#!/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_2033).
input_ndx_path (str) (Optional): Path to the input index NDX file. File type: input. Accepted formats: ndx (edam:format_2033).
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()