Energy correction model¶

TCKDB backend app models energy correction (encorr) module

class tckdb.backend.app.models.encorr.EnCorr(**kwargs)[source]¶

A class for representing a TCKDB EnCorr item

AEC and BAC Example:

EnCorr(level_id=1, supported_elements=['H', 'C', 'N', 'O', 'S'], energy_unit='Hartree',
       aec={'H': -0.499459, 'C': -37.786694, 'N': -54.524279,
            'O': -74.992097, 'S': -397.648733},
       bac={'C-H': -0.46, 'C-C': -0.68, 'C=C': -1.9, 'C#C': -3.13, 'O-H': -0.51,
            'C-O': -0.23, 'C=O': -0.69, 'O-O': -0.02, 'C-N': -0.67, 'C=N': -1.46,
            'C#N': -2.79, 'N-O': 0.74, 'N_O': -0.23, 'N=O': -0.51, 'N-H': -0.69,
            'N-N': -0.47, 'N=N': -1.54, 'N#N': -2.05, 'S-H': 0.87, 'C-S': 0.42,
            'C=S': 0.51, 'S-S': 0.86, 'O-S': 0.23, 'O=S': -0.53})

Isodesmic reactions Example:

EnCorr(level_id=1, supported_elements=['H', 'C', 'N', 'O', 'S'], energy_unit='kcal/mol',
       isodesmic_reactions=([{'reactants': ['[CH2]CCCC', '[CH]'],
                              'products': ['[C]C', 'C[CH]CC'],
                              'stoichiometry': [1, 1, 1, 1], 'DHrxn298': 17.076},
                             {'reactants': ['[CH2]CCCC', '[CH3]'],
                              'products': ['C[CH2]', '[CH2]C(C)C'],
                              'stoichiometry': [1, 1, 1, 1], 'DHrxn298': 14.507}]),
       isodesmic_high_level_id=2)

id¶

The primary key (not a user input)

Type: int

level_id¶

The level of theory key for the Level table.

Note

This argument is facilitated by querying the Level table.

Type: int

supported_elements¶

Entries are atomic symbols of elements supported by this energy correction instance.

Type: List[str]

energy_unit¶

The energy units, default: ‘Hartree’

Type: str

aec¶

Atomic energy corrections (including SOC). Keys are element symbols, values are energy corrections in the specified energy_unit.

Type: Dict[str, float]

bac¶

Bond additivity corrections. Keys are strings representing two elements and the bond between them (e.g., ‘C=O’). Values are energy corrections in the specified energy_unit. Allowed bond descriptors are '-', '=', '#', '--', and '&' for single, double, triple, hydrogen, and aromatic bonds, respectively.

Type: Dict[str, float]

isodesmic_reactions¶

The isodesmic reactions used for the energy correction. If specified, ‘AEC’ and ‘BAC’ must be None, and vice versa. Entries are dictionaries representing reactions. Each reaction dict has ‘reactants’, ‘products’, ‘stoichiometry’, and ‘DHrxn298’ keys. The values of the ‘reactants’ and ‘products’ are lists of string species identifier (SMILES or InChI). The value of ‘stoichiometry’ is a list with stoichiometric coefficients of the reactants and products (in that order). The value of ‘DHrxn298’ is the enthalpy change of reaction at the “low level” in the specified energy_unit. See example above.

Type: List[Dict[str, Union[List[Union[int, str]], float]]]

isodesmic_high_level_id¶

The high level of theory used for all other species. A level of theory key for the Level table. Required if isodesmic_reactions is specified, None otherwise.

Type: int

species¶

A One to Many relationship between EnCorr and Species.

Type: relationship

reviewer_flags¶

Backend flags to assist the review process (not a user input).

Type: Dict[str, str]