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:
biobb_common.generic.biobb_object.BiobbObject
biobb_vs BindingSiteThis 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: benner6, benner22, benner74, blosum100, blosum30, blosum35, blosum40, blosum45, blosum50, blosum55, blosum60, blosum62, blosum65, blosum70, blosum75, blosum80, blosum85, blosum90, blosum95, feng, fitch, genetic, gonnet, grant, ident, johnson, levin, mclach, miyata, nwsgappep, pam120, pam180, pam250, pam30, pam300, pam60, pam90, rao, risler, structure.
- 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.
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
-
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, **kwargs) → int[source]¶ Execute the
BindingSite
class and execute thelaunch()
method.
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:
biobb_common.generic.biobb_object.BiobbObject
biobb_vs BoxThis 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.
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
- input_pdb_path (str) –
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:
biobb_common.generic.biobb_object.BiobbObject
biobb_vs BoxResiduesThis 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.
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
-
launch
() → int[source]¶ Execute the
BoxResidues
utils.box_residues.BoxResidues object.
- input_pdb_path (str) –
-
utils.box_residues.
box_residues
(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
BoxResidues
class and execute thelaunch()
method.
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:
biobb_common.generic.biobb_object.BiobbObject
biobb_vs ExtractModelPDBQTExtracts a model from a PDBQT file with several models.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.
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
-
launch
() → int[source]¶ Execute the
ExtractModelPDBQT
utils.extract_model_pdbqt.ExtractModelPDBQT object.
- input_pdbqt_path (str) –
-
utils.extract_model_pdbqt.
extract_model_pdbqt
(input_pdbqt_path: str, output_pdbqt_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
ExtractModelPDBQT
class and execute thelaunch()
method.