Source code for gromacs.grompp_mdrun

#!/usr/bin/env python3

"""Module containing the GromppMDrun class and the command line interface."""
import argparse
from pathlib import Path
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_md.gromacs.grompp import grompp
from biobb_md.gromacs.mdrun import mdrun


[docs]class GromppMdrun(BiobbObject): """ | biobb_md GromppMdrun | Wrapper of the `GROMACS grompp <http://manual.gromacs.org/current/onlinehelp/gmx-grompp.html>`_ module and the `GROMACS mdrun <http://manual.gromacs.org/current/onlinehelp/gmx-mdrun.html>`_ module. | Grompp The GROMACS preprocessor module needs to be fed with the input system and the dynamics parameters to create a portable binary run input file TPR. The simulation parameters can be specified by two methods: 1.The predefined mdp settings defined at simulation_type property or 2.A custom mdp file defined at the input_mdp_path argument. These two methods are mutually exclusive. In both cases can be further modified by adding parameters to the mdp section in the yaml configuration file. The simulation parameter names and default values can be consulted in the `official MDP specification <http://manual.gromacs.org/current/user-guide/mdp-options.html>`_. MDRun is the main computational chemistry engine within GROMACS. It performs Molecular Dynamics simulations, but it can also perform Stochastic Dynamics, Energy Minimization, test particle insertion or (re)calculation of energies. Args: input_gro_path (str): Path to the input GROMACS structure GRO file. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/grompp.gro>`_. Accepted formats: gro (edam:format_2033). input_top_zip_path (str): Path to the input GROMACS topology TOP and ITP files in zip format. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/grompp.zip>`_. Accepted formats: zip (edam:format_3987). output_trr_path (str): Path to the GROMACS uncompressed raw trajectory file TRR. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_mdrun.trr>`_. Accepted formats: trr (edam:format_3910). output_gro_path (str): Path to the output GROMACS structure GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_mdrun.gro>`_. Accepted formats: gro (edam:format_2033). output_edr_path (str): Path to the output GROMACS portable energy file EDR. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_mdrun.edr>`_. Accepted formats: edr (edam:format_2330). output_log_path (str): Path to the output GROMACS trajectory log file LOG. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_gmx_mdrun.log>`_. Accepted formats: log (edam:format_2330). input_cpt_path (str) (Optional): Path to the input GROMACS checkpoint file CPT. File type: input. Accepted formats: cpt (edam:format_2333). input_ndx_path (str) (Optional): Path to the input GROMACS index files NDX. File type: input. Accepted formats: ndx (edam:format_2330). input_mdp_path (str) (Optional): Path to the input GROMACS `MDP file <http://manual.gromacs.org/current/user-guide/mdp-options.html>`_. File type: input. Accepted formats: mdp (edam:format_2330). output_xtc_path (str) (Optional): Path to the GROMACS compressed trajectory file XTC. File type: output. Accepted formats: xtc (edam:format_3875). output_cpt_path (str) (Optional): Path to the output GROMACS checkpoint file CPT. File type: output. Accepted formats: cpt (edam:format_2333). output_dhdl_path (str) (Optional): Path to the output dhdl.xvg file only used when free energy calculation is turned on. File type: output. Accepted formats: xvg (edam:format_2033). