#!/usr/bin/env python3
"""Module containing the PMX merge_ff class and the command line interface."""
import os
import sys
from pathlib import Path
import glob
import argparse
from pmx import ligand_alchemy
from typing import Mapping
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 Pmxmerge_ff(BiobbObject):
"""
| biobb_pmx Pmxmerge_ff
| Wrapper class for the `PMX merge_ff <https://github.com/deGrootLab/pmx>`_ module.
Args:
input_topology_path (str): Path to the input ligand topologies as a zip file containing a list of itp files. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand_itps.zip>`_. Accepted formats: zip (edam:format_3987).
output_topology_path (str): Path to the merged ligand topology file. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.itp>`_. Accepted formats: itp (edam:format_3883).
properties (dic):
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **container_path** (*str*) - (None) Path to the binary executable of your container.
* **container_image** (*str*) - (None) Container Image identifier.
* **container_volume_path** (*str*) - ("/inout") Path to an internal directory in the container.
* **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
* **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
* **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
Examples:
This is a use example of how to use the building block from Python::
from biobb_pmx.pmxbiobb.pmxmerge_ff import pmxmerge_ff
prop = {
'remove_tmp' : True
}
pmxmerge_ff(input_topology_path='/path/to/myTopologies.zip',
output_topology_path='/path/to/myMergedTopology.itp',
properties=prop)
Info:
* wrapped_software:
* name: PMX merge_ff
* version: >=1.0.1
* license: GNU
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_topology_path: str, output_topology_path: str, properties: Mapping = 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_topology_path": input_topology_path},
"out": {"output_topology_path": output_topology_path}
}
# Properties specific for BB
# None yet
# Properties common in all PMX BB
self.gmx_lib = properties.get('gmx_lib', None)
if not self.gmx_lib and os.environ.get('CONDA_PREFIX'):
python_version = f"{sys.version_info.major}.{sys.version_info.minor}"
self.gmx_lib = str(
Path(os.environ.get('CONDA_PREFIX')).joinpath(f"lib/python{python_version}/site-packages/pmx/data/mutff/"))
if properties.get('container_path'):
self.gmx_lib = str(Path('/usr/local/').joinpath("lib/python3.7/site-packages/pmx/data/mutff/"))
self.binary_path = properties.get('binary_path', 'pmx')
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`Pmxmerge_ff <pmx.pmxmerge_ff.Pmxmerge_ff>` pmx.pmxmerge_ff.Pmxmerge_ff object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Creating temporary folder
self.tmp_folder = fu.create_unique_dir()
self.out_log.info('Creating %s temporary folder' % self.tmp_folder)
fu.unzip_list(self.stage_io_dict["in"]["input_topology_path"], self.tmp_folder, out_log=self.out_log)
files = glob.glob(self.tmp_folder+"/*.itp")
ffsIn_list = []
for itp in files:
ffsIn_list.append(itp)
self.out_log.info('Running merge_FF_files from pmx package...\n')
ligand_alchemy._merge_FF_files(self.stage_io_dict["out"]["output_topology_path"], ffsIn=ffsIn_list)
# ffsIn=[self.stage_io_dict["in"]["input_topology1_path"],self.stage_io_dict["in"]["input_topology2_path"]] )
self.out_log.info('Exit code 0\n')
if self.gmx_lib:
self.env_vars_dict['GMXLIB'] = self.gmx_lib
# Run Biobb block
# self.run_biobb()
# Copy files to host
self.copy_to_host()
self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def pmxmerge_ff(input_topology_path: str, output_topology_path: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`Pmxmerge_ff <pmx.pmxmerge_ff.Pmxmerge_ff>` class and
execute the :meth:`launch() <pmx.pmxmerge_ff.Pmxmerge_ff.launch> method."""
return Pmxmerge_ff(input_topology_path=input_topology_path,
output_topology_path=output_topology_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="Run PMX merge_ff 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_topology_path', required=True, help="Path to the input ligand topologies as a zip file containing a list of itp files.")
required_args.add_argument('--output_topology_path', required=True, help="Path to the merged ligand topology file")
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
pmxmerge_ff(input_topology_path=args.input_topology_path,
output_topology_path=args.output_topology_path,
properties=properties)
if __name__ == '__main__':
main()