Source code for gromacs.genrestr

#!/usr/bin/env python3

"""Module containing the Genrestr class and the command line interface."""
import os
import argparse
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 Genrestr(BiobbObject): """ | biobb_md Genrestr | Wrapper of the `GROMACS genrestr <http://manual.gromacs.org/current/onlinehelp/gmx-genrestr.html>`_ module. | The GROMACS genrestr module, produces an #include file for a topology containing a list of atom numbers and three force constants for the x-, y-, and z-direction based on the contents of the -f file. A single isotropic force constant may be given on the command line instead of three components. Args: input_structure_path (str): Path to the input structure PDB, GRO or TPR format. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/genrestr.gro>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033), tpr (edam:format_2333). output_itp_path (str): Path the output ITP topology file with restrains. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_genrestr.itp>`_. Accepted formats: itp (edam:format_3883). input_ndx_path (str) (Optional): Path to the input GROMACS index file, NDX format. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/genrestr.ndx>`_. Accepted formats: ndx (edam:format_2330). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **restrained_group** (*str*) - ("system") Index group that will be restrained. * **force_constants** (*str*) - ("500 500 500") Array of three floats defining the force constants * **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.genrestr import genrestr prop = { 'restrained_group': 'system', 'force_constants': '500 500 500' } genrestr(input_structure_path='/path/to/myStructure.gro', output_itp_path='/path/to/newTopologyAddOn.itp', properties=prop) Info: * wrapped_software: * name: GROMACS Genrestr * version: >5.1 * license: LGPL 2.1 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_structure_path: str, output_itp_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_structure_path": input_structure_path, "input_ndx_path": input_ndx_path}, "out": {"output_itp_path": output_itp_path} } # Properties specific for BB self.force_constants = str(properties.get('force_constants', '500 500 500')) self.restrained_group = properties.get('restrained_group', 'system') # 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:`Grompp <gromacs.grompp.Grompp>` object.""" # Setup Biobb if self.check_restart(): return 0 self.stage_files() self.cmd = ['echo', '\"'+self.restrained_group+'\"', '|', self.gmx_path, "genrestr", "-f", self.stage_io_dict["in"]["input_structure_path"], "-o", self.stage_io_dict["out"]["output_itp_path"], "-fc", self.force_constants] if self.stage_io_dict["in"].get("input_ndx_path"): self.cmd.append('-n') self.cmd.append(self.stage_io_dict["in"]["input_ndx_path"]) 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() # Remove temporal files self.tmp_files.append(self.stage_io_dict.get("unique_dir")) self.remove_tmp_files() return self.return_code
[docs]def genrestr(input_structure_path: str, output_itp_path: str, input_ndx_path: str = None, properties: dict = None, **kwargs) -> int: """Create :class:`Genrestr <gromacs.genrestr.Genrestr>` class and execute the :meth:`launch() <gromacs.genrestr.Genrestr.launch>` method.""" return Genrestr(input_structure_path=input_structure_path, output_itp_path=output_itp_path, input_ndx_path=input_ndx_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_structure_path', required=True) required_args.add_argument('--output_itp_path', required=True) parser.add_argument('--input_ndx_path', required=False) 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 genrestr(input_structure_path=args.input_structure_path, input_ndx_path=args.input_ndx_path, output_itp_path=args.output_itp_path, properties=properties)
if __name__ == '__main__': main()