utils package¶
Submodules¶
utils.cat_pdb module¶
Module containing the CatPDB class and the command line interface.
-
class
utils.cat_pdb.
CatPDB
(input_structure1, input_structure2, output_structure_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils CatPDBClass to concat two PDB structures in a single PDB file.Parameters: - input_structure1 (str) – Input structure 1 file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- input_structure2 (str) –
Input structure 2 file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- output_structure_path (str) –
Output protein file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.cat_pdb import cat_pdb prop = { } cat_pdb(input_structure1='/path/to/myInputStr1.pdb', input_structure2='/path/to/myInputStr2.pdb', output_structure_path='/path/to/newStructure.pdb', properties=prop)
- Info:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
utils.closest_residues module¶
Module containing the ClosestResidues class and the command line interface.
-
class
utils.closest_residues.
ClosestResidues
(input_structure_path, output_residues_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils ClosestResiduesClass to search closest residues from a 3D structure using Biopython.Return all residues that have at least one atom within radius of center from a list of given residues.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- output_residues_path (str) –
Output molcules file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- residues (list) - (None) List of comma separated res_id or list of dictionaries with the name | res_id | chain | model of the residues to find the closest neighbours. Format: [{“name”: “HIS”, “res_id”: “72”, “chain”: “A”, “model”: “1”}].
- radius (float) - (5) Distance in Ångströms to neighbours of the given list of residues.
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.closest_residues import closest_residues prop = { 'residues': [ { 'name': 'HIS', 'res_id': '72', 'chain': 'A', 'model': '1' } ], 'radius': 5, 'preserve_target': False } closest_residues(input_structure_path='/path/to/myStructure.pdb', output_residues_path='/path/to/newResidues.pdb', properties=prop)
- Info:
- wrapped_software:
- name: In house using Biopython
- version: >=1.79
- license: other
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
ClosestResidues
utils.closest_residues.ClosestResidues object.
- input_structure_path (str) –
-
utils.closest_residues.
closest_residues
(input_structure_path: str, output_residues_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
ClosestResidues
class and execute thelaunch()
method.
utils.extract_atoms module¶
Module containing the ExtractAtoms class and the command line interface.
-
class
utils.extract_atoms.
ExtractAtoms
(input_structure_path, output_structure_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils ExtractAtomsClass to extract atoms from a 3D structure.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
- output_structure_path (str) –
Output structure file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.extract_atoms import extract_atoms prop = { 'regular_expression_pattern': '^D' } extract_atoms(input_structure_path='/path/to/myStructure.pdb', output_structure_path='/path/to/newStructure.pdb', properties=prop)
- Info:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
ExtractAtoms
utils.extract_atoms.ExtractAtoms object.
- input_structure_path (str) –
-
utils.extract_atoms.
extract_atoms
(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
ExtractAtoms
class and execute thelaunch()
method.
utils.extract_chain module¶
Module containing the ExtractChain class and the command line interface.
-
class
utils.extract_chain.
ExtractChain
(input_structure_path, output_structure_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils ExtractAtomsThis class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure.Wrapper for the Structure Checking tool to extract a chain from a 3D structure.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- output_structure_path (str) –
Output structure file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- chains (list) - (None) List of chains to be extracted from the input_structure_path file. If empty, all the chains of the structure will be returned.
- permissive (bool) - (False) Use non standard PDB files.
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.extract_chain import extract_chain prop = { 'chains': [ 'A', 'B' ] } extract_chain(input_structure_path='/path/to/myStructure.pdb', output_structure_path='/path/to/newStructure.pdb', properties=prop)
- Info:
- wrapped_software:
- name: Structure Checking from MDWeb
- version: >=3.0.3
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
ExtractChain
utils.extract_chain.ExtractChain object.
- input_structure_path (str) –
-
utils.extract_chain.
extract_chain
(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
ExtractChain
class and execute thelaunch()
method.
utils.extract_heteroatoms module¶
Module containing the ExtractHeteroAtoms class and the command line interface.
-
class
utils.extract_heteroatoms.
ExtractHeteroAtoms
(input_structure_path, output_heteroatom_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils ExtractHeteroAtomsClass to extract hetero-atoms from a 3D structure using Biopython.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- output_heteroatom_path (str) –
Output heteroatom file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- heteroatoms (list) - (None) List of dictionaries with the name | res_id | chain | model of the heteroatoms to be extracted. Format: [{“name”: “ZZ7”, “res_id”: “302”, “chain”: “B”, “model”: “1”}]. If empty, all the heteroatoms of the structure will be returned.
