#!/usr/bin/env python3
"""Module containing the PMX atom_mapping class and the command line interface."""
import os
import sys
from pathlib import Path
import shutil
import argparse
from typing import Mapping
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
[docs]class Pmxatom_mapping(BiobbObject):
"""
| biobb_pmx Pmxatom_mapping
| Wrapper class for the `PMX atom_mapping <https://github.com/deGrootLab/pmx>`_ module.
Args:
input_structure1_path (str): Path to the input ligand structure file 1. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.pdb>`_. Accepted formats: pdb (edam:format_1476).
input_structure2_path (str): Path to the input ligand structure file 2. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_pairs1_path (str): Path to the output pairs for the ligand structure 1. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_mapping_pairs.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).
output_pairs2_path (str): Path to the output pairs for the ligand structure 2. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_mapping_pairs.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).
output_log_path (str): Path to the log file. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/atom_mapping.log>`_. Accepted formats: log (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).
output_structure1_path (str) (Optional): Path to the superimposed structure for the ligand structure 1. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/superimposed_ligand.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_structure2_path (str) (Optional): Path to the superimposed structure for the ligand structure 2. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/superimposed_ligand.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_morph1_path (str) (Optional): Path to the morphable atoms for the ligand structure 1. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/superimposed_ligand.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_morph2_path (str) (Optional): Path to the morphable atoms for the ligand structure 2. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/superimposed_ligand.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_scaffold1_path (str) (Optional): Path to the index of atoms to consider for the ligand structure 1. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/atoms_to_consider.ndx>`_. Accepted formats: ndx (edam:format_2033).
output_scaffold2_path (str) (Optional): Path to the index of atoms to consider for the ligand structure 2. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/atoms_to_consider.ndx>`_. Accepted formats: ndx (edam:format_2033).
output_score_path (str) (Optional): Path to the morphing score. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/morph_score.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).
properties (dic):
* **noalignment** (*bool*) - (False) Should the alignment method be disabled.
* **nomcs** (*bool*) - (False) Should the MCS method be disabled.
* **noH2H** (*bool*) - (True) Should non-polar hydrogens be discarded from morphing into any other hydrogen.
* **H2Hpolar** (*bool*) - (False) Should polar hydrogens be morphed into polar hydrogens.
* **H2Heavy** (*bool*) - (False) Should hydrogen be morphed into a heavy atom.
* **RingsOnly** (*bool*) - (False) Should rings only be used in the MCS search and alignemnt.
* **dMCS** (*bool*) - (False) Should the distance criterium be also applied in the MCS based search.
* **swap** (*bool*) - (False) Try swapping the molecule order which would be a cross-check and require double execution time.
* **nochirality** (*bool*) - (True) Perform chirality check for MCS mapping.
* **distance** (*float*) - (0.05) Distance (nm) between atoms to consider them morphable for alignment approach.
* **timeout** (*int*) - (10) Maximum time (s) for an MCS search.
* **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.pmxatom_mapping import pmxatom_mapping
prop = {
'no-alignment' : True,
'distance': 0.05
}
pmxatom_mapping(input_structure1_path='/path/to/myStructure1.pdb',
input_structure2_path='/path/to/myStructure2.pdb',
output_pairs1_path='/path/to/myPairs1.dat',
output_pairs2_path='/path/to/myPairs2.dat',
output_log_path='/path/to/myLog.log',
properties=prop)
Info:
* wrapped_software:
* name: PMX atom_mapping
* version: >=1.0.1
* license: GNU
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_structure1_path: str, input_structure2_path: str, output_pairs1_path: str, output_pairs2_path: str,
output_log_path: str, output_structure1_path: str = None, output_structure2_path: str = None, output_morph1_path: str = None,
output_morph2_path: str = None, output_scaffold1_path: str = None, output_scaffold2_path: str = None, output_score_path: str = None,
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_structure1_path": input_structure1_path, "input_structure2_path": input_structure2_path},
"out": {"output_pairs1_path": output_pairs1_path, "output_pairs2_path": output_pairs2_path,
"output_log_path": output_log_path,
"output_structure1_path": output_structure1_path, "output_structure2_path": output_structure2_path,
"output_morph1_path": output_morph1_path, "output_morph2_path": output_morph2_path,
"output_scaffold1_path": output_scaffold1_path, "output_scaffold2_path": output_scaffold2_path,
"output_score_path": output_score_path}
}
# Properties specific for BB
# self.noalignment = properties.get('noalignment', False)
# self.nomcs = properties.get('nomcs', False)
# self.noH2H = properties.get('noH2H', True)
# self.H2Hpolar = properties.get('H2Hpolar', False)
# self.H2Heavy = properties.get('H2Heavy', False)
# self.RingsOnly = properties.get('RingsOnly', False)
# self.dMCS = properties.get('dMCS', False)
# self.swap = properties.get('swap', False)
# self.nochirality = properties.get('nochirality', True)
# self.distance = properties.get('distance', 0.05)
# self.timeout = properties.get('timeout', 10)
self.noalignment = properties.get('noalignment')
self.nomcs = properties.get('nomcs')
self.noH2H = properties.get('noH2H')
self.H2Hpolar = properties.get('H2Hpolar')
