#!/usr/bin/env python3
"""Module containing the AppendLigand class and the command line interface."""
import re
import argparse
import shutil
from pathlib import Path
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
[docs]class AppendLigand(BiobbObject):
"""
| biobb_md AppendLigand
| This class takes a ligand ITP file and inserts it in a topology.
| This module automatizes the process of inserting a ligand ITP file in a GROMACS topology.
Args:
input_top_zip_path (str): Path the input topology TOP and ITP files zipball. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs_extra/ndx2resttop.zip>`_. Accepted formats: zip (edam:format_3987).
input_itp_path (str): Path to the ligand ITP file to be inserted in the topology. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs_extra/pep_ligand.itp>`_. Accepted formats: itp (edam:format_3883).
output_top_zip_path (str): Path/Name the output topology TOP and ITP files zipball. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs_extra/ref_appendligand.zip>`_. Accepted formats: zip (edam:format_3987).
input_posres_itp_path (str) (Optional): Path to the position restriction ITP file. File type: input. Accepted formats: itp (edam:format_3883).
properties (dic):
* **posres_name** (*str*) - ("POSRES_LIGAND") String to be included in the ifdef clause.
* **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_md.gromacs_extra.append_ligand import append_ligand
prop = { 'posres_name': 'POSRES_LIGAND' }
append_ligand(input_top_zip_path='/path/to/myTopology.zip',
input_itp_path='/path/to/myTopologyAddOn.itp',
output_top_zip_path='/path/to/newTopology.zip',
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_top_zip_path: str, input_itp_path: str, output_top_zip_path: str,
input_posres_itp_path: str = None, properties: dict = None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {"input_top_zip_path": input_top_zip_path, "input_itp_path": input_itp_path,
"input_posres_itp_path": input_posres_itp_path},
"out": {"output_top_zip_path": output_top_zip_path}
}
# Properties specific for BB
self.posres_name = properties.get('posres_name', 'POSRES_LIGAND')
# Check the properties
self.check_properties(properties)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`AppendLigand <gromacs_extra.append_ligand.AppendLigand>` object."""
# Setup Biobb
if self.check_restart(): return 0
# Unzip topology
top_file = fu.unzip_top(zip_file=self.io_dict['in'].get("input_top_zip_path"), out_log=self.out_log)
top_dir = str(Path(top_file).parent)
itp_name = str(Path(self.io_dict['in'].get("input_itp_path")).name)
with open(top_file) as top_f:
top_lines = top_f.readlines()
top_f.close()
fu.rm(top_file)
forcefield_pattern = r'#include.*forcefield.itp\"'
if top_lines:
for index, line in enumerate(top_lines):
if re.search(forcefield_pattern, line):
break
else:
fu.log(f'FATAL: Input topfile {top_file} from input_top_zip_path {self.io_dict["in"].get("input_top_zip_path")} is empty.', self.out_log, self.global_log)
return 1
top_lines.insert(index+1, '\n')
top_lines.insert(index+2, '; Including ligand ITP\n')
top_lines.insert(index+3, '#include "' + itp_name + '"\n')
top_lines.insert(index+4, '\n')
if self.io_dict['in'].get("input_posres_itp_path"):
top_lines.insert(index+5, '; Ligand position restraints'+'\n')
top_lines.insert(index+6, '#ifdef '+self.posres_name+'\n')
top_lines.insert(index+7, '#include "'+str(Path(self.io_dict['in'].get("input_posres_itp_path")).name)+'"\n')
top_lines.insert(index+8, '#endif'+'\n')
top_lines.insert(index+9, '\n')
inside_moleculetype_section = False
with open(self.io_dict['in'].get("input_itp_path")) as itp_file:
moleculetype_pattern = r'\[ moleculetype \]'
for line in itp_file:
if re.search(moleculetype_pattern, line):
inside_moleculetype_section = True
continue
if inside_moleculetype_section and not line.startswith(';'):
moleculetype = line.strip().split()[0].strip()
break
molecules_pattern = r'\[ molecules \]'
inside_molecules_section = False
index_molecule = None
molecule_string = moleculetype+(20-len(moleculetype))*' '+'1'+'\n'
for index, line in enumerate(top_lines):
if re.search(molecules_pattern, line):
inside_molecules_section = True
continue
if inside_molecules_section and not line.startswith(';') and line.upper().startswith('PROTEIN'):
index_molecule = index
if index_molecule:
top_lines.insert(index_molecule+1, molecule_string)
else:
top_lines.append(molecule_string)
new_top = fu.create_name(path=top_dir, prefix=self.prefix, step=self.step, name='ligand.top')
with open(new_top, 'w') as new_top_f:
new_top_f.write("".join(top_lines))
shutil.copy2(self.io_dict['in'].get("input_itp_path"), top_dir)
if self.io_dict['in'].get("input_posres_itp_path"):
shutil.copy2(self.io_dict['in'].get("input_posres_itp_path"), top_dir)
# zip topology
fu.log('Compressing topology to: %s' % self.io_dict['out'].get("output_top_zip_path"), self.out_log, self.global_log)
fu.zip_top(zip_file=self.io_dict['out'].get("output_top_zip_path"), top_file=new_top, out_log=self.out_log)
# Remove temporal files
self.tmp_files.append(top_dir)
self.remove_tmp_files()
return 0
[docs]def append_ligand(input_top_zip_path: str, input_itp_path: str, output_top_zip_path: str,
input_posres_itp_path: str = None, properties: dict = None, **kwargs) -> int:
"""Create :class:`AppendLigand <gromacs_extra.append_ligand.AppendLigand>` class and
execute the :meth:`launch() <gromacs_extra.append_ligand.AppendLigand.launch>` method."""
return AppendLigand(input_top_zip_path=input_top_zip_path,
input_itp_path=input_itp_path,
output_top_zip_path=output_top_zip_path,
input_posres_itp_path=input_posres_itp_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="Wrapper of the GROMACS editconf module.",
formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_top_zip_path', required=True)
required_args.add_argument('--input_itp_path', required=True)
required_args.add_argument('--output_top_zip_path', required=True)
parser.add_argument('--input_posres_itp_path', required=False)
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
append_ligand(input_top_zip_path=args.input_top_zip_path, input_itp_path=args.input_itp_path,
output_top_zip_path=args.output_top_zip_path, input_posres_itp_path=args.input_posres_itp_path,
properties=properties)
if __name__ == '__main__':
main()