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.extract_heteroatoms import extract_heteroatoms prop = { 'heteroatoms': [ { 'name': 'ZZ7', 'res_id': '302', 'chain': 'B', 'model': '1' } ] } extract_heteroatoms(input_structure_path='/path/to/myStructure.pdb', output_heteroatom_path='/path/to/newHeteroatom.pdb', properties=prop)
- Info:
- wrapped_software:
- name: In house using Biopython
- version: >=1.76
- license: other
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
ExtractHeteroAtoms
utils.extract_heteroatoms.ExtractHeteroAtoms object.
- input_structure_path (str) –
-
utils.extract_heteroatoms.
extract_heteroatoms
(input_structure_path: str, output_heteroatom_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
ExtractHeteroAtoms
class and execute thelaunch()
method.
utils.extract_residues module¶
Module containing the ExtractResidues class and the command line interface.
-
class
utils.extract_residues.
ExtractResidues
(input_structure_path, output_residues_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils ExtractResiduesClass to extract residues from a 3D structure using Biopython.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- output_residues_path (str) –
Output residues file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.extract_residues import extract_residues prop = { 'residues': [ { 'name': 'HIS', 'res_id': '72', 'chain': 'A', 'model': '1' } ] } extract_residues(input_structure_path='/path/to/myStructure.pdb', output_residues_path='/path/to/newResidues.pdb', properties=prop)
- Info:
- wrapped_software:
- name: In house using Biopython
- version: >=1.79
- license: other
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
ExtractResidues
utils.extract_residues.ExtractResidues object.
- input_structure_path (str) –
-
utils.extract_residues.
extract_residues
(input_structure_path: str, output_residues_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
ExtractResidues
class and execute thelaunch()
method.
utils.remove_molecules module¶
Module containing the RemoveMolecules class and the command line interface.
-
class
utils.remove_molecules.
RemoveMolecules
(input_structure_path, output_molecules_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils RemoveMoleculesClass to remove molecules from a 3D structure using Biopython.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- output_molecules_path (str) –
Output molcules file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.remove_molecules import remove_molecules prop = { 'molecules': [ { 'name': 'HIS', 'res_id': '72', 'chain': 'A', 'model': '1' } ] } remove_molecules(input_structure_path='/path/to/myStructure.pdb', output_molecules_path='/path/to/newMolecules.pdb', properties=prop)
- Info:
- wrapped_software:
- name: In house using Biopython
- version: >=1.79
- license: other
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
RemoveMolecules
utils.remove_molecules.RemoveMolecules object.
- input_structure_path (str) –
-
utils.remove_molecules.
main
()[source]¶ Command line execution of this building block. Please check the command line documentation.
-
utils.remove_molecules.
remove_molecules
(input_structure_path: str, output_molecules_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
RemoveMolecules
class and execute thelaunch()
method.
utils.extract_model module¶
Module containing the ExtractModel class and the command line interface.
-
class
utils.extract_model.
ExtractModel
(input_structure_path, output_structure_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils ExtractModelThis class is a wrapper of the Structure Checking tool to extract a model from a 3D structure.Wrapper for the Structure Checking tool to extract a model from a 3D structure.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- output_structure_path (str) –
Output structure file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- models (list) - (None) List of models to be extracted from the input_structure_path file. If empty, all the models of the structure will be returned.
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.extract_model import extract_model prop = { 'models': [ 1, 2, 3 ] } extract_model(input_structure_path='/path/to/myStructure.pdb', output_structure_path='/path/to/newStructure.pdb', properties=prop)
- Info:
- wrapped_software:
- name: Structure Checking from MDWeb
- version: >=3.0.3
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
ExtractModel
utils.extract_model.ExtractModel object.
- input_structure_path (str) –
-
utils.extract_model.
extract_model
(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
ExtractModel
class and execute thelaunch()
method.
utils.extract_molecule module¶
Module containing the ExtractMolecule class and the command line interface.
-
class
utils.extract_molecule.
ExtractMolecule
(input_structure_path, output_molecule_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils ExtractMoleculeThis class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure.Wrapper for the Structure Checking tool to extract a molecule from a 3D structure.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- output_molecule_path (str) –
Output molecule file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- molecule_type (string) - (“all”) type of molecule to be extracted. If all, only waters and ligands will be removed from the original structure. Values: all, protein, na, dna, rna, chains.
