#!/usr/bin/env python3
"""Module containing the Genrestr class and the command line interface."""
from pathlib import Path
from typing import Optional, Union
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_gromacs.gromacs.common import get_gromacs_version
[docs]
class Genrestr(BiobbObject):
"""
| biobb_gromacs Genrestr
| Wrapper of the `GROMACS genrestr <http://manual.gromacs.org/current/onlinehelp/gmx-genrestr.html>`_ module.
| The GROMACS genrestr module, produces an #include file for a topology containing a list of atom numbers and three force constants for the x-, y-, and z-direction based on the contents of the -f file. A single isotropic force constant may be given on the command line instead of three components.
Args:
input_structure_path (str): Path to the input structure PDB, GRO or TPR format. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genrestr.gro>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033), tpr (edam:format_2333).
output_itp_path (str): Path the output ITP topology file with restrains. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_genrestr.itp>`_. Accepted formats: itp (edam:format_3883).
input_ndx_path (str) (Optional): Path to the input GROMACS index file, NDX format. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genrestr.ndx>`_. Accepted formats: ndx (edam:format_2033).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **restrained_group** (*str*) - ("system") Index group that will be restrained.
* **force_constants** (*str*) - ("500 500 500") Array of three floats defining the force constants
* **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
* **binary_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.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
* **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_gromacs.gromacs.genrestr import genrestr
prop = { 'restrained_group': 'system',
'force_constants': '500 500 500' }
genrestr(input_structure_path='/path/to/myStructure.gro',
output_itp_path='/path/to/newTopologyAddOn.itp',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS Genrestr
* version: 2025.2
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_structure_path: Union[str, Path],
output_itp_path: Union[str, Path],
input_ndx_path: Optional[Union[str, Path]] = None,
properties: Optional[dict] = None,
**kwargs,
) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {
"input_structure_path": input_structure_path,
"input_ndx_path": input_ndx_path,
},
"out": {"output_itp_path": output_itp_path},
}
# Properties specific for BB
self.force_constants = str(properties.get("force_constants", "500 500 500"))
self.restrained_group = properties.get("restrained_group", "system")
# Properties common in all GROMACS BB
self.gmx_lib = properties.get("gmx_lib", None)
self.binary_path = properties.get("binary_path", "gmx")
self.gmx_nobackup = properties.get("gmx_nobackup", True)
self.gmx_nocopyright = properties.get("gmx_nocopyright", True)
if self.gmx_nobackup:
self.binary_path = f"{self.binary_path} -nobackup"
if self.gmx_nocopyright:
self.binary_path = f"{self.binary_path} -nocopyright"
if not self.container_path:
self.gmx_version = get_gromacs_version(str(self.binary_path))
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Grompp <gromacs.grompp.Grompp>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file(f"{self.restrained_group}")
self.stage_files()
self.cmd = [
str(self.binary_path),
"genrestr",
"-f",
self.stage_io_dict["in"]["input_structure_path"],
"-o",
self.stage_io_dict["out"]["output_itp_path"],
]
if not isinstance(self.force_constants, str):
self.force_constants = " ".join(map(str, self.force_constants))
self.cmd.append("-fc")
self.cmd.append(self.force_constants)
if self.stage_io_dict["in"].get("input_ndx_path"):
self.cmd.append("-n")
self.cmd.append(self.stage_io_dict["in"]["input_ndx_path"])
# Add stdin input file
self.cmd.append("<")
self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
if self.gmx_lib:
self.env_vars_dict["GMXLIB"] = self.gmx_lib
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.tmp_files.append(str(self.io_dict["in"].get("stdin_file_path")))
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def genrestr(
input_structure_path: Union[str, Path],
output_itp_path: Union[str, Path],
input_ndx_path: Optional[Union[str, Path]] = None,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Genrestr <gromacs.genrestr.Genrestr>` class and
execute the :meth:`launch() <gromacs.genrestr.Genrestr.launch>` method."""
return Genrestr(**dict(locals())).launch()
genrestr.__doc__ = Genrestr.__doc__
main = Genrestr.get_main(genrestr, "Wrapper for the GROMACS genrestr module.")
if __name__ == "__main__":
main()