Source code for gromacs.make_ndx

#!/usr/bin/env python3

"""Module containing the MakeNdx class and the command line interface."""
import os
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 MakeNdx(BiobbObject): """ | biobb_md MakeNdx | Wrapper of the `GROMACS make_ndx <http://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html>`_ module. | The GROMACS make_ndx module, generates an index file using the atoms of the selection. Args: input_structure_path (str): Path to the input GRO/PDB/TPR file. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/make_ndx.tpr>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476), tpr (edam:format_2333). output_ndx_path (str): Path to the output index NDX file. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_make_ndx.ndx>`_. Accepted formats: ndx (edam:format_2330). 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): * **selection** (*str*) - ("a CA C N O") Heavy atoms. Atom selection string. * **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.make_ndx import make_ndx prop = { 'selection': 'a CA C N O' } make_ndx(input_structure_path='/path/to/myStructure.gro', output_ndx_path='/path/to/newIndex.ndx', properties=prop) Info: * wrapped_software: * name: GROMACS MakeNdx * version: >5.1 * license: LGPL 2.1 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_structure_path: str, output_ndx_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_ndx_path": output_ndx_path} } # Properties specific for BB self.selection = properties.get('selection', "a CA C N O") # 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 fu.check_properties(self, properties)
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` object.""" # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Create command line self.cmd = ['echo', '-e', '\'' + self.selection + '\\nq' + '\'', '|', self.gmx_path, 'make_ndx', '-f', self.stage_io_dict["in"]["input_structure_path"], '-o', self.stage_io_dict["out"]["output_ndx_path"] ] 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.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) # create_cmd_line and execute_command self.run_biobb() # Retrieve results 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 make_ndx(input_structure_path: str, output_ndx_path: str, input_ndx_path: str = None, properties: dict = None, **kwargs) -> int: """Create :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` class and execute the :meth:`launch() <gromacs.make_ndx.MakeNdx.launch>` method.""" return MakeNdx(input_structure_path=input_structure_path, output_ndx_path=output_ndx_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 make_ndx 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_ndx_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 make_ndx(input_structure_path=args.input_structure_path, output_ndx_path=args.output_ndx_path, input_ndx_path=args.input_ndx_path, properties=properties)
if __name__ == '__main__': main()