- chains (list) - (None) if chains selected in molecule_type, specify them here, e.g: [“A”, “C”, “N”].
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.extract_molecule import extract_molecule prop = { 'molecule_type': 'chains', 'chains': ['A', 'N', 'F'] } extract_molecule(input_structure_path='/path/to/myStructure.pdb', output_molecule_path='/path/to/newMolecule.pdb', properties=prop)
- Info:
- wrapped_software:
- name: Structure Checking from MDWeb
- version: >=3.0.3
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
create_command_list
(command_list_path)[source]¶ Creates a command list file as a input for structure checking
-
launch
() → int[source]¶ Execute the
ExtractMolecule
utils.extract_molecule.ExtractMolecule object.
- input_structure_path (str) –
-
utils.extract_molecule.
extract_molecule
(input_structure_path: str, output_molecule_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
ExtractMolecule
class and execute thelaunch()
method.
utils.remove_ligand module¶
Module containing the RemoveLigand class and the command line interface.
-
class
utils.remove_ligand.
RemoveLigand
(input_structure_path, output_structure_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils RemoveLigandClass to remove the selected ligand atoms from a 3D structure.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
- output_structure_path (str) –
Output structure file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.remove_ligand import remove_ligand prop = { 'ligand': 'AQ4' } remove_ligand(input_structure_path='/path/to/myStructure.pdb', output_structure_path='/path/to/newStructure.pdb', properties=prop)
- Info:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
RemoveLigand
utils.remove_ligand.RemoveLigand object.
- input_structure_path (str) –
-
utils.remove_ligand.
main
()[source]¶ Command line execution of this building block. Please check the command line documentation.
-
utils.remove_ligand.
remove_ligand
(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
RemoveLigand
class and execute thelaunch()
method.
utils.remove_pdb_water module¶
Module containing the RemovePdbWater class and the command line interface.
-
class
utils.remove_pdb_water.
RemovePdbWater
(input_pdb_path, output_pdb_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils RemovePdbWaterThis class is a wrapper of the Structure Checking tool to remove water molecules from PDB 3D structures.Wrapper for the Structure Checking tool to remove water molecules from PDB 3D structures.Parameters: - input_pdb_path (str) –
Input PDB file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).
- output_pdb_path (str) –
Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.remove_pdb_water import remove_pdb_water prop = { } remove_pdb_water(input_pdb_path='/path/to/myStructure.pdb', output_pdb_path='/path/to/newStructure.pdb', properties=prop)
- Info:
- wrapped_software:
- name: Structure Checking from MDWeb
- version: >=3.0.3
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
RemovePdbWater
utils.remove_pdb_water.RemovePdbWater object.
- input_pdb_path (str) –
-
utils.remove_pdb_water.
main
()[source]¶ Command line execution of this building block. Please check the command line documentation.
-
utils.remove_pdb_water.
remove_pdb_water
(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
RemovePdbWater
class and execute thelaunch()
method.
utils.renumber_structure module¶
Module containing the RenumberStructure class and the command line interface.
-
class
utils.renumber_structure.
RenumberStructure
(input_structure_path, output_structure_path, output_mapping_json_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils RenumberStructureClass to renumber atomic indexes from a 3D structure.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
- output_structure_path (str) –
Output structure file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
- output_mapping_json_path (str) –
Output mapping json file path. File type: output. Sample file. Accepted formats: json (edam:format_3464).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- renumber_residues (bool) - (True) Residue code of the ligand to be removed.
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.renumber_structure import renumber_structure prop = { 'renumber_residues': True, 'renumber_residues_per_chain': True } renumber_structure(input_structure_path='/path/to/myInputStr.pdb', output_structure_path='/path/to/newStructure.pdb', output_mapping_json_path='/path/to/newMapping.json', properties=prop)
- Info:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
RenumberStructure
utils.renumber_structure.RenumberStructure object.
- input_structure_path (str) –
-
utils.renumber_structure.
main
()[source]¶ Command line execution of this building block. Please check the command line documentation.
-
utils.renumber_structure.
renumber_structure
(input_structure_path: str, output_structure_path: str, output_mapping_json_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
RenumberStructure
class and execute thelaunch()
method.
utils.sort_gro_residues module¶
Module containing the SortGroResidues class and the command line interface.
-
class
utils.sort_gro_residues.
