#!/usr/bin/env python3
"""Module containing the Genion class and the command line interface."""
import os
import shutil
import argparse
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
from biobb_md.gromacs.common import get_gromacs_version
from biobb_md.gromacs.common import GromacsVersionError
[docs]class Genion(BiobbObject):
"""
| biobb_md Genion
| Wrapper class for the `GROMACS genion <http://manual.gromacs.org/current/onlinehelp/gmx-genion.html>`_ module.
| The GROMACS genion module randomly replaces solvent molecules with monoatomic ions. The group of solvent molecules should be continuous and all molecules should have the same number of atoms.
Args:
input_tpr_path (str): Path to the input portable run input TPR file. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/genion.tpr>`_. Accepted formats: tpr (edam:format_2333).
output_gro_path (str): Path to the input structure GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_genion.gro>`_. Accepted formats: gro (edam:format_2033).
input_top_zip_path (str): Path the input TOP topology in zip format. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/genion.zip>`_. Accepted formats: zip (edam:format_3987).
output_top_zip_path (str): Path 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/ref_genion.zip>`_. Accepted formats: zip (edam:format_3987).
input_ndx_path (str) (Optional): Path to the input index NDX file. File type: input. Accepted formats: ndx (edam:format_2033).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **replaced_group** (*str*) - ("SOL") Group of molecules that will be replaced by the solvent.
* **neutral** (*bool*) - (False) Neutralize the charge of the system.
* **concentration** (*float*) - (0.05) [0~10|0.01] Concentration of the ions in (mol/liter).
* **seed** (*int*) - (1993) Seed for random number generator.
* **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
* **gmx_path** (*str*) - ("gmx") Path to the GROMACS 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) Path to the binary executable of your container.
* **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
* **container_volume_path** (*str*) - ("/data") 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_md.gromacs.genion import genion
prop = { 'concentration': 0.05,
'replaced_group': 'SOL'}
genion(input_tpr_path='/path/to/myPortableBinaryRunInputFile.tpr',
output_gro_path='/path/to/newStructure.gro',
input_top_zip_path='/path/to/myTopology.zip',
output_top_zip_path='/path/to/newTopology.zip',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS Genion
* version: >5.1
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_tpr_path: str, output_gro_path: str, input_top_zip_path: str,
output_top_zip_path: str, input_ndx_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_tpr_path": input_tpr_path, "input_ndx_path": input_ndx_path},
"out": {"output_gro_path": output_gro_path, "output_top_zip_path": output_top_zip_path}
}
# Should not be copied inside container
self.input_top_zip_path = input_top_zip_path
# Properties specific for BB
self.output_top_path = properties.get('output_top_path', 'gio.top') # Not in documentation for clarity
self.replaced_group = properties.get('replaced_group', 'SOL')
self.neutral = properties.get('neutral', False)
self.concentration = properties.get('concentration', 0.05)
self.seed = properties.get('seed', 1993)
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`Genion <gromacs.genion.Genion>` object."""
# Setup Biobb
if self.check_restart(): return 0
self.stage_files()
# Unzip topology to topology_out
top_file = fu.unzip_top(zip_file=self.input_top_zip_path, out_log=self.out_log)
top_dir = str(Path(top_file).parent)
if self.container_path:
shutil.copytree(top_dir, Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(top_dir).name))
top_file = str(Path(self.container_volume_path).joinpath(Path(top_dir).name, Path(top_file).name))
self.cmd = ['echo', '\"'+self.replaced_group+'\"', '|',
self.gmx_path, 'genion',
'-s', self.stage_io_dict["in"]["input_tpr_path"],
'-o', self.stage_io_dict["out"]["output_gro_path"],
'-p', top_file]
if self.stage_io_dict["in"].get("input_ndx_path") and Path(
self.stage_io_dict["in"].get("input_ndx_path")).exists():
self.cmd.append('-n')
self.cmd.append(self.stage_io_dict["in"].get("input_ndx_path"))
if self.neutral:
self.cmd.append('-neutral')
if self.concentration:
self.cmd.append('-conc')
self.cmd.append(str(self.concentration))
fu.log('To reach up %g mol/litre concentration' % self.concentration, self.out_log, self.global_log)
if self.seed is not None:
self.cmd.append('-seed')
self.cmd.append(str(self.seed))
if self.gmx_lib:
self.environment = os.environ.copy()
self.environment['GMXLIB'] = self.gmx_lib
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError("Gromacs version should be 5.1.2 or newer %d detected" % self.gmx_version)
fu.log("GROMACS %s %d version detected" % (self.__class__.__name__, self.gmx_version), self.out_log)
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
if self.container_path:
top_file = str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(top_dir).name, Path(top_file).name))
# zip topology
fu.log('Compressing topology to: %s' % self.stage_io_dict["out"]["output_top_zip_path"],
self.out_log, self.global_log)
fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"], top_file=top_file, out_log=self.out_log)
# Remove temporal files
self.tmp_files.extend([self.stage_io_dict.get("unique_dir"), top_dir])
self.remove_tmp_files()
return self.return_code
[docs]def genion(input_tpr_path: str, output_gro_path: str, input_top_zip_path: str,
output_top_zip_path: str, properties: dict = None, **kwargs) -> int:
"""Create :class:`Genion <gromacs.genion.Genion>` class and
execute the :meth:`launch() <gromacs.genion.Genion.launch>` method."""
return Genion(input_tpr_path=input_tpr_path, output_gro_path=output_gro_path,
input_top_zip_path=input_top_zip_path, output_top_zip_path=output_top_zip_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 for the GROMACS genion 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_tpr_path', required=True)
required_args.add_argument('--output_gro_path', required=True)
required_args.add_argument('--input_top_zip_path', required=True)
required_args.add_argument('--output_top_zip_path', required=True)
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
genion(input_tpr_path=args.input_tpr_path, output_gro_path=args.output_gro_path,
input_top_zip_path=args.input_top_zip_path, output_top_zip_path=args.output_top_zip_path,
properties=properties)
if __name__ == '__main__':
main()