| """OpenMM Molecular Dynamics refinement module for HADDOCK3.
|
|
|
| The potential of OpenMM can be exploited to perform potentially different
|
| tasks, such as:
|
|
|
| * Run MD simulation for each model from previous step;
|
| * Refine the models in the middle of a docking run. For example, it can be used
|
| to refine the models coming from a `[rigidbody]` module before `[flexref]` is
|
| executed, or to replace the `[mdref]` step.
|
| * Generate conformers prior to their use in a thorough docking run.
|
|
|
| To get a list of all possible parameters, run:
|
|
|
| >>> haddock3-cfg -m openmm
|
|
|
| Module workflow:
|
|
|
| * Generate openmm topology and fix atoms
|
| * Build solvation box
|
| * Equilibration solvation box restraining the protein
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| * Run MD simulation: increase temperature, run MD, reduce temperature.
|
| * Either generate an ensemble of multiple frames or return the last frame.
|
|
|
| This module will refine all models coming from the previous workflow step and
|
| send them to the next step in the workflow. If you want to use other modules
|
| such as `flexref` or `emref` after the OpenMM module, you need to recreate the
|
| topologies by simply adding a `[topoaa]` step in the workflow.
|
| See examples in `examples/thirdparty/openmm` folder.
|
|
|
| For more details about this module, please `refer to the haddock3 user manual
|
| <https://www.bonvinlab.org/haddock3-user-manual/modules/refinement.html#openmm-module>`_
|
| """
|
| import os
|
| import shutil
|
|
|
| from contextlib import suppress
|
| from pathlib import Path
|
| from subprocess import run as subprocrun
|
|
|
| from haddock.core.defaults import MODULE_DEFAULT_YAML
|
| from haddock.core.exceptions import ThirdPartyIntallationError
|
| from haddock.libs.libontology import PDBFile
|
| from haddock.modules import BaseHaddockModule, get_engine
|
|
|
|
|
| with suppress(ImportError):
|
| from haddock.modules.refinement.openmm.openmm import OPENMM
|
|
|
|
|
| RECIPE_PATH = Path(__file__).resolve().parent
|
| DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML)
|
|
|
|
|
| class HaddockModule(BaseHaddockModule):
|
| """HADDOCK3 OpenMM module."""
|
|
|
| name = RECIPE_PATH.name
|
|
|
| def __init__(self, order, path, initial_params=DEFAULT_CONFIG):
|
| super().__init__(order, path, initial_params)
|
|
|
| def create_directories(self) -> dict[str, str]:
|
| """Create the necessary directories and provides the paths."""
|
| directory_list = (
|
| "pdbfixer",
|
| "solvation_boxes",
|
| "intermediates",
|
| "md_raw_output",
|
| "openmm_output",
|
| "simulation_stats",
|
| )
|
|
|
| directory_dict: dict[str, str] = {}
|
| for dir in directory_list:
|
| self.log(f"Creating directory {dir}")
|
| os.mkdir(dir)
|
| directory_dict[dir] = dir
|
|
|
| return directory_dict
|
|
|
| def remove_directories(self) -> None:
|
| """Remove unnecessary directories full of heavy files."""
|
| directory_list = (
|
| "pdbfixer",
|
| "md_raw_output",
|
| "solvation_boxes",
|
| )
|
| for dir in directory_list:
|
| self.log(f"Removing temporary directory {dir}")
|
| shutil.rmtree(dir)
|
| return None
|
|
|
| @classmethod
|
| def confirm_installation(cls) -> None:
|
| """Confirm installation of openmm and pdfixer.
|
|
|
| Raises
|
| ------
|
| ThirdPartyIntallationError
|
| When OpenMM is not installed
|
| ThirdPartyIntallationError
|
| When OpenMM pdbfixer is not installed
|
| """
|
| try:
|
| import openmm
|
| except ModuleNotFoundError:
|
| raise ThirdPartyIntallationError(
|
| "OpenMM is not installed."
|
| )
|
| try:
|
| import pdbfixer
|
| except ModuleNotFoundError:
|
| raise ThirdPartyIntallationError(
|
| "OpenMM pdbfixer is not installed."
|
| )
|
| return None
|
|
|
| @staticmethod
|
| def set_max_cpu(nbcpu: int) -> None:
|
| from openmm import Platform
|
| cpu_platform = Platform.getPlatformByName('CPU')
|
| cpu_platform.setPropertyDefaultValue('Threads', str(nbcpu))
|
|
|
| def _run(self) -> None:
|
| """Execute module."""
|
|
|
| previous_models = self.previous_io.retrieve_models(
|
| individualize=True,
|
| )
|
|
|
|
|
| directory_dict = self.create_directories()
|
|
|
|
|
| self.set_max_cpu(self.params["ncores"])
|
|
|
|
|
| openmm_jobs: list[OPENMM] = []
|
| for i, model_to_be_simulated in enumerate(previous_models, start=1):
|
|
|
| openmm_job_i = OPENMM(
|
| i,
|
| model_to_be_simulated,
|
| Path("."),
|
| directory_dict,
|
| self.params,
|
| )
|
|
|
| openmm_jobs.append(openmm_job_i)
|
|
|
|
|
| scheduling_engine = get_engine(self.params["mode"], self.params)
|
| scheduler = scheduling_engine(openmm_jobs)
|
| scheduler.run()
|
|
|
|
|
| output_pdbs = list(Path(directory_dict["openmm_output"]).glob("*.pdb"))
|
|
|
|
|
| if len(output_pdbs) == 0:
|
| self.finish_with_error(
|
| "No output models generated. "
|
| "Check Openmm Execution and logfile."
|
| )
|
|
|
|
|
| self.log("Removing unnecessary directories...")
|
|
|
|
|
|
|
| self.log("Completed OpenMM module run.")
|
| self.log(
|
| "If you want to continue the haddock3 workflow after "
|
| "the OpenMM module, the next module should be `[topoaa]`, "
|
| "to rebuild the CNS molecular topologies."
|
| )
|
|
|
|
|
| self.output_models = [
|
| PDBFile(openmmout)
|
| for openmmout in sorted(output_pdbs)
|
| ]
|
|
|
| self.export_io_models()
|
|
|
