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 CatPDB
Class 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).
  • input_structure2 (str) –

    Input structure 2 file path. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_structure_path (str) –

    Output protein 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) –
    • 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:
launch() → int[source]

Execute the CatPDB utils.cat_pdb.CatPDB object.

utils.cat_pdb.cat_pdb(input_structure1: str, input_structure2: str, output_structure_path: str, properties: dict = None, **kwargs) → int[source]

Execute the CatPDB class and execute the launch() method.

utils.cat_pdb.main()[source]

Command line execution of this building block. Please check the command line documentation.

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 ExtractAtoms
Class 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:
launch() → int[source]

Execute the ExtractAtoms utils.extract_atoms.ExtractAtoms object.

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 the launch() method.

utils.extract_atoms.main()[source]

Command line execution of this building block. Please check the command line documentation.

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 ExtractAtoms
This 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).

  • output_structure_path (str) –

    Output structure 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) –
    • 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.
    • check_structure_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:
launch() → int[source]

Execute the ExtractChain utils.extract_chain.ExtractChain object.

utils.extract_chain.check_format_chains(chains, out_log)[source]

Check format of chains list

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 the launch() method.

utils.extract_chain.main()[source]

Command line execution of this building block. Please check the command line documentation.

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 ExtractHeteroAtoms
Class 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).

  • output_heteroatom_path (str) –

    Output heteroatom 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) –
    • 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:
launch() → int[source]

Execute the ExtractHeteroAtoms utils.extract_heteroatoms.ExtractHeteroAtoms object.

utils.extract_heteroatoms.check_format_heteroatoms(hets, out_log)[source]

Check format of heteroatoms list

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 the launch() method.

utils.extract_heteroatoms.main()[source]

Command line execution of this building block. Please check the command line documentation.

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 ExtractModel
This 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).

  • output_structure_path (str) –

    Output structure 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) –
    • 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.
    • check_structure_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:
launch() → int[source]

Execute the ExtractModel utils.extract_model.ExtractModel object.

utils.extract_model.check_format_models(models, out_log)[source]

Check format of models list

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 the launch() method.

utils.extract_model.main()[source]

Command line execution of this building block. Please check the command line documentation.

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 ExtractMolecule
This 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).

  • output_molecule_path (str) –

    Output molecule 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) –
    • 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”].
    • check_structure_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:
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.

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 the launch() method.

utils.extract_molecule.main()[source]

Command line execution of this building block. Please check the command line documentation.

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 RemoveLigand
Class 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:
launch() → int[source]

Execute the RemoveLigand utils.remove_ligand.RemoveLigand object.

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 the launch() 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 RemovePdbWater
This 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) –
    • check_structure_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:
launch() → int[source]

Execute the RemovePdbWater utils.remove_pdb_water.RemovePdbWater object.

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 the launch() 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 RenumberStructure
Class 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:
launch() → int[source]

Execute the RenumberStructure utils.renumber_structure.RenumberStructure object.

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 the launch() 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 SortGroResidues
Class 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:
launch() → int[source]

Execute the SortGroResidues utils.sort_gro_residues.SortGroResidues object.

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 the launch() 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 StrCheckAddHydrogens
This 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) Wether or not to add charges to the output file. If True the output is in PDBQT format.
    • mode (string) - (None) 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.
    • check_structure_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:
launch() → int[source]

Execute the StrCheckAddHydrogens utils.str_check_add_hydrogens.StrCheckAddHydrogens object.

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 the launch() 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 StructureCheck
This 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).

  • 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).
    • check_structure_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:
launch() → int[source]

Execute the StructureCheck utils.structure_check.StructureCheck object.

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 the launch() method.