[FEATURE] New sandbox_path property

Author: PauAndrio

biobb_structure_utils/docs/jupyter/command_line_template.ipynb

@@ -21,6 +21,7 @@ class CatPDB(BiobbObject):
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/cat_pdb.py

@@ -25,6 +25,7 @@ class ClosestResidues(BiobbObject):
             * **preserve_target** (*bool*) - (True) Whether or not to preserve the target residues in the output structure.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/closest_residues.py

@@ -25,6 +25,7 @@ class ExtractAtoms(BiobbObject):
             * **regular_expression_pattern** (*str*) - ("^D") Python style regular expression matching the selected atom names.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/extract_atoms.py

@@ -25,6 +25,7 @@ class ExtractChain(BiobbObject):
             * **binary_path** (*string*) - ("check_structure") path to the check_structure application
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/extract_chain.py

@@ -24,6 +24,7 @@ class ExtractHeteroAtoms(BiobbObject):
             * **water** (*bool*) - (False) Add or not waters.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/extract_heteroatoms.py

@@ -24,6 +24,7 @@ class ExtractModel(BiobbObject):
             * **binary_path** (*string*) - ("check_structure") path to the check_structure application
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/extract_model.py

@@ -24,6 +24,7 @@ class ExtractMolecule(BiobbObject):
             * **binary_path** (*string*) - ("check_structure") path to the check_structure application
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/extract_molecule.py

@@ -23,6 +23,7 @@ class ExtractResidues(BiobbObject):
             * **residues** (*list*) - (None) List of comma separated res_id (will extract all residues that match the res_id) or list of dictionaries with the name | res_id  | chain | model of the residues to be extracted. Format: [{"name": "HIS", "res_id": "72", "chain": "A", "model": "1"}].
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/extract_residues.py

@@ -23,6 +23,7 @@ class RemoveLigand(BiobbObject):
             * **ligand** (*str*) - ("AQ4") Residue code of the ligand to be removed.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/remove_ligand.py

@@ -23,6 +23,7 @@ class RemoveMolecules(BiobbObject):
             * **molecules** (*list*) - (None) List of comma separated res_id (will remove all molecules that match the res_id) or list of dictionaries with the name | res_id  | chain | model of the molecules to be removed. Format: [{"name": "HIS", "res_id": "72", "chain": "A", "model": "1"}].
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/remove_molecules.py

@@ -20,6 +20,7 @@ class RemovePdbWater(BiobbObject):
             * **binary_path** (*string*) - ("check_structure") path to the check_structure application
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/remove_pdb_water.py

@@ -27,6 +27,7 @@ class RenumberStructure(BiobbObject):
             * **renumber_residues_per_chain** (*bool*) - (True) Restart residue enumeration every time a new chain is detected.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/renumber_structure.py

@@ -21,6 +21,7 @@ class SortGroResidues(BiobbObject):
             * **residue_name_list** (*list*) - (["NA", "CL", "SOL"]) Ordered residue name list.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/sort_gro_residues.py

@@ -26,6 +26,7 @@ class StrCheckAddHydrogens(BiobbObject):
             * **binary_path** (*string*) - ("check_structure") path to the check_structure application
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::

biobb_structure_utils/utils/str_check_add_hydrogens.py

@@ -23,6 +23,7 @@ class StructureCheck(BiobbObject):
             * **binary_path** (*string*) - ("check_structure") path to the check_structure application
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::