| """Explicit solvent MD refinement with CNS. |
| |
| The ``[mdref]`` module (also known as ``itw`` in HADDOCK2.X series), is a small |
| molecular dynamics simulation, in cartesian space, using explicit solvent. |
| |
| A layer of solvent (8A for water, 12.5A for DMSO) is generated around |
| surface residues. |
| |
| The `mdref` protocol is composed of 4 sequential steps: |
| 1. Short energy minimization |
| 2. 3 stages of molecular dynamics to reach 300K (at 100, 200 and 300K) |
| 3. Molecular dynamics at 300K. |
| 4. 3 stages of molecular dynamics, to reach 100K (at 300, 200 and 100K) |
| |
| Using this protocol, with default parameters, no spectacular changes are |
| expected, however, the scoring of the various structures might be improved. |
| |
| |
| Number of MD steps can be modified using the ``waterheatsteps``, ``watersteps`` |
| and ``watercoolsteps``. |
| |
| For more details about this module, please `refer to the haddock3 user manual |
| <https://www.bonvinlab.org/haddock3-user-manual/modules/refinement.html#mdref-module>`_ |
| """ |
|
|
| from pathlib import Path |
|
|
| from haddock.core.defaults import MODULE_DEFAULT_YAML |
| from haddock.core.typing import FilePath |
| from haddock.gear.haddockmodel import HaddockModel |
| from haddock.libs.libcns import prepare_cns_input, prepare_expected_pdb |
| from haddock.libs.libontology import PDBFile |
| from haddock.libs.libsubprocess import CNSJob |
| from haddock.modules import get_engine |
| from haddock.modules.base_cns_module import BaseCNSModule |
|
|
|
|
| RECIPE_PATH = Path(__file__).resolve().parent |
| DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML) |
|
|
|
|
| class HaddockModule(BaseCNSModule): |
| """HADDOCK3 module for water refinement.""" |
|
|
| name = RECIPE_PATH.name |
|
|
| def __init__( |
| self, order: int, path: Path, initial_params: FilePath = DEFAULT_CONFIG |
| ) -> None: |
| cns_script = Path(RECIPE_PATH, "cns", "mdref.cns") |
| super().__init__(order, path, initial_params, cns_script=cns_script) |
|
|
| @classmethod |
| def confirm_installation(cls) -> None: |
| """Confirm if module is installed.""" |
| return |
|
|
| def _run(self) -> None: |
| """Execute module.""" |
| |
| jobs: list[CNSJob] = [] |
|
|
| |
| try: |
| models_to_refine = self.previous_io.retrieve_models() |
| except Exception as e: |
| self.finish_with_error(e) |
|
|
| self.output_models: list[PDBFile] = [] |
|
|
| sampling_factor = self.params["sampling_factor"] |
| if sampling_factor > 1: |
| self.log(f"sampling_factor={sampling_factor}") |
| if sampling_factor == 0: |
| self.log("[Warning] sampling_factor cannot be 0, setting it to 1") |
| sampling_factor = 1 |
| if sampling_factor > 100: |
| self.log("[Warning] sampling_factor is larger than 100") |
|
|
| max_nmodels = self.params["max_nmodels"] |
| nmodels = len(models_to_refine) * sampling_factor |
| if nmodels > max_nmodels: |
| self.finish_with_error( |
| f"Too many models ({nmodels}) to refine, max_nmodels =" |
| f" {max_nmodels}. Please reduce the number of models or" |
| " decrease the sampling_factor." |
| ) |
|
|
| |
| try: |
| prev_ambig_fnames = [mod.restr_fname for mod in models_to_refine] |
| except Exception as e: |
| |
| prev_ambig_fnames = [None for mod in models_to_refine] |
|
|
| ambig_fnames = self.get_ambig_fnames(prev_ambig_fnames) |
|
|
| model_idx = 0 |
| idx = 1 |
| for model in models_to_refine: |
| |
| if ambig_fnames: |
| ambig_fname = ambig_fnames[model_idx] |
| else: |
| ambig_fname = self.params["ambig_fname"] |
| model_idx += 1 |
|
|
| for s_ind in range(sampling_factor): |
| |
| |
| |
| if isinstance(model, PDBFile) and model.seed is not None: |
| offsetted_seed = model.seed + s_ind |
| else: |
| offsetted_seed = None |
| mdref_input = prepare_cns_input( |
| idx, |
| model, |
| self.path, |
| self.recipe_str, |
| self.params, |
| "mdref", |
| ambig_fname=ambig_fname, |
| native_segid=True, |
| debug=self.params["debug"], |
| seed=offsetted_seed, |
| ) |
| out_file = f"mdref_{idx}.out" |
| err_fname = f"mdref_{idx}.cnserr" |
|
|
| |
| expected_pdb = prepare_expected_pdb(model, idx, ".", "mdref") |
| expected_pdb.restr_fname = ambig_fname |
| try: |
| expected_pdb.ori_name = model.file_name |
| except AttributeError: |
| expected_pdb.ori_name = None |
| self.output_models.append(expected_pdb) |
|
|
| job = CNSJob(mdref_input, out_file, err_fname, envvars=self.envvars) |
|
|
| jobs.append(job) |
|
|
| idx += 1 |
|
|
| |
| self.log(f"Running CNS Jobs n={len(jobs)}") |
| Engine = get_engine(self.params["mode"], self.params) |
| engine = Engine(jobs) |
| engine.run() |
| self.log("CNS jobs have finished") |
|
|
| |
| _weight_keys = ("w_vdw", "w_elec", "w_desolv", "w_air", "w_bsa") |
| weights = {e: self.params[e] for e in _weight_keys} |
|
|
| for pdb in self.output_models: |
| if pdb.is_present(): |
| haddock_model = HaddockModel(pdb.file_name) |
| pdb.unw_energies = haddock_model.energies |
|
|
| haddock_score = haddock_model.calc_haddock_score(**weights) |
| pdb.score = haddock_score |
|
|
| |
| self.export_io_models(faulty_tolerance=self.params["tolerance"]) |
|
|
