spycci.wrappers.crest sub-module
tautomer_search class
- spycci.wrappers.crest.tautomer_search(mol, ncores=None, maxcore=None, solvent=None, remove_tdir=True, optionals='', CRESTPATH=None)
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:
conformer_search class
- spycci.wrappers.crest.conformer_search(mol, ncores=None, maxcore=None, solvent=None, remove_tdir=True, optionals='', CRESTPATH=None)
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:
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:
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:
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: