utils package

Submodules

utils.bindingsite module

Module containing the BindingSite class and the command line interface.

class utils.bindingsite.BindingSite(input_pdb_path, input_clusters_zip, output_pdb_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_vs BindingSite
This class finds the binding site of the input_pdb.
Finds the binding site of the input_pdb_path file based on the ligands’ location of similar structures (members of the sequence identity cluster)

Parameters:

input_pdb_path (str) – Path to the PDB structure where the binding site is to be found. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).
input_clusters_zip (str) –
Path to the ZIP file with all the PDB members of the identity cluster. File type: input. Sample file. Accepted formats: zip (edam:format_3987).
output_pdb_path (str) –
Path to the PDB containig the residues belonging to the binding site. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- ligand (str) - (None) Ligand to be found in the protein structure. If no ligand provided, the largest one will be selected, if more than one.
- radius (float) - (5.0) [0.1~1000|0.1] Cut-off distance (Ångstroms) around ligand atoms to consider a protein atom as a binding site atom.
- max_num_ligands (int) - (15) [0~1000|1] Total number of superimposed ligands to be extracted from the identity cluster. For populated clusters, the restriction avoids to superimpose redundant structures. If 0, all ligands extracted will be considered.
- matrix_name (str) - (“BLOSUM62”) Substitution matrices for use in alignments. Values: BENNER22, BENNER6, BENNER74, BLASTN, BLASTP, BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, DAYHOFF, FENG, GENETIC, GONNET1992, HOXD70, JOHNSON, JONES, LEVIN, MCLACHLAN, MDM78, MEGABLAST, NUC.4.4, PAM250, PAM30, PAM70, RAO, RISLER, SCHNEIDER, STR, TRANS.
- gap_open (float) - (-10.0) [-1000~1000|0.1] Gap open penalty.
- gap_extend (float) - (-0.5) [-1000~1000|0.1] Gap extend penalty.
- 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:

from biobb_vs.utils.bindingsite import bindingsite
prop = {
    'ligand': 'PGA',
    'matrix_name': 'BLOSUM62',
    'gap_open': -10.0,
    'gap_extend': -0.5,
    'max_num_ligands': 15,
    'radius': 5
}
bindingsite(input_pdb_path='/path/to/myStructure.pdb',
            input_clusters_zip='/path/to/myCluster.zip',
            output_pdb_path='/path/to/newStructure.pdb',
            properties=prop)

Info:

wrapped_software:
- name: In house using Biopython
- version: >=1.76
- license: Apache-2.0
ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl

check_data_params(out_log, err_log)[source]: Checks all the input/output paths and parameters

launch() → int[source]: Execute the BindingSite utils.bindingsite.BindingSite object.

utils.bindingsite.bindingsite(input_pdb_path: str, input_clusters_zip: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]: Execute the BindingSite class and execute the launch() method.

utils.bindingsite.main()[source]: Command line execution of this building block. Please check the command line documentation.

utils.box module

Module containing the Box class and the command line interface.

class utils.box.Box(input_pdb_path, output_pdb_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_vs Box
This class sets the center and the size of a rectangular parallelepiped box around a set of residues or a pocket.
Sets the center and the size of a rectangular parallelepiped box around a set of residues from a given PDB or a pocket from a given PQR.

Parameters:

input_pdb_path (str) –
PDB file containing a selection of residue numbers or PQR file containing the pocket. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), pqr (edam:format_1476).
output_pdb_path (str) –
PDB including the annotation of the box center and size as REMARKs. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- offset (float) - (2.0) [0.1~1000|0.1] Extra distance (Angstroms) between the last residue atom and the box boundary.
- box_coordinates (bool) - (False) Add box coordinates as 8 ATOM records.
- 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:

from biobb_vs.utils.box import box
prop = {
    'offset': 2,
    'box_coordinates': True
}
box(input_pdb_path='/path/to/myPocket.pqr',
    output_pdb_path='/path/to/newBox.pdb',
    properties=prop)

