rdmc.conformer_generation.ts_generators#

Modules for TS conformer generation workflows.

class rdmc.conformer_generation.ts_generators.TSConformerGenerator(rxn_smiles: str, multiplicity: int | None = None, use_smaller_multiplicity: bool = True, embedder: TSInitialGuesser | None = None, optimizer: TSOptimizer | None = None, pruner: ConfGenPruner | None = None, verifiers: TSVerifier | List[TSVerifier] | None = None, sampler: TorisonalSampler | None = None, final_modules: TSOptimizer | TSVerifier | List[TSVerifier] | None = None, save_dir: str | None = None)#

Bases: object

The class used to define a workflow for generating a set of TS conformers.

Parameters:

  • rxn_smiles (str) – The SMILES of the reaction. The SMILES should be formatted similar to "reactant1.reactant2>>product1.product2.".

  • multiplicity (int, optional) – The spin multiplicity of the reaction. The spin multiplicity will be interpreted from the reaction smiles if this is not given by the user.

  • use_smaller_multiplicity (bool, optional) – Whether to use the smaller multiplicity when the interpreted multiplicity from the reaction smiles is inconsistent between reactants and products. Defaults to True.

  • embedder (TSInitialGuesser, optional) – Instance of a TSInitialGuesser. Available options are TSEGNNGuesser, TSGCNGuesser, AutoNEBGuesser, RMSDPPGuesser, and DEGSMGuesser.

  • optimizer (TSOptimizer, optional) – Instance of a TSOptimizer. Available options are SellaOptimizer, OrcaOptimizer, GaussianOptimizer, and QChemOptimizer.

  • pruner (ConfGenPruner, optional) – The pruner used to prune conformers based on geometric similarity after optimization. Instance of a ConfGenPruner. Available options are CRESTPruner and TorsionPruner.

  • verifiers (TSVerifier or list of TSVerifiers, optional) – The verifier or a list of verifiers used to verify the obtained TS conformer. Instance of a TSVerifier. Available options are XTBFrequencyVerifier, GaussianIRCVerifier, OrcaIRCVerifier, QChemIRCVerifier, and TSScreener.

  • sampler (TorisonalSampler, optional) – The sampler used to do automated conformer search for the obtained TS conformer. You can use TorsionalSampler to define your own sampler.

  • final_modules (TSOptimizer, TSVerifier or list of TSVerifiers, optional) – The final modules can include optimizer in different LoT than previous one and verifier(s) used to verify the obtained TS conformer.

  • save_dir (str or Pathlike object, optional) – The path to save the intermediate files and outputs generated during the generation. Defaults to None.

embed_stable_species(smiles: str) → RDKitMol#

Embed the reactant and product complex according to the SMILES provided.

Parameters:

smiles (str) – The reactant or product complex in SMILES. if multiple molecules involve, use "." to separate them.

Returns:

RDKitMol – An RDKitMol of the reactant or product complex with 3D geometry embedded.

generate_seed_mols(rxn_smiles: str, n_conformers: int = 20, shuffle: bool = False) → list#

Genereate seeds of reactant/product pairs to be passed to the following steps.

Parameters:

  • rxn_smiles (str) – The reaction smiles of the reaction.

  • n_conformers (int, optional) – The maximum number of conformers to be generated. Defaults to 20.

  • shuffle (bool, optional) – Whether or not to shuffle the embedded mols. Defaults to False.

Returns:

list – A list of reactant/product pairs in RDKitMol.

set_filter(ts_mol: RDKitMol, n_conformers: int) → RDKitMol#

Assign the indices of reactions to track whether the conformers are passed to the following steps.

Parameters:

  • ts_mol ('RDKitMol') – The TS in RDKitMol object with 3D geometries embedded.

  • n_conformers (int) – The maximum number of conformers to be passed to the following steps.

Returns:

RDKitMol – with KeepIDs as a list of True and False indicating whether a conformer passes the check.