#!/usr/bin/env python3
"""Module containing the Box 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
[docs]class Box(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.
Args:
input_pdb_path (str): PDB file containing a selection of residue numbers or PQR file containing the pocket. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box.pqr>`_. 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 <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box.pdb>`_. 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
"""
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.offset = float(properties.get('offset', 2.0))
self.box_coordinates = float(properties.get('box_coordinates', False))
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:`Box <utils.box.Box>` utils.box.Box 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()
# check if cavity (pdb) or pocket (pqr)
input_type = PurePath(self.io_dict["in"]["input_pdb_path"]).suffix.lstrip('.')
if input_type == 'pdb':
fu.log('Loading residue PDB selection from %s' % (self.io_dict["in"]["input_pdb_path"]), self.out_log, self.global_log)
else:
fu.log('Loading pocket PQR selection from %s' % (self.io_dict["in"]["input_pdb_path"]), self.out_log, self.global_log)
# get input_pdb_path atoms coordinates
selection_atoms_num = 0
x_coordslist = []
y_coordslist = []
z_coordslist = []
with open(self.io_dict["in"]["input_pdb_path"]) as infile:
for line in infile:
if line.startswith("HETATM") or line.startswith("ATOM"):
x_coordslist.append(float(line[31:38].strip()))
y_coordslist.append(float(line[39:46].strip()))
z_coordslist.append(float(line[47:54].strip()))
selection_atoms_num = selection_atoms_num + 1
# Compute binding site box size
# compute box center
selection_box_center = [np.average(x_coordslist), np.average(y_coordslist), np.average(z_coordslist)]
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([x_coordslist, y_coordslist, z_coordslist], axis=1)
selection_box_size = selection_coords_max - selection_box_center
if self.offset:
fu.log('Adding %.1f Angstroms offset' % (self.offset), self.out_log, self.global_log)
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()
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def box(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`Box <utils.box.Box>` class and
execute the :meth:`launch() <utils.box.Box.launch>` method."""
return Box(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 set of residues from a given PDB or a pocket from a given PQR.", 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 file containing a selection of residue numbers or PQR file containing the pocket. Accepted formats: pdb, pqr.')
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(input_pdb_path=args.input_pdb_path,
output_pdb_path=args.output_pdb_path,
properties=properties)
if __name__ == '__main__':
main()