Source code for gromacs.gmxselect

#!/usr/bin/env python3

"""Module containing the Select 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 Gmxselect(BiobbObject): """ | biobb_md Gmxselect | Wrapper of the `GROMACS select <http://manual.gromacs.org/current/onlinehelp/gmx-select.html>`_ module. | The GROMACS select module writes out basic data about dynamic selections. It can be used for some simple analyses, or the output can be combined with output from other programs and/or external analysis programs to calculate more complex things. 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: pdb (edam:format_1476), gro (edam:format_2033), 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_select.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. * **append** (*bool*) - (False) Append the content of the input_ndx_path to the output_ndx_path. * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary. * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable. * **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.gmxselect import gmxselect prop = { 'selection': '"Mynewgroup" group "Protein-H" and not same residue as within 0.4 of resname ARG' } gmxselect(input_structure_path='/path/to/myStructure.gro', output_ndx_path='/path/to/newIndex.ndx', properties=prop) Info: * wrapped_software: * name: GROMACS Gmxselect * 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") self.append = properties.get('append', False) # 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:`Gmxselect <gromacs.gmxselect.Gmxselect>` object.""" # Setup Biobb if self.check_restart(): return 0 self.stage_files() self.cmd = [self.gmx_path, 'select', '-s', self.stage_io_dict["in"]["input_structure_path"], '-on', 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")) self.cmd.append('-select') self.cmd.append("\'"+self.selection+"\'") 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.io_dict["in"].get("input_ndx_path"): if self.append: fu.log(f"Appending {self.io_dict['in'].get('input_ndx_path')} to {self.io_dict['out']['output_ndx_path']}", self.out_log, self.global_log) with open(self.io_dict["out"]["output_ndx_path"], 'a') as out_ndx_file: out_ndx_file.write('\n') with open(self.io_dict["in"].get("input_ndx_path")) as in_ndx_file: for line in in_ndx_file: out_ndx_file.write(line) # Remove temporal files self.tmp_files.append(self.stage_io_dict.get("unique_dir")) self.remove_tmp_files() return self.return_code
[docs]def gmxselect(input_structure_path: str, output_ndx_path: str, input_ndx_path: str = None, properties: dict = None, **kwargs) -> int: """Create :class:`Gmxselect <gromacs.gmxselect.Gmxselect>` class and execute the :meth:`launch() <gromacs.gmxselect.Gmxselect.launch>` method.""" return Gmxselect(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 select 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 gmxselect(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()