Source code for gromacs.solvate

#!/usr/bin/env python3

"""Module containing the Editconf 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 Solvate(BiobbObject): """ | biobb_md Solvate | Wrapper of the `GROMACS solvate <http://manual.gromacs.org/current/onlinehelp/gmx-solvate.html>`_ module. | The GROMACS solvate module, generates a box of solvent around the selected structure. Args: input_solute_gro_path (str): Path to the input GRO file. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/solvate.gro>`_. Accepted formats: gro (edam:format_2033). output_gro_path (str): Path to the output GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_solvate.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/solvate.zip>`_. Accepted formats: zip (edam:format_3987). output_top_zip_path (str): Path the output topology in zip format. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_solvate.zip>`_. Accepted formats: zip (edam:format_3987). input_solvent_gro_path (str) (Optional): (spc216.gro) Path to the GRO file containing the structure of the solvent. File type: input. Accepted formats: gro (edam:format_2033). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **shell** (*float*) - (0.0) [0~100|0.1] Thickness in nanometers of optional water layer around solute. * **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.solvate import Solvate prop = { 'shell': 1.0 } solvate(input_solute_gro_path='/path/to/myStructure.gro', 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 Solvate * version: >5.1 * license: LGPL 2.1 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str, output_top_zip_path: str, input_solvent_gro_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_solute_gro_path": input_solute_gro_path, "input_solvent_gro_path": input_solvent_gro_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.shell = properties.get('shell') if not self.io_dict["in"].get('input_solvent_gro_path'): self.io_dict["in"]['input_solvent_gro_path'] = 'spc216.gro' # 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:`Solvate <gromacs.solvate.Solvate>` 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, str(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 = [self.gmx_path, 'solvate', '-cp', self.stage_io_dict["in"]["input_solute_gro_path"], '-cs', self.stage_io_dict["in"]["input_solvent_gro_path"], '-o', self.stage_io_dict["out"]["output_gro_path"], '-p', top_file] if self.shell: self.cmd.append("-shell") self.cmd.append(str(self.shell)) 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 solvate(input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str, output_top_zip_path: str, input_solvent_gro_path: str = None, properties: dict = None, **kwargs) -> int: """Create :class:`Solvate <gromacs.solvate.Solvate>` class and execute the :meth:`launch() <gromacs.solvate.Solvate.launch>` method.""" return Solvate(input_solute_gro_path=input_solute_gro_path, output_gro_path=output_gro_path, input_top_zip_path=input_top_zip_path, output_top_zip_path=output_top_zip_path, input_solvent_gro_path=input_solvent_gro_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 solvate 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_solute_gro_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) parser.add_argument('--input_solvent_gro_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 solvate(input_solute_gro_path=args.input_solute_gro_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, input_solvent_gro_path=args.input_solvent_gro_path, properties=properties)
if __name__ == '__main__': main()