spycci.wrappers.crest sub-module

tautomer_search class

Tautomer search using CREST.

Parameters:
  • mol (System object) – input molecule to use in the calculation

  • ncores (int, optional) – number of cores, by default all available cores

  • maxcore (dummy variable) – dummy variable used for compatibility with Orca calculations

  • solvent (str, optional) – ALPB solvent, by default no solvent (vacuum)

  • remove_tdir (bool, optional) – temporary work directory will be removed, by default True

  • optionals (str, optional) – optional flags for calculation

  • CRESTPATH (str, optional) – the path to the crest executable. If set to None (default) the crest executable will be loaded automatically.

Returns:

tautomers – Ensemble containing the found tautomers, in order of ascending energy

Return type:

Ensemble


conformer_search class

Conformer search using CREST.

Parameters:
  • mol (System object) – input molecule to use in the calculation

  • ncores (int, optional) – number of cores, by default all available cores

  • maxcore (dummy) – dummy variable used for compatibility with Orca calculations

  • solvent (str, optional) – ALPB solvent, by default no solvent (vacuum)

  • remove_tdir (bool, optional) – temporary work directory will be removed, by default True

  • optionals (str, optional) – optional flags for calculation

  • CRESTPATH (str, optional) – the path to the crest executable. If set to None (default) the crest executable will be loaded automatically.

Returns:

conformers – Ensemble containing the found conformers, in order of ascending energy

Return type:

Ensemble


deprotonate class

spycci.wrappers.crest.deprotonate(mol, ncores=None, maxcore=None, solvent=None, remove_tdir=True, optionals='', CRESTPATH=None)

Deprotomer search using CREST.

Parameters:
  • mol (System object) – input molecule to use in the calculation

  • ncores (int, optional) – number of cores, by default all available cores

  • maxcore (dummy) – dummy variable used for compatibility with Orca calculations

  • solvent (str, optional) – ALPB solvent, by default no solvent (vacuum)

  • remove_tdir (bool, optional) – temporary work directory will be removed, by default True

  • optionals (str, optional) – optional flags for calculation

  • CRESTPATH (str, optional) – the path to the crest executable. If set to None (default) the crest executable will be loaded automatically.

Returns:

deprotomers – Ensemble containing the found deprotomers, in order of ascending energy

Return type:

Ensemble


protonate class

spycci.wrappers.crest.protonate(mol, ncores=None, maxcore=None, solvent=None, remove_tdir=True, optionals='', CRESTPATH=None)

Protomer search using CREST.

Parameters:
  • mol (System object) – input molecule to use in the calculation

  • ncores (int, optional) – number of cores, by default all available cores

  • maxcore (dummy) – dummy variable used for compatibility with Orca calculations

  • solvent (str, optional) – ALPB solvent, by default no solvent (vacuum)

  • remove_tdir (bool, optional) – temporary work directory will be removed, by default True

  • optionals (str, optional) – optional flags for calculation

  • CRESTPATH (str, optional) – the path to the crest executable. If set to None (default) the crest executable will be loaded automatically.

Returns:

protomers – Ensemble containing the found protomers, in order of ascending energy

Return type:

Ensemble


qcg_grow class

spycci.wrappers.crest.qcg_grow(solute, solvent, charge=None, spin=None, method='gfn2', nsolv=0, ncores=None, maxcore=None, alpb_solvent=None, optionals='', remove_tdir=True, CRESTPATH=None)

Quantum Cluster Growth using CREST.

Parameters:
  • solute (System object) – solute molecule to use in the calculation

  • solvent (System object) – solvent molecule to use in the calculation

  • charge (int, optional) – total charge of the system. Default is taken from the solute molecule.

  • spin (int, optional) – total spin of the system. Default is taken from the solute molecule.

  • method (str) – method for the geometry optimizations, by default gfn2 Alternative options: gfn1, gfnff

  • nsolv (int) – number of solvent molecules to add to the cluster, by default 0 (unconstrained). If a number is not specified, the program will keep adding solvent molecules until convergence is reached, or 150 molecules are added.

  • ncores (int, optional) – number of cores, by default all available cores

  • maxcore (dummy) – dummy variable used for compatibility with Orca calculations

  • alpb_solvent (str, optional) – ALPB solvent, by default no solvent (vacuum)

  • optionals (str, optional) – optional flags for calculation

  • remove_tdir (bool, optional) – temporary work directory will be removed, by default True

  • CRESTPATH (str, optional) – the path to the crest executable. If set to None (default) the crest executable will be loaded automatically.

Returns:

cluster – System object containing the explicitly solvated input molecule

Return type:

System object


qcg_ensemble class

spycci.wrappers.crest.qcg_ensemble(solute, solvent, charge=None, spin=None, method='gfn2', enslvl='gfn2', ensemble_choice='full_ensemble', nsolv=0, ncores=None, maxcore=None, alpb_solvent=None, optionals='', remove_tdir=True, CRESTPATH=None)

Quantum Cluster Growth + ensemble generation using CREST.

Parameters:
  • solute (System object) – solute molecule to use in the calculation

  • solvent (System object) – solvent molecule to use in the calculation

  • charge (int, optional) – total charge of the molecule. Default is taken from the solute molecule.

  • spin (int, optional) – total spin of the molecule. Default is taken from the solute molecule.

  • method (str) – method for the geometry optimizations, by default gfn2 Alternative options: gfn1, gfnff

  • enslvl (str) – method for the ensemble optimization, by default gfn2 Alternative options: gfn1, gfnff

  • ensemble_choice (str) – file containing the chosen ensemble after generation, by default “full_ensemble”. Available options are: - “full_ensemble” - “final_ensemble” - “crest_best”

  • nsolv (int) – number of solvent molecules to add to the cluster, by default 0 (unconstrained). If a number is not specified, the program will keep adding solvent molecules until convergence is reached, or 150 molecules are added.

  • ncores (int, optional) – number of cores, by default all available cores

  • maxcore (dummy) – dummy variable used for compatibility with Orca calculations

  • alpb_solvent (str, optional) – ALPB solvent, by default no solvent (vacuum)

  • optionals (str, optional) – optional flags for calculation

  • remove_tdir (bool, optional) – temporary work directory will be removed, by default True

  • CRESTPATH (str, optional) – the path to the crest executable. If set to None (default) the crest executable will be loaded automatically.

Returns:

ensemble – Ensemble object containing the explicitly solvated input molecule, with updated energy coming from enseble generation (electronic contribution only). The vibronic contribution is taken from the input solute molecule (if present), while the electronic contribution is taken as the weighted average of all generated ensembles.

Return type:

Ensemble