self.H2Heavy = properties.get('H2Heavy')
self.RingsOnly = properties.get('RingsOnly')
self.dMCS = properties.get('dMCS')
self.swap = properties.get('swap')
self.nochirality = properties.get('nochirality')
self.distance = properties.get('distance')
self.timeout = properties.get('timeout')
# 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:`Pmxmutate <pmx.pmxmutate.Pmxmutate>` pmx.pmxmutate.Pmxmutate object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Check if executable exists
if not self.container_path:
if not Path(self.binary_path).is_file():
if not shutil.which(self.binary_path):
raise FileNotFoundError(
'Executable %s not found. Check if it is installed in your system and correctly defined in the properties' % self.binary_path)
self.cmd = [self.binary_path, 'atomMapping',
'-i1', self.stage_io_dict["in"]["input_structure1_path"],
'-i2', self.stage_io_dict["in"]["input_structure2_path"],
'-o1', self.stage_io_dict["out"]["output_pairs1_path"],
'-o2', self.stage_io_dict["out"]["output_pairs2_path"],
'-log', self.stage_io_dict["out"]["output_log_path"]
]
if self.stage_io_dict["out"].get("output_structure1_path"):
self.cmd.append('-opdb1')
self.cmd.append(self.stage_io_dict["out"]["output_structure1_path"])
if self.stage_io_dict["out"].get("output_structure2_path"):
self.cmd.append('-opdb2')
self.cmd.append(self.stage_io_dict["out"]["output_structure2_path"])
if self.stage_io_dict["out"].get("output_morph1_path"):
self.cmd.append('-opdbm1')
self.cmd.append(self.stage_io_dict["out"]["output_morph1_path"])
if self.stage_io_dict["out"].get("output_morph2_path"):
self.cmd.append('-opdbm2')
self.cmd.append(self.stage_io_dict["out"]["output_morph2_path"])
if self.stage_io_dict["out"].get("output_scaffold1_path"):
self.cmd.append('-n1')
self.cmd.append(self.stage_io_dict["out"]["output_scaffold1_path"])
if self.stage_io_dict["out"].get("output_scaffold2_path"):
self.cmd.append('-n2')
self.cmd.append(self.stage_io_dict["out"]["output_scaffold2_path"])
if self.stage_io_dict["out"].get("output_score_path"):
self.cmd.append('-score')
self.cmd.append(self.stage_io_dict["out"]["output_score_path"])
if self.noalignment:
self.cmd.append('--no-alignment')
if self.nomcs:
self.cmd.append('--no-mcs')
if self.noH2H:
self.cmd.append('--no-H2H')
if self.H2Hpolar:
self.cmd.append('--H2Hpolar')
if self.H2Heavy:
self.cmd.append('--H2Heavy')
if self.RingsOnly:
self.cmd.append('--RingsOnly')
if self.dMCS:
self.cmd.append('--dMCS')
if self.swap:
self.cmd.append('--swap')
if self.nochirality:
self.cmd.append('--no-chirality')
if self.distance:
self.cmd.append('--d')
self.cmd.append(str(self.distance))
if self.timeout:
self.cmd.append('--timeout')
self.cmd.append(str(self.timeout))
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 pmxatom_mapping(input_structure1_path: str, input_structure2_path: str, output_pairs1_path: str, output_pairs2_path: str,
output_log_path: str, output_structure1_path: str = None, output_structure2_path: str = None, output_morph1_path: str = None,
output_morph2_path: str = None, output_scaffold1_path: str = None, output_scaffold2_path: str = None, output_score_path: str = None,
properties: dict = None, **kwargs) -> int:
"""Execute the :class:`Pmxatom_mapping <pmx.pmxmutate.Pmxatom_mapping>` class and
execute the :meth:`launch() <pmx.pmxatom_mapping.Pmxatom_mapping.launch> method."""
return Pmxatom_mapping(input_structure1_path=input_structure1_path, input_structure2_path=input_structure2_path,
output_pairs1_path=output_pairs1_path, output_pairs2_path=output_pairs2_path,
output_log_path=output_log_path,
output_structure1_path=output_structure1_path, output_structure2_path=output_structure2_path,
output_morph1_path=output_morph1_path, output_morph2_path=output_morph2_path,
output_scaffold1_path=output_scaffold1_path, output_scaffold2_path=output_scaffold2_path,
output_score_path=output_score_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 atom mapping 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_structure1_path', required=True, help="Path to the input ligand structure file 1")
required_args.add_argument('--input_structure2_path', required=True, help="Path to the input ligand structure file 2")
required_args.add_argument('--output_pairs1_path', required=True, help="Path to the output pairs for the ligand structure 1")
required_args.add_argument('--output_pairs2_path', required=True, help="Path to the output pairs for the ligand structure 2")
required_args.add_argument('--output_log_path', required=True, help="Path to the log file")
parser.add_argument('--output_structure1_path', required=False, help="Path to the superimposed structure for the ligand structure 1")
parser.add_argument('--output_structure2_path', required=False, help="Path to the superimposed structure for the ligand structure 2")
parser.add_argument('--output_morph1_path', required=False, help="Path to the morphable atoms for the ligand structure 1")
parser.add_argument('--output_morph2_path', required=False, help="Path to the morphable atoms for the ligand structure 2")
parser.add_argument('--output_scaffold1_path', required=False, help="Path to the index of atoms to consider for the ligand structure 1")
parser.add_argument('--output_scaffold2_path', required=False, help="Path to the index of atoms to consider for the ligand structure 2")
parser.add_argument('--output_score_path', required=False, help="Path to the morphing score. File type: output")
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
pmxatom_mapping(input_structure1_path=args.input_structure1_path, input_structure2_path=args.input_structure2_path,
output_pairs1_path=args.output_pairs1_path, output_pairs2_path=args.output_pairs2_path,
output_log_path=args.output_log_path,
output_structure1_path=args.output_structure1_path, output_structure2_path=args.output_structure2_path,
output_morph1_path=args.output_morph1_path, output_morph2_path=args.output_morph2_path,
output_scaffold1_path=args.output_scaffold1_path, output_scaffold2_path=args.output_scaffold2_path,
output_score_path=args.output_score_path,
properties=properties)
if __name__ == '__main__':
main()