 
     Args:
         input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/2vgb.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).

diff --git a/biobb_structure_utils/utils/extract_heteroatoms.py b/biobb_structure_utils/utils/extract_heteroatoms.py
@@ -14,6 +14,7 @@ class ExtractHeteroAtoms(BiobbObject):
     """
     | biobb_structure_utils ExtractHeteroAtoms
     | Class to extract hetero-atoms from a 3D structure using Biopython.
+    | Extracts a list of heteroatoms from a 3D structure using Biopython.
 
     Args:
         input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).

diff --git a/biobb_structure_utils/utils/extract_residues.py b/biobb_structure_utils/utils/extract_residues.py
@@ -14,6 +14,7 @@ class ExtractResidues(BiobbObject):
     """
     | biobb_structure_utils ExtractResidues
     | Class to extract residues from a 3D structure using Biopython.
+    | Extracts a list of residues from a 3D structure using Biopython.
 
     Args:
         input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).

diff --git a/biobb_structure_utils/utils/remove_ligand.py b/biobb_structure_utils/utils/remove_ligand.py
@@ -14,6 +14,7 @@ class RemoveLigand(BiobbObject):
     """
     | biobb_structure_utils RemoveLigand
     | Class to remove the selected ligand atoms from a 3D structure.
+    | Remove the selected ligand atoms from a 3D structure.
 
     Args:
         input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/WT_aq4_md_1.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).

diff --git a/biobb_structure_utils/utils/remove_molecules.py b/biobb_structure_utils/utils/remove_molecules.py
@@ -14,6 +14,7 @@ class RemoveMolecules(BiobbObject):
     """
     | biobb_structure_utils RemoveMolecules
     | Class to remove molecules from a 3D structure using Biopython.
+    | Remove a list of molecules from a 3D structure using Biopython.
 
     Args:
         input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/2vgb.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).

diff --git a/biobb_structure_utils/utils/renumber_structure.py b/biobb_structure_utils/utils/renumber_structure.py
@@ -16,6 +16,7 @@ class RenumberStructure(BiobbObject):
     """
     | biobb_structure_utils RenumberStructure
     | Class to renumber atomic indexes from a 3D structure.
+    | Renumber atomic indexes from a 3D structure.
 
     Args:
         input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/cl3.noH.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).

diff --git a/biobb_structure_utils/utils/sort_gro_residues.py b/biobb_structure_utils/utils/sort_gro_residues.py
@@ -12,6 +12,7 @@ class SortGroResidues(BiobbObject):
     """
     | biobb_structure_utils SortGroResidues
     | Class to sort the selected residues from a GRO 3D structure.
+    | Sorts the selected residues from a GRO 3D structure.
 
     Args:
         input_gro_path (str): Input GRO file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/WT_aq4_md_1.gro>`_. Accepted formats: gro (edam:format_2033).