#!/usr/bin/env python3
"""Module containing the AcpypeParamsGMX class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
from biobb_chemistry.acpype.common import get_binary_path, check_input_path, check_output_path, get_basename, get_charge, create_unique_name, get_default_value, process_output_gmx
[docs]class AcpypeParamsGMX(BiobbObject):
"""
| biobb_chemistry AcpypeParamsGMX
| This class is a wrapper of `Acpype <https://github.com/alanwilter/acpype>`_ tool for generation of topologies for GROMACS.
| Generation of topologies for GROMACS. Acpype is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA. `Visit the official page <https://github.com/alanwilter/acpype>`_.
Args:
input_path (str): Path to the input file. File type: input. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/acpype/acpype.params.mol2>`_. Accepted formats: pdb (edam:format_1476), mdl (edam:format_3815), mol2 (edam:format_3816).
output_path_gro (str): Path to the GRO output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.gro>`_. Accepted formats: gro (edam:format_2033).
output_path_itp (str): Path to the ITP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.itp>`_. Accepted formats: itp (edam:format_3883).
output_path_top (str): Path to the TOP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.top>`_. Accepted formats: top (edam:format_3880).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **basename** (*str*) - ("BBB") A basename for the project (folder and output files).
* **charge** (*int*) - (0) [-20~20|1] Net molecular charge, for gas default is 0. If None the charge is guessed by acpype.
* **binary_path** (*str*) - ("acpype") Path to the acpype executable binary.
* **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) Container path definition.
* **container_image** (*str*) - ('acpype/acpype:2022.7.21') Container image definition.
* **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
* **container_working_dir** (*str*) - (None) Container working directory definition.
* **container_user_id** (*str*) - (None) Container user_id definition.
* **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
Examples:
This is a use example of how to use the building block from Python::
from biobb_chemistry.acpype.acpype_params_gmx import acpype_params_gmx
prop = {
'basename': 'BBB',
'charge': 0
}
acpype_params_gmx(input_path='/path/to/myStructure.mol2',
output_path_gro='/path/to/newGRO.gro',
output_path_itp='/path/to/newITP.itp',
output_path_top='/path/to/newTOP.top',
properties=prop)
Info:
* wrapped_software:
* name: Acpype
* version: 2019.10.05.12.26
* license: GNU
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_path, output_path_gro, output_path_itp, output_path_top,
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_path": input_path},
"out": {"output_path_gro": output_path_gro, "output_path_itp": output_path_itp, "output_path_top": output_path_top}
}
# Properties specific for BB
self.basename = properties.get('basename', 'BBB')
self.charge = properties.get('charge', '')
self.binary_path = get_binary_path(properties, 'binary_path')
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_path"] = check_input_path(self.io_dict["in"]["input_path"], out_log, self.__class__.__name__)
self.io_dict["out"]["output_path_gro"] = check_output_path(self.io_dict["out"]["output_path_gro"], 'gro', out_log, self.__class__.__name__)
self.io_dict["out"]["output_path_itp"] = check_output_path(self.io_dict["out"]["output_path_itp"], 'itp', out_log, self.__class__.__name__)
self.io_dict["out"]["output_path_top"] = check_output_path(self.io_dict["out"]["output_path_top"], 'top', out_log, self.__class__.__name__)
self.output_files = {
'gro': self.io_dict["out"]["output_path_gro"],
'itp': self.io_dict["out"]["output_path_itp"],
'top': self.io_dict["out"]["output_path_top"],
}
[docs] def create_cmd(self, container_io_dict, out_log, err_log):
"""Creates the command line instruction using the properties file settings"""
instructions_list = []
# generating output path
if self.container_path:
out_pth = self.container_volume_path + '/' + get_basename(self.basename, out_log) + '.' + self.unique_name
else:
out_pth = get_basename(self.basename, out_log) + '.' + self.unique_name
# executable path
instructions_list.append(self.binary_path)
# generating input
ipath = '-i ' + container_io_dict["in"]["input_path"]
instructions_list.append(ipath)
# generating output
basename = '-b ' + out_pth
instructions_list.append(basename)
# adding charge if not None
charge = get_charge(self.charge, out_log)
if charge:
charge = '-n ' + charge
instructions_list.append(charge)
return instructions_list
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`AcpypeParamsGMX <acpype.acpype_params_gmx.AcpypeParamsGMX>` acpype.acpype_params_gmx.AcpypeParamsGMX 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()
# create unique name for temporary folder (created by acpype)
self.unique_name = create_unique_name(6)
# create command line instruction
self.cmd = self.create_cmd(self.stage_io_dict, self.out_log, self.err_log)
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# move files to output_path and removes temporary folder
if self.container_path:
process_output_gmx(self.unique_name,
self.stage_io_dict['unique_dir'],
self.remove_tmp,
self.basename,
get_default_value(self.__class__.__name__),
self.output_files, self.out_log)
else:
process_output_gmx(self.unique_name,
self.basename + "." + self.unique_name + ".acpype",
self.remove_tmp,
self.basename,
get_default_value(self.__class__.__name__),
self.output_files, self.out_log)
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def acpype_params_gmx(input_path: str, output_path_gro: str, output_path_itp: str, output_path_top: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`AcpypeParamsGMX <acpype.acpype_params_gmx.AcpypeParamsGMX>` class and
execute the :meth:`launch() <acpype.acpype_params_gmx.AcpypeParamsGMX.launch>` method."""
return AcpypeParamsGMX(input_path=input_path,
output_path_gro=output_path_gro,
output_path_itp=output_path_itp,
output_path_top=output_path_top,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Small molecule parameterization for GROMACS MD package.", 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_path', required=True, help='Path to the input file. Accepted formats: pdb, mdl, mol2.')
required_args.add_argument('--output_path_gro', required=True, help='Path to the GRO output file. Accepted formats: gro.')
required_args.add_argument('--output_path_itp', required=True, help='Path to the ITP output file. Accepted formats: itp.')
required_args.add_argument('--output_path_top', required=True, help='Path to the TOP output file. Accepted formats: top.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
acpype_params_gmx(input_path=args.input_path,
output_path_gro=args.output_path_gro,
output_path_itp=args.output_path_itp,
output_path_top=args.output_path_top,
properties=properties)
if __name__ == '__main__':
main()