Info:

wrapped_software:
- name: In house
- license: Apache-2.0
ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl

check_data_params(out_log, err_log)[source]: Checks all the input/output paths and parameters

launch() → int[source]: Execute the Box utils.box.Box object.

utils.box.box(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]: Execute the Box class and execute the launch() method.

utils.box.main()[source]: Command line execution of this building block. Please check the command line documentation.

utils.box_residues module

Module containing the BoxResidues class and the command line interface.

class utils.box_residues.BoxResidues(input_pdb_path, output_pdb_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_vs BoxResidues
This class sets the center and the size of a rectangular parallelepiped box around a set of residues.
Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB. The residue identifiers that compose the selection (i.e. binding site) are provided by a property list.

Parameters:

input_pdb_path (str) –
PDB protein structure for which the box will be build. Its size and center will be set around the ‘resid_list’ property once mapped against this PDB. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).
output_pdb_path (str) –
PDB including the annotation of the box center and size as REMARKs. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- resid_list (list) - (None) List with all the residue numbers to form a cavity or binding site. Mandatory property.
- offset (float) - (2.0) [0.1~1000|0.1] Extra distance (Angstroms) between the last residue atom and the box boundary.
- box_coordinates (bool) - (False) Add box coordinates as 8 ATOM records.
- residue_offset (int) - (0) [0~1000|1] Residue id offset.
- 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:

from biobb_vs.utils.box_residues import box_residues
prop = {
    'resid_list': [718, 743, 745, 762, 766, 796, 790, 791, 793, 794, 788],
    'offset': 2,
    'box_coordinates': True
}
box_residues(input_pdb_path='/path/to/myStructure.pdb',
            output_pdb_path='/path/to/newBox.pdb',
            properties=prop)

Info:

wrapped_software:
- name: In house using Biopython
- version: >=1.76
- license: Apache-2.0
ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl

check_data_params(out_log, err_log)[source]: Checks all the input/output paths and parameters

launch() → int[source]: Execute the BoxResidues utils.box_residues.BoxResidues object.

utils.box_residues.box_residues(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]: Execute the BoxResidues class and execute the launch() method.

utils.box_residues.main()[source]: Command line execution of this building block. Please check the command line documentation.

utils.extract_model_pdbqt module

Module containing the ExtractModelPDBQT class and the command line interface.

class utils.extract_model_pdbqt.ExtractModelPDBQT(input_pdbqt_path, output_pdbqt_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_vs ExtractModelPDBQT
Extracts a model from a PDBQT file with several models.
Extracts a model from a PDBQT file with several models. The model number to extract is defined by the user.

Parameters:

input_pdbqt_path (str) –
Input PDBQT file. File type: input. Sample file. Accepted formats: pdbqt (edam:format_1476).
output_pdbqt_path (str) –
Output PDBQT file. File type: output. Sample file. Accepted formats: pdbqt (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- model (int) - (1) [0~1000|1] Model number to extract from input_pdbqt_path.
- 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:

from biobb_vs.utils.extract_model_pdbqt import extract_model_pdbqt
prop = {
    'model': 1
}
extract_model_pdbqt(input_pdbqt_path='/path/to/myStructure.pdbqt',
                    output_pdbqt_path='/path/to/newStructure.pdbqt',
                    properties=prop)

Info:

wrapped_software:
- name: In house using Biopython
- version: >=1.76
- license: Apache-2.0
ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl

check_data_params(out_log, err_log)[source]: Checks all the input/output paths and parameters

launch() → int[source]: Execute the ExtractModelPDBQT utils.extract_model_pdbqt.ExtractModelPDBQT object.

utils.extract_model_pdbqt.extract_model_pdbqt(input_pdbqt_path: str, output_pdbqt_path: str, properties: dict | None = None, **kwargs) → int[source]: Execute the ExtractModelPDBQT class and execute the launch() method.

utils.extract_model_pdbqt.main()[source]: Command line execution of this building block. Please check the command line documentation.