Source code for gromacs.editconf

#!/usr/bin/env python3

"""Module containing the Editconf 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 import file_utils as fu
from import launchlogger
from biobb_md.gromacs.common import get_gromacs_version
from biobb_md.gromacs.common import GromacsVersionError

[docs]class Editconf(BiobbObject): """ | biobb_md Editconf | Wrapper class for the `GROMACS editconf <>`_ module. | The GROMACS solvate module generates a box around the selected structure. Args: input_gro_path (str): Path to the input GRO file. File type: input. `Sample file <>`_. Accepted formats: gro (edam:format_2033). output_gro_path (str): Path to the output GRO file. File type: output. `Sample file <>`_. Accepted formats: gro (edam:format_2033). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **distance_to_molecule** (*float*) - (1.0) [0~100|0.1] Distance of the box from the outermost atom in nm. ie 1.0nm = 10 Angstroms. * **box_type** (*str*) - ("cubic") Geometrical shape of the solvent box. Values: cubic (rectangular box with all sides equal), triclinic (triclinic box), dodecahedron (rhombic dodecahedron), octahedron (truncated octahedron). * **center_molecule** (*bool*) - (True) Center molecule in the box. * **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.editconf import editconf prop = { 'distance_to_molecule': 1.0, 'box_type': 'cubic'} editconf(input_gro_path='/path/to/structure.gro', output_gro_path='/path/to/newStructure.gro', properties=prop) Info: * wrapped_software: * name: GROMACS Solvate * version: >5.1 * license: LGPL 2.1 * ontology: * name: EDAM * schema: """ def __init__(self, input_gro_path: str, output_gro_path: str, properties: dict = None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) # Input/Output files self.io_dict = { "in": {"input_gro_path": input_gro_path}, "out": {"output_gro_path": output_gro_path} } # Properties specific for BB self.distance_to_molecule = properties.get('distance_to_molecule', 1.0) self.box_type = properties.get('box_type', 'cubic') self.center_molecule = properties.get('center_molecule', True) # 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:`Editconf <gromacs.editconf.Editconf>` object.""" # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Create command line self.cmd = [self.gmx_path, 'editconf', '-f', self.stage_io_dict["in"]["input_gro_path"], '-o', self.stage_io_dict["out"]["output_gro_path"], '-d', str(self.distance_to_molecule), '-bt', self.box_type] if self.center_molecule: self.cmd.append('-c') fu.log('Centering molecule in the box.', self.out_log, self.global_log) fu.log("Distance of the box to molecule: %6.2f" % self.distance_to_molecule, self.out_log, self.global_log) fu.log("Box type: %s" % self.box_type, self.out_log, self.global_log) 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 editconf(input_gro_path: str, output_gro_path: str, properties: dict = None, **kwargs) -> int: """Create :class:`Editconf <gromacs.editconf.Editconf>` class and execute the :meth:`launch() <gromacs.editconf.Editconf.launch>` method.""" return Editconf(input_gro_path=input_gro_path, output_gro_path=output_gro_path, properties=properties, **kwargs).launch()
[docs]def main(): parser = argparse.ArgumentParser(description="Wrapper of the GROMACS gmx editconf 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_gro_path', required=True) required_args.add_argument('--output_gro_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 editconf(input_gro_path=args.input_gro_path, output_gro_path=args.output_gro_path, properties=properties)
if __name__ == '__main__': main()