#!/usr/bin/env python3
"""Module containing the BoxResidues class and the command line interface."""
import argparse
import numpy as np
from pathlib import PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_vs.utils.common import check_input_path, check_output_path, get_box_coordinates
from Bio import BiopythonDeprecationWarning
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonDeprecationWarning)
import Bio.PDB
import Bio.pairwise2
# try:
# import Bio.SubsMat.MatrixInfo
# except ImportError:
import Bio.Align.substitution_matrices
[docs]class BoxResidues(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.
Args:
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 <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box_residues.pdb>`_. 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 <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box_residues.pdb>`_. 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
"""
def __init__(self, input_pdb_path, output_pdb_path,
properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_pdb_path": input_pdb_path},
"out": {"output_pdb_path": output_pdb_path}
}
# Properties specific for BB
self.resid_list = properties.get('resid_list', [])
self.offset = float(properties.get('offset', 2.0))
self.box_coordinates = float(properties.get('box_coordinates', False))
self.residue_offset = properties.get('residue_offset', 0)
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", self.out_log, self.__class__.__name__)
self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, self.out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` utils.box_residues.BoxResidues object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Parse structure
fu.log('Loading input PDB structure %s' % (self.io_dict["in"]["input_pdb_path"]), self.out_log, self.global_log)
structure_name = PurePath(self.io_dict["in"]["input_pdb_path"]).name
parser = Bio.PDB.PDBParser(QUIET=True)
structPDB = parser.get_structure(structure_name, self.io_dict["in"]["input_pdb_path"])
if len(structPDB):
structPDB = structPDB[0]
# Mapping residue structure into input structure
fu.log('Mapping residue structure into input structure', self.out_log, self.global_log)
# Listing residues to be selected from the residue structure
residPDB_res_list = []
for residPDB_res in self.resid_list:
if self.residue_offset:
residPDB_res_list.append((' ', residPDB_res+self.residue_offset, ' '))
else:
residPDB_res_list.append((' ', residPDB_res, ' '))
selection_res_list = []
selection_atoms_num = 0
for struct_chain in structPDB:
for struct_res in struct_chain:
if struct_res.get_id() in residPDB_res_list:
selection_res_list.append(struct_res)
selection_atoms_num += len(struct_res.get_list())
if len(selection_res_list) == 0:
fu.log(self.__class__.__name__ + ': Cannot match any of the residues listed in [%s] into %s' % (', '.join(str(v) for v in self.resid_list), self.io_dict["in"]["input_pdb_path"]), self.out_log)
raise SystemExit(self.__class__.__name__ + ': Cannot match any of the residues listed in [%s] into %s' % (', '.join(str(v) for v in self.resid_list), self.io_dict["in"]["input_pdb_path"]))
elif len(selection_res_list) != len(residPDB_res_list):
fu.log('Cannot match all the residues listed in %s into %s. Found %s out of %s' % (', '.join(str(v) for v in self.resid_list), self.io_dict["in"]["input_pdb_path"], len(selection_res_list), len(residPDB_res_list)), self.out_log)
else:
fu.log('Selection of residues successfully matched', self.out_log, self.global_log)
# Compute binding site box size
# compute box center
selection_box_center = sum(atom.coord for res in selection_res_list for atom in res.get_atoms()) / selection_atoms_num
fu.log('Binding site center (Angstroms): %10.3f%10.3f%10.3f' % (selection_box_center[0], selection_box_center[1], selection_box_center[2]), self.out_log, self.global_log)
# compute box size
selection_coords_max = np.amax([atom.coord for res in selection_res_list for atom in res.get_atoms()], axis=0)
selection_box_size = selection_coords_max - selection_box_center
if self.offset:
selection_box_size = [c + self.offset for c in selection_box_size]
fu.log('Binding site size (Angstroms): %10.3f%10.3f%10.3f' % (selection_box_size[0], selection_box_size[1], selection_box_size[2]), self.out_log, self.global_log)
# compute volume
vol = np.prod(selection_box_size) * 2**3
fu.log('Volume (cubic Angstroms): %.0f' % (vol), self.out_log, self.global_log)
# add box details as PDB remarks
remarks = "REMARK BOX CENTER:%10.3f%10.3f%10.3f" % (selection_box_center[0], selection_box_center[1], selection_box_center[2])
remarks += " SIZE:%10.3f%10.3f%10.3f" % (selection_box_size[0], selection_box_size[1], selection_box_size[2])
selection_box_coords_txt = ""
# add (optional) box coordinates as 8 ATOM records
if self.box_coordinates:
fu.log('Adding box coordinates', self.out_log, self.global_log)
selection_box_coords_txt = get_box_coordinates(selection_box_center, selection_box_size)
with open(self.io_dict["out"]["output_pdb_path"], 'w') as f:
f.seek(0, 0)
f.write(remarks.rstrip('\r\n') + '\n' + selection_box_coords_txt)
fu.log('Saving output PDB file (with box setting annotations): %s' % (self.io_dict["out"]["output_pdb_path"]), self.out_log, self.global_log)
# Copy files to host
self.copy_to_host()
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir")
])
self.remove_tmp_files()
return 0
[docs]def box_residues(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` class and
execute the :meth:`launch() <utils.box_residues.BoxResidues.launch>` method."""
return BoxResidues(input_pdb_path=input_pdb_path,
output_pdb_path=output_pdb_path,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_pdb_path', required=True, help='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. Accepted formats: pdb.')
required_args.add_argument('--output_pdb_path', required=True, help='PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
box_residues(input_pdb_path=args.input_pdb_path,
output_pdb_path=args.output_pdb_path,
properties=properties)
if __name__ == '__main__':
main()