#!/usr/bin/env python3
"""Module containing the GMX Energy class and the command line interface."""
from pathlib import PurePath
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
from biobb_analysis.gromacs.common import (
_from_string_to_list,
check_energy_path,
check_out_xvg_path,
get_binary_path,
get_default_value,
get_terms,
get_xvg,
)
[docs]
class GMXEnergy(BiobbObject):
"""
| biobb_analysis GMXEnergy
| Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file.
| `GROMACS energy <http://manual.gromacs.org/current/onlinehelp/gmx-energy.html>`_ extracts energy components from an energy file. The user is prompted to interactively select the desired energy terms.
Args:
input_energy_path (str): Path to the input EDR file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/energy.edr>`_. Accepted formats: edr (edam:format_2330).
output_xvg_path (str): Path to the XVG output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_energy.xvg>`_. Accepted formats: xvg (edam:format_2030).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **xvg** (*str*) - ("none") XVG plot formatting. Values: xmgrace, xmgr, none.
* **terms** (*list*) - (["Potential"]) Energy terms. Values: Angle, Proper-Dih., Improper-Dih., LJ-14, Coulomb-14, LJ-\(SR\), Coulomb-\(SR\), Coul.-recip., Position-Rest., Potential, Kinetic-En., Total-Energy, Temperature, Pressure, Constr.-rmsd, Box-X, Box-Y, Box-Z, Volume, Density, pV, Enthalpy, Vir-XX, Vir-XY, Vir-XZ, Vir-YX, Vir-YY, Vir-YZ, Vir-ZX, Vir-ZY, Vir-ZZ, Pres-XX, Pres-XY, Pres-XZ, Pres-YX, Pres-YY, Pres-YZ, Pres-ZX, Pres-ZY, Pres-ZZ, #Surf*SurfTen, Box-Vel-XX, Box-Vel-YY, Box-Vel-ZZ, Mu-X, Mu-Y, Mu-Z, T-Protein, T-non-Protein, Lamb-Protein, Lamb-non-Protein.
* **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) Container path definition.
* **container_image** (*str*) - ('gromacs/gromacs:2022.2') Container image definition.
* **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
* **container_working_dir** (*str*) - (None) Container working directory definition.
* **container_user_id** (*str*) - (None) Container user_id definition.
* **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
Examples:
This is a use example of how to use the building block from Python::
from biobb_analysis.gromacs.gmx_energy import gmx_energy
prop = {
'xvg': 'xmgr',
'terms': ['Potential', 'Pressure']
}
gmx_energy(input_energy_path='/path/to/myEnergyFile.edr',
output_xvg_path='/path/to/newXVG.xvg',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS energy
* version: >=2024.5
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self, input_energy_path, output_xvg_path, properties=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_energy_path": input_energy_path},
"out": {"output_xvg_path": output_xvg_path},
}
# Properties specific for BB
self.xvg = properties.get("xvg", "none")
self.terms = _from_string_to_list(properties.get("terms", ["Potential"]))
self.instructions_file = get_default_value("instructions_file")
self.properties = properties
# Properties common in all GROMACS BB
self.binary_path = get_binary_path(properties, "binary_path")
# Check the properties
self.check_init(properties)
[docs]
def check_data_params(self, out_log, err_log):
"""Checks all the input/output paths and parameters"""
self.io_dict["in"]["input_energy_path"] = check_energy_path(
self.io_dict["in"]["input_energy_path"], out_log, self.__class__.__name__
)
self.io_dict["out"]["output_xvg_path"] = check_out_xvg_path(
self.io_dict["out"]["output_xvg_path"], out_log, self.__class__.__name__
)
self.xvg = get_xvg(self.properties, out_log, self.__class__.__name__)
self.terms = get_terms(self.properties, out_log, self.__class__.__name__)
[docs]
def create_instructions_file(self):
"""Creates an input file using the properties file settings"""
instructions_list = []
# Different path if container execution or not
if self.container_path:
self.instructions_file = str(PurePath(self.stage_io_dict['unique_dir']).joinpath("instructions.in"))
self.instructions_file_path = str(PurePath(self.container_volume_path).joinpath("instructions.in"))
else:
self.instructions_file = self.create_tmp_file(self.instructions_file)
self.instructions_file_path = self.instructions_file
for t in self.terms:
instructions_list.append(t)
# create instructions file
with open(self.instructions_file, "w") as mdp:
for line in instructions_list:
mdp.write(line.strip() + "\n")
return self.instructions_file_path
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`GMXEnergy <gromacs.gmx_energy.GMXEnergy>` object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# create instructions file
self.create_instructions_file()
self.cmd = [
self.binary_path,
"energy",
"-f",
self.stage_io_dict["in"]["input_energy_path"],
"-o",
self.stage_io_dict["out"]["output_xvg_path"],
"-xvg",
self.xvg,
"<",
self.instructions_file_path,
]
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def gmx_energy(
input_energy_path: str,
output_xvg_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create the :class:`GMXEnergy <gromacs.gmx_energy.GMXEnergy>` class and
execute the :meth:`launch() <gromacs.gmx_energy.GMXEnergy.launch>` method."""
return GMXEnergy(**dict(locals())).launch()
gmx_energy.__doc__ = GMXEnergy.__doc__
main = GMXEnergy.get_main(gmx_energy, "Extracts energy components from a given GROMACS energy file.")
if __name__ == "__main__":
main()