# !/usr/bin/env python3
"""Module containing the PMX ligand_hybrid 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 Pmxligand_hybrid(BiobbObject):
"""
| biobb_pmx Pmxligand_hybrid
| Wrapper class for the `PMX ligand_hybrid <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).
input_topology1_path (str): Path to the input ligand topology file 1. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.itp>`_. Accepted formats: itp (edam:format_3883).
input_topology2_path (str): Path to the input ligand topology file 2. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.itp>`_. Accepted formats: itp (edam:format_3883).
input_pairs_path (str) (Optional): Path to the input atom pair mapping. File type: input. `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).
input_scaffold1_path (str) (Optional): Path to the index of atoms to consider for the ligand structure 1. File type: input. `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).
input_scaffold2_path (str) (Optional): Path to the index of atoms to consider for the ligand structure 2. File type: input. `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_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): Path to the output hybrid structure based on the ligand 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): Path to the output hybrid structure based on the ligand 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_topology_path (str): Path to the output hybrid topology. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ligand_hybrid.itp>`_. Accepted formats: itp (edam:format_3883).
output_atomtypes_path (str): Path to the atom types for the output hybrid topology. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ligand_hybrid_atomtypes.itp>`_. Accepted formats: itp (edam:format_3883).
properties (dic):
* **fit** (*bool*) - (False) Fit ligand structure 1 onto ligand structure 2 (Only used if input_pairs_path is provided).
* **split** (*bool*) - (False) Split the topology into separate transitions.
* **scDUMm** (*float*) - (1.0) Scale dummy masses using the counterpart atoms.
* **scDUMa** (*float*) - (1.0) Scale bonded dummy angle parameters.
* **scDUMd** (*float*) - (1.0) Scale bonded dummy dihedral parameters.
* **deAng** (*bool*) - (False) Decouple angles composed of 1 dummy and 2 non-dummies.
* **distance** (*float*) - (0.05) Distance (nm) between atoms to consider them morphable for alignment approach (Only used if input_pairs_path is not provided).
* **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.pmxligand_hybrid import pmxligand_hybrid
prop = {
'fit' : True,
'distance': 0.05
}
pmxligand_hybrid(input_structure1_path='/path/to/myStructure1.pdb',
input_structure2_path='/path/to/myStructure2.pdb',
input_topology1_path='/path/to/myTopology1.pdb',
input_topology2_path='/path/to/myTopology2.pdb',
input_pairs_path='/path/to/myPairs.dat',
output_log_path='/path/to/myLog.log',
output_structure1_path='/path/to/myStructureOutput1.pdb',
output_structure2_path='/path/to/myStructureOutput2.pdb',
output_topology_path='/path/to/myTopologyOutput.pdb',
output_atomtypes_path='/path/to/myAtomTypesOutput.pdb',
properties=prop)
Info:
* wrapped_software:
* name: PMX ligand_hybrid
* 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, input_topology1_path: str, input_topology2_path: str,
output_log_path: str, output_structure1_path: str, output_structure2_path: str, output_topology_path: str, output_atomtypes_path: str,
input_scaffold1_path: str = None, input_scaffold2_path: str = None, input_pairs_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,
"input_topology1_path": input_topology1_path, "input_topology2_path": input_topology2_path,
"input_scaffold1_path": input_scaffold1_path, "input_scaffold2_path": input_scaffold2_path,
"input_pairs_path": input_pairs_path},
"out": {"output_structure1_path": output_structure1_path, "output_structure2_path": output_structure2_path,
"output_topology_path": output_topology_path, "output_atomtypes_path": output_atomtypes_path,
"output_log_path": output_log_path}
}
# Properties specific for BB
# self.fit = properties.get('fit', False)
# self.split = properties.get('split', False)
# self.scDUMm = properties.get('scDUMm', 1.0)
# self.scDUMa = properties.get('scDUMa', 1.0)
# self.scDUMd = properties.get('scDUMd', 1.0)
# self.deAng = properties.get('deAng', False)
# self.distance = properties.get('distance', 0.05)
self.fit = properties.get('fit')
self.split = properties.get('split')
self.scDUMm = properties.get('scDUMm')
self.scDUMa = properties.get('scDUMa')
self.scDUMd = properties.get('scDUMd')
