#!/usr/bin/env python3
"""Module containing the Editconf class and the command line interface."""
from typing import Optional
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 Editconf(BiobbObject):
"""
| biobb_gromacs Editconf
| Wrapper class for the `GROMACS editconf <http://manual.gromacs.org/current/onlinehelp/gmx-editconf.html>`_ module.
| The GROMACS editconf converts generic structure format to .gro, .g96 or .pdb.
Args:
input_gro_path (str): Path to the input GRO file. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/editconf.gro>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476).
output_gro_path (str): Path to the output GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_editconf.gro>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **distance_to_molecule** (*float*) - (1.0) [0~100|0.1] Distance of the box from the outermost atom in nm. ie 1.0nm = 10 Angstroms.
* **box_vector_lenghts** (*str*) - (None) Array of floats defining the box vector lenghts ie "0.5 0.5 0.5". If this option is used the distance_to_molecule property will be ignored.
* **box_type** (*str*) - ("cubic") Geometrical shape of the solvent box. Values: cubic (rectangular box with all sides equal), triclinic (triclinic box), dodecahedron (rhombic dodecahedron), octahedron (truncated octahedron).
* **center_molecule** (*bool*) - (True) Center molecule in the box.
* **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*) - (None) 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.editconf import editconf
prop = { 'distance_to_molecule': 1.0,
'box_type': 'cubic'}
editconf(input_gro_path='/path/to/structure.gro',
output_gro_path='/path/to/newStructure.gro',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS Solvate
* version: 2025.2
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_gro_path: str,
output_gro_path: str,
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_gro_path": input_gro_path},
"out": {"output_gro_path": output_gro_path},
}
# Properties specific for BB
self.distance_to_molecule = properties.get("distance_to_molecule", 1.0)
self.box_vector_lenghts = properties.get("box_vector_lenghts")
self.box_type = properties.get("box_type", "cubic")
self.center_molecule = properties.get("center_molecule", True)
# Properties common in all GROMACS BB
self.gmx_lib = properties.get("gmx_lib", None)
self.binary_path: str = 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 += " -nobackup"
if self.gmx_nocopyright:
self.binary_path += " -nocopyright"
if not self.container_path:
self.gmx_version = get_gromacs_version(self.binary_path)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Editconf <gromacs.editconf.Editconf>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Create command line
self.cmd = [
self.binary_path,
"editconf",
"-f",
self.stage_io_dict["in"]["input_gro_path"],
"-o",
self.stage_io_dict["out"]["output_gro_path"],
"-bt",
self.box_type,
]
if self.box_vector_lenghts:
if not isinstance(self.box_vector_lenghts, str):
self.box_vector_lenghts = " ".join(map(str, self.box_vector_lenghts))
self.cmd.append("-box")
self.cmd.append(self.box_vector_lenghts)
else:
self.cmd.append("-d")
self.cmd.append(str(self.distance_to_molecule))
fu.log(
"Distance of the box to molecule: %6.2f" % self.distance_to_molecule,
self.out_log,
self.global_log,
)
if self.center_molecule:
self.cmd.append("-c")
fu.log("Centering molecule in the box.", self.out_log, self.global_log)
fu.log("Box type: %s" % self.box_type, self.out_log, self.global_log)
if self.gmx_lib:
self.env_vars_dict = self.gmx_lib
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.remove_tmp_files()
# self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def editconf(
input_gro_path: str,
output_gro_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`Editconf <gromacs.editconf.Editconf>` class and
execute the :meth:`launch() <gromacs.editconf.Editconf.launch>` method."""
return Editconf(**dict(locals())).launch()
editconf.__doc__ = Editconf.__doc__
main = Editconf.get_main(editconf, "Wrapper of the GROMACS gmx editconf module.")
if __name__ == "__main__":
main()