#!/usr/bin/env python3
"""Module containing the Genion class and the command line interface."""
import shutil
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 Genion(BiobbObject):
"""
| biobb_gromacs Genion
| Wrapper class for the `GROMACS genion <http://manual.gromacs.org/current/onlinehelp/gmx-genion.html>`_ module.
| The GROMACS genion module randomly replaces solvent molecules with monoatomic ions. The group of solvent molecules should be continuous and all molecules should have the same number of atoms.
Args:
input_tpr_path (str): Path to the input portable run input TPR file. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genion.tpr>`_. Accepted formats: tpr (edam:format_2333).
output_gro_path (str): Path to the input structure GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_genion.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_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genion.zip>`_. Accepted formats: zip (edam:format_3987).
output_top_zip_path (str): Path the output topology TOP and ITP files zipball. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_genion.zip>`_. Accepted formats: zip (edam:format_3987).
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):
* **replaced_group** (*str*) - ("SOL") Group of molecules that will be replaced by the solvent.
* **neutral** (*bool*) - (False) Neutralize the charge of the system.
* **concentration** (*float*) - (0.0) [0~10|0.01] Concentration of the ions in (mol/liter).
* **seed** (*int*) - (1993) Seed for random number generator.
* **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.genion import genion
prop = { 'concentration': 0.05,
'replaced_group': 'SOL'}
genion(input_tpr_path='/path/to/myPortableBinaryRunInputFile.tpr',
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 Genion
* version: 2025.2
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_tpr_path: Union[str, Path],
output_gro_path: Union[str, Path],
input_top_zip_path: Union[str, Path],
output_top_zip_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_tpr_path": input_tpr_path, "input_ndx_path": input_ndx_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.output_top_path = properties.get(
"output_top_path", "gio.top"
) # Not in documentation for clarity
self.replaced_group = properties.get("replaced_group", "SOL")
self.neutral = properties.get("neutral", False)
self.concentration = properties.get("concentration", 0.0)
self.seed = properties.get("seed", 1993)
# 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:`Genion <gromacs.genion.Genion>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file(f"{self.replaced_group}")
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,
Path(str(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 = [
str(self.binary_path),
"genion",
"-s",
self.stage_io_dict["in"]["input_tpr_path"],
"-o",
self.stage_io_dict["out"]["output_gro_path"],
"-p",
top_file,
]
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.neutral:
self.cmd.append("-neutral")
if self.concentration:
self.cmd.append("-conc")
self.cmd.append(str(self.concentration))
fu.log(
"To reach up %g mol/litre concentration" % self.concentration,
self.out_log,
self.global_log,
)
if self.seed is not None:
self.cmd.append("-seed")
self.cmd.append(str(self.seed))
# 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()
if self.container_path:
top_file = str(
Path(str(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_original_files=self.remove_tmp
)
# Remove temporal files
self.tmp_files.extend([top_dir, str(self.io_dict["in"].get("stdin_file_path"))])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=True)
return self.return_code
[docs]
def genion(
input_tpr_path: Union[str, Path],
output_gro_path: Union[str, Path],
input_top_zip_path: Union[str, Path],
output_top_zip_path: Union[str, Path],
input_ndx_path: Optional[Union[str, Path]] = None,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Genion <gromacs.genion.Genion>` class and
execute the :meth:`launch() <gromacs.genion.Genion.launch>` method."""
return Genion(**dict(locals())).launch()
genion.__doc__ = Genion.__doc__
main = Genion.get_main(genion, "Wrapper for the GROMACS genion module.")
if __name__ == "__main__":
main()