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **mdp** (*dict*) - ({}) MDP options specification. * **simulation_type** (*str*) - ("minimization") Default options for the mdp file. Each creates a different mdp file. Values: `minimization <https://biobb-md.readthedocs.io/en/latest/_static/mdp/minimization.mdp>`_ (Energy minimization using steepest descent algorithm is used), `nvt <https://biobb-md.readthedocs.io/en/latest/_static/mdp/nvt.mdp>`_ (substance N Volume V and Temperature T are conserved), `npt <https://biobb-md.readthedocs.io/en/latest/_static/mdp/npt.mdp>`_ (substance N pressure P and Temperature T are conserved), `free <https://biobb-md.readthedocs.io/en/latest/_static/mdp/free.mdp>`_ (No design constraints applied; Free MD), `ions <https://biobb-md.readthedocs.io/en/latest/_static/mdp/minimization.mdp>`_ (Synonym of minimization), index (Creates an empty mdp file). * **maxwarn** (*int*) - (10) [0~1000|1] Maximum number of allowed warnings. * **mpi_bin** (*str*) - (None) Path to the MPI runner. Usually "mpirun" or "srun". * **mpi_np** (*str*) - (None) Number of MPI processes. Usually an integer bigger than 1. * **mpi_hostlist** (*str*) - (None) Path to the MPI hostlist file. * **checkpoint_time** (*int*) - (15) [0~1000|1] Checkpoint writing interval in minutes. Only enabled if an output_cpt_path is provided. * **num_threads** (*int*) - (0) [0-1000|1] Let GROMACS guess. The number of threads that are going to be used. * **num_threads_mpi** (*int*) - (0) [0-1000|1] Let GROMACS guess. The number of GROMACS MPI threads that are going to be used. * **num_threads_omp** (*int*) - (0) [0-1000|1] Let GROMACS guess. The number of GROMACS OPENMP threads that are going to be used. * **num_threads_omp_pme** (*int*) - (0) [0-1000|1] Let GROMACS guess. The number of GROMACS OPENMP_PME threads that are going to be used. * **use_gpu** (*bool*) - (False) Use settings appropriate for GPU. Adds: -nb gpu -pme gpu * **gpu_id** (*str*) - (None) List of unique GPU device IDs available to use. * **gpu_tasks** (*str*) - (None) List of GPU device IDs, mapping each PP task on each node to a device. * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable. * **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) 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_md.gromacs.grompp_mdrun import grompp_mdrun prop = { 'num_threads': 0, 'gmx_path': 'gmx', 'mdp': { 'simulation_type': 'minimization', 'emtol':'500', 'nsteps':'5000'} } grompp_mdrun(input_gro_path='/path/to/myStructure.gro', input_top_zip_path='/path/to/myTopology.zip', output_trr_path='/path/to/newTrajectory.trr', output_gro_path='/path/to/newStructure.gro', output_edr_path='/path/to/newEnergy.edr', output_log_path='/path/to/newSimulationLog.log', properties=prop) Info: * wrapped_software: * name: GROMACS Grompp & MDRun * version: >5.1 * license: LGPL 2.1 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_gro_path: str, input_top_zip_path: str, output_trr_path: str, output_gro_path: str, output_edr_path: str, output_log_path: str, input_cpt_path: str = None, input_ndx_path: str = None, input_mdp_path: str = None, output_xtc_path: str = None, output_cpt_path: str = None, output_dhdl_path: str = None, properties: dict = None, **kwargs) -> None: # Properties management properties = properties or {} # Call parent class constructor super().__init__(properties) grompp_properties_keys = ['mdp', 'maxwarn', 'simulation_type'] mdrun_properties_keys = ['mpi_bin', 'mpi_np', 'mpi_hostlist', 'checkpoint_time', 'num_threads', 'num_threads_mpi', 'num_threads_omp', 'num_threads_omp_pme', 'use_gpu', 'gpu_id', 'gpu_tasks', 'dev'] self.properties_grompp = {} self.properties_mdrun = {} if properties: self.global_log = properties.get('global_log', None) self.properties_grompp = properties.copy() for key in mdrun_properties_keys: self.properties_grompp.pop(key, None) self.properties_mdrun = properties.copy() for key in grompp_properties_keys: self.properties_mdrun.pop(key, None) # Grompp arguments self.input_gro_path = input_gro_path self.input_top_zip_path = input_top_zip_path self.output_tpr_path = str(Path(fu.create_unique_dir()).joinpath('internal.tpr')) self.input_cpt_path = input_cpt_path self.input_ndx_path = input_ndx_path self.input_mdp_path = input_mdp_path # MDRun arguments self.input_tpr_path = self.output_tpr_path self.output_trr_path = output_trr_path self.output_gro_path = output_gro_path self.output_edr_path = output_edr_path self.output_log_path = output_log_path self.output_xtc_path = output_xtc_path self.output_cpt_path = output_cpt_path self.output_dhdl_path = output_dhdl_path