self.deAng = properties.get('deAng')
self.distance = properties.get('distance')
# 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, 'ligandHybrid',
'-i1', self.stage_io_dict["in"]["input_structure1_path"],
'-i2', self.stage_io_dict["in"]["input_structure2_path"],
'-itp1', self.stage_io_dict["in"]["input_topology1_path"],
'-itp2', self.stage_io_dict["in"]["input_topology2_path"],
'-pairs', self.stage_io_dict["in"]["input_pairs_path"],
'-oA', self.stage_io_dict["out"]["output_structure1_path"],
'-oB', self.stage_io_dict["out"]["output_structure2_path"],
'-oitp', self.stage_io_dict["out"]["output_topology_path"],
'-offitp', self.stage_io_dict["out"]["output_atomtypes_path"],
'-log', self.stage_io_dict["out"]["output_log_path"]
]
if self.stage_io_dict["in"].get("output_scaffold1_path"):
self.cmd.append('-n1')
self.cmd.append(self.stage_io_dict["in"]["output_scaffold1_path"])
if self.stage_io_dict["in"].get("output_scaffold2_path"):
self.cmd.append('-n2')
self.cmd.append(self.stage_io_dict["in"]["output_scaffold2_path"])
if self.fit:
self.cmd.append('--fit')
if self.split:
self.cmd.append('--split')
if self.deAng:
self.cmd.append('--deAng')
if self.distance:
self.cmd.append('--d')
self.cmd.append(str(self.distance))
if self.scDUMm:
self.cmd.append('--scDUMm')
self.cmd.append(str(self.scDUMm))
if self.scDUMa:
self.cmd.append('--scDUMa')
self.cmd.append(str(self.scDUMa))
if self.scDUMd:
self.cmd.append('--scDUMd')
self.cmd.append(str(self.scDUMd))
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 pmxligand_hybrid(input_structure1_path: str, input_structure2_path: str, input_topology1_path: str, input_topology2_path: str,
output_log_path: str, output_structure1_path: str, output_structure2_path: str, output_topology_path: str, output_atomtypes_path: str,
input_scaffold1_path: str = None, input_scaffold2_path: str = None, input_pairs_path: str = None,
properties: dict = None, **kwargs) -> int:
"""Execute the :class:`Pmxligand_hybrid <pmx.pmxmutate.Pmxligand_hybrid>` class and
execute the :meth:`launch() <pmx.pmxligand_hybrid.Pmxligand_hybrid.launch> method."""
return Pmxligand_hybrid(input_structure1_path=input_structure1_path, input_structure2_path=input_structure2_path,
input_topology1_path=input_topology1_path, input_topology2_path=input_topology2_path,
output_log_path=output_log_path,
output_structure1_path=output_structure1_path, output_structure2_path=output_structure2_path,
output_topology_path=output_topology_path, output_atomtypes_path=output_atomtypes_path,
input_scaffold1_path=input_scaffold1_path, input_scaffold2_path=input_scaffold2_path,
input_pairs_path=input_pairs_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 ligand hybrid 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('--input_topology1_path', required=True, help="Path to the input ligand topology file 1")
required_args.add_argument('--input_topology2_path', required=True, help="Path to the input ligand topology file 2")
required_args.add_argument('--output_structure1_path', required=True, help="Path to the output ligand structure file 1")
required_args.add_argument('--output_structure2_path', required=True, help="Path to the output ligand structure file 2")
required_args.add_argument('--output_topology1_path', required=True, help="Path to the output ligand topology file 1")
required_args.add_argument('--output_topology2_path', required=True, help="Path to the output ligand topology file 2")
required_args.add_argument('--output_log_path', required=True, help="Path to the log file")
parser.add_argument('--input_scaffold1_path', required=False, help="Path to the index of atoms to consider for the ligand structure 1")
parser.add_argument('--input_scaffold2_path', required=False, help="Path to the index of atoms to consider for the ligand structure 2")
parser.add_argument('--input_pairs_path', required=False, help="Path to the input atom pair mapping.")
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
pmxligand_hybrid(input_structure1_path=args.input_structure1_path, input_structure2_path=args.input_structure2_path,
input_topology1_path=args.input_topology1_path, input_topology2_path=args.input_topology2_path,
input_scaffold1_path=args.input_scaffold1_path, input_scaffold2_path=args.input_scaffold2_path,
input_pairs_path=args.input_pairs_path, output_log_path=args.output_log_path,
output_structure1_path=args.output_structure1_path, output_structure2_path=args.output_structure2_path,
output_topology1_path=args.output_topology1_path, output_topology2_path=args.output_topology2_path,
properties=properties)
if __name__ == '__main__':
main()