Source code for gromacs.genion

#!/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_2330). 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()