SortGroResidues
(input_gro_path, output_gro_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils SortGroResiduesClass to sort the selected residues from a GRO 3D structure.Parameters: - input_gro_path (str) –
Input GRO file path. File type: input. Sample file. Accepted formats: gro (edam:format_2033).
- output_gro_path (str) –
Output sorted GRO file path. File type: output. Sample file. Accepted formats: gro (edam:format_2033).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.sort_gro_residues import sort_gro_residues prop = { 'residue_name_list': ['NA', 'CL', 'SOL'] } sort_gro_residues(input_gro_path='/path/to/myInputStr.gro', output_gro_path='/path/to/newStructure.gro', properties=prop)
- Info:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
SortGroResidues
utils.sort_gro_residues.SortGroResidues object.
- input_gro_path (str) –
-
utils.sort_gro_residues.
main
()[source]¶ Command line execution of this building block. Please check the command line documentation.
-
utils.sort_gro_residues.
sort_gro_residues
(input_gro_path: str, output_gro_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
SortGroResidues
class and execute thelaunch()
method.
utils.str_check_add_hydrogens module¶
Module containing the StrCheckAddHydrogens class and the command line interface.
-
class
utils.str_check_add_hydrogens.
StrCheckAddHydrogens
(input_structure_path, output_structure_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils StrCheckAddHydrogensThis class is a wrapper of the Structure Checking tool to add hydrogens to a 3D structure.Wrapper for the Structure Checking tool to add hydrogens to a 3D structure.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).
- output_structure_path (str) –
Output structure file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- charges (bool) - (False) Whether or not to add charges to the output file. If True the output is in PDBQT format.
- mode (string) - (auto) Selection mode. Values: auto, list, ph
- ph (float) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH. Only in case mode ph selected.
- list (string) - (“”) List of residues to modify separated by commas (i.e HISA234HID,HISB33HIE). Only in case mode list selected.
- keep_canonical_resnames (bool) - (False) Whether or not keep canonical residue names
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.str_check_add_hydrogens import str_check_add_hydrogens prop = { 'charges': False, 'mode': 'auto' } str_check_add_hydrogens(input_structure_path='/path/to/myInputStr.pdb', output_structure_path='/path/to/newStructure.pdb', properties=prop)
- Info:
- wrapped_software:
- name: Structure Checking from MDWeb
- version: >=3.0.3
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
StrCheckAddHydrogens
utils.str_check_add_hydrogens.StrCheckAddHydrogens object.
- input_structure_path (str) –
-
utils.str_check_add_hydrogens.
main
()[source]¶ Command line execution of this building block. Please check the command line documentation.
-
utils.str_check_add_hydrogens.
str_check_add_hydrogens
(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
StrCheckAddHydrogens
class and execute thelaunch()
method.
utils.structure_check module¶
Module containing the StructureCheck class and the command line interface.
-
class
utils.structure_check.
StructureCheck
(input_structure_path, output_summary_path, properties=None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_structure_utils StructureCheckThis class is a wrapper of the Structure Checking tool to generate summary checking results on a json file.Wrapper for the Structure Checking tool to generate summary checking results on a json file from a given structure and a list of features.Parameters: - input_structure_path (str) –
Input structure file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
- output_summary_path (str) –
Output summary checking results. File type: output. Sample file. Accepted formats: json (edam:format_3464).
- properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- features (list) - (None) Features to summarize. If None, all the features will be computed. Values: models (multiple molecules or coordinate sets in a single file), chains (multiple chains in a single file), altloc (atom alternative conformation given an alternate location indicator and occupancy), metals (metals present in the structure), ligands (heteroatoms present in the structure), chiral (to say that a structure is chiral is to say that its mirror image is not the same as it self), getss (detect SS bonds or disulfides), cistransbck (detact cis/trans backbone), backbone (detect backbone breaks), amide (detect too close amides), clashes (detect clashes).
- 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_structure_utils.utils.structure_check import structure_check prop = { 'features': ['models', 'chains', 'ligands'] } structure_check(input_structure_path='/path/to/myInputStr.pdb', output_summary_path='/path/to/newSummary.json', properties=prop)
- Info:
- wrapped_software:
- name: Structure Checking from MDWeb
- version: >=3.0.3
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
StructureCheck
utils.structure_check.StructureCheck object.
- input_structure_path (str) –
-
utils.structure_check.
main
()[source]¶ Command line execution of this building block. Please check the command line documentation.
-
utils.structure_check.
structure_check
(input_structure_path: str, output_summary_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
StructureCheck
class and execute thelaunch()
method.