Source code for gromacs.gmx_energy

#!/usr/bin/env python3

"""Module containing the GMX Energy class and the command line interface."""
import argparse
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_analysis.gromacs.common import *


[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. * **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) Container path definition. * **container_image** (*str*) - ('gromacs/gromacs:latest') 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: >=2019.1 * 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) # 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 = properties.get('terms', ["Potential"]) self.instructions_file = get_default_value('instructions_file') self.properties = properties # Properties common in all GROMACS BB self.gmx_path = get_binary_path(properties, 'gmx_path') # Check the properties self.check_properties(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.container_volume_path).joinpath(self.instructions_file)) else: self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file)) #self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file)) fu.create_name(prefix=self.prefix, step=self.step, name=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
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`GMXEnergy <gromacs.gmx_energy.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() # if container execution, copy intructions file to container if self.container_path: copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict.get("unique_dir")) self.cmd = [self.gmx_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] # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() # if container execution, remove temporary folder if self.container_path: self.tmp_files.append(self.stage_io_dict.get("unique_dir")) self.remove_tmp_files() if self.remove_tmp: self.tmp_files.append(str(PurePath(self.instructions_file).parent)) self.remove_tmp_files() return self.return_code
[docs]def gmx_energy(input_energy_path: str, output_xvg_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`GMXEnergy <gromacs.gmx_energy.GMXEnergy>` class and execute the :meth:`launch() <gromacs.gmx_energy.GMXEnergy.launch>` method.""" return GMXEnergy(input_energy_path=input_energy_path, output_xvg_path=output_xvg_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="Extracts energy components from a given GROMACS energy file.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') #Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_energy_path', required=True, help='Path to the input EDR file. Accepted formats: edr.') required_args.add_argument('--output_xvg_path', required=True, help='Path to the XVG output file. Accepted formats: xvg.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() #Specific call of each building block gmx_energy(input_energy_path=args.input_energy_path, output_xvg_path=args.output_xvg_path, properties=properties)
if __name__ == '__main__': main()