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`GromppMdrun <gromacs.grompp_mdrun.GromppMdrun>` object.""" fu.log(f'Calling Grompp class', self.out_log, self.global_log) grompp_return_code = grompp(input_gro_path=self.input_gro_path, input_top_zip_path=self.input_top_zip_path, output_tpr_path=self.output_tpr_path, input_cpt_path=self.input_cpt_path, input_ndx_path=self.input_ndx_path, input_mdp_path=self.input_mdp_path, properties=self.properties_grompp) fu.log(f'Grompp return code: {grompp_return_code}', self.out_log, self.global_log) if not grompp_return_code: fu.log(f'Grompp return code is correct. Calling MDRun class', self.out_log, self.global_log) mdrun_return_code = mdrun(input_tpr_path=self.output_tpr_path, output_trr_path=self.output_trr_path, output_gro_path=self.output_gro_path, output_edr_path=self.output_edr_path, output_log_path=self.output_log_path, output_xtc_path=self.output_xtc_path, output_cpt_path=self.output_cpt_path, output_dhdl_path=self.output_dhdl_path, properties=self.properties_mdrun) fu.log(f'MDRun return code: {mdrun_return_code}', self.out_log, self.global_log) else: return 1 return mdrun_return_code
[docs]def grompp_mdrun(input_gro_path: str, input_top_zip_path: str, output_trr_path: str, output_gro_path: str, output_edr_path: str, output_log_path: str, input_cpt_path: str = None, input_ndx_path: str = None, input_mdp_path: str = None, output_xtc_path: str = None, output_cpt_path: str = None, output_dhdl_path: str = None, properties: dict = None, **kwargs) -> int: return GromppMdrun(input_gro_path=input_gro_path, input_top_zip_path=input_top_zip_path, output_trr_path=output_trr_path, output_gro_path=output_gro_path, output_edr_path=output_edr_path, output_log_path=output_log_path, input_cpt_path=input_cpt_path, input_ndx_path=input_ndx_path, input_mdp_path=input_mdp_path, output_xtc_path=output_xtc_path, output_cpt_path=output_cpt_path, output_dhdl_path=output_dhdl_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="Wrapper for the GROMACS grompp_mdrun module.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_gro_path', required=True) required_args.add_argument('--input_top_zip_path', required=True) required_args.add_argument('--output_trr_path', required=True) required_args.add_argument('--output_gro_path', required=True) required_args.add_argument('--output_edr_path', required=True) required_args.add_argument('--output_log_path', required=True) parser.add_argument('--input_cpt_path', required=False) parser.add_argument('--input_ndx_path', required=False) parser.add_argument('--input_mdp_path', required=False) parser.add_argument('--output_xtc_path', required=False) parser.add_argument('--output_cpt_path', required=False) parser.add_argument('--output_dhdl_path', required=False) args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block grompp_mdrun(input_gro_path=args.input_gro_path, input_top_zip_path=args.input_top_zip_path, output_trr_path=args.output_trr_path, output_gro_path=args.output_gro_path, output_edr_path=args.output_edr_path, output_log_path=args.output_log_path, input_cpt_path=args.input_cpt_path, input_ndx_path=args.input_ndx_path, input_mdp_path=args.input_mdp_path, output_xtc_path=args.output_xtc_path, output_cpt_path=args.output_cpt_path, output_dhdl_path=args.output_dhdl_path, properties=properties)
if __name__ == '__main__': main()