bonafide.features

bonafide.features.alfabet_

Bond dissociation energy features from ALFABET.

class bonafide.features.alfabet_.Alfabet2DBondBondDissociationEnergy

Bases: _Alfabet2DBond

Feature factory for the 2D bond feature “bond_dissociation_energy”, calculated with alfabet.

The index of this feature is 0 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “alfabet” in the _feature_config.toml file.

class bonafide.features.alfabet_.Alfabet2DBondBondDissociationFreeEnergy

Bases: _Alfabet2DBond

Feature factory for the 2D bond feature “bond_dissociation_free_energy”, calculated with alfabet.

The index of this feature is 1 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “alfabet” in the _feature_config.toml file.

class bonafide.features.alfabet_._Alfabet2DBond

Bases: BaseFeaturizer

Parent feature factory for the 2D atom ALFABET features.

For details, please refer to the ALFABET repository (https://github.com/NREL/alfabet, last accessed on 09.09.2025).

_read_output_file(mapping_dict)

Read the ALFABET output pandas DataFrame and write the results to the results dictionary.

Only the bonds that can be predicted by ALFABET will have an entry in the DataFrame. If molecules with no hydrogen atoms added are passed to BONAFIDE, the X-H dissociation energies still will be predicted by ALFABET, but the results will not appear in the final BONAFIDE output, as the bonds do not exist in the actual input molecule. Add hydrogen atoms to the molecule before passing it to BONAFIDE to avoid this.

Parameters:

mapping_dictDict[int, int]

The mapping dictionary to map the bond indices from the canonical SMILES string to the bond indices of the input molecule. This is included for security to ensure that the bond indices are handled correctly.

Returns:

None

calculate()

Calculate the alfabet2D-bond-bond_dissociation_energy and alfabet2D-bond-bond_dissociation_free_energy feature.

python_interpreter_path

bonafide.features.autocorrelation

Autocorrelation features for atoms in 2D molecules.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationAbsDifference

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_abs_difference”, implemented within this package.

The index of this feature is 5 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_abs_difference feature.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationDifference

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_difference”, implemented within this package.

The index of this feature is 6 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_difference feature.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationMean

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_mean”, implemented within this package.

The index of this feature is 7 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_mean feature.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationProduct

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_product”, implemented within this package.

The index of this feature is 8 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_product feature.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledAbsDifference

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_scaled_abs_difference”, implemented within this package.

The index of this feature is 9 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_scaled_abs_difference feature.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledDifference

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_scaled_difference”, implemented within this package.

The index of this feature is 10 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_scaled_difference feature.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledMean

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_scaled_mean”, implemented within this package.

The index of this feature is 11 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_scaled_mean feature.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledProduct

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_scaled_product”, implemented within this package.

The index of this feature is 12 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_scaled_product feature.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledSum

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_scaled_sum”, implemented within this package.

The index of this feature is 13 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_scaled_sum feature.

class bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationSum

Bases: _Bonafide2DAtomAutocorrelation

Feature factory for the 2D atom feature “autocorrelation_sum”, implemented within this package.

The index of this feature is 14 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.autocorrelation” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-autocorrelation_sum feature.

class bonafide.features.autocorrelation._Bonafide2DAtomAutocorrelation

Bases: BaseFeaturizer

Parent feature factory for the 2D atom autocorrelation features.

static _abs_diff(num, arr)

Calculate the absolute difference between a number and an array.

Parameters:

numfloat

The number (i.e., the property of the root atom).

arrNDArray[np.float64]

The array (i.e., the property vector of all atoms in the molecule).

Returns:

NDArray[np.float64]

The absolute difference between the number and each element in the array.

_get_autocorrelation_vector(dist_vector, property_vector, operant, scale)

Calculate the autocorrelation vector.

Parameters:

dist_vectorNDArray[np.float64]

The vector of the shortest distances in bonds from the root atom to all other atoms in the molecule.

property_vectorNDArray[np.float64]

The property vector for the requested feature for all atoms in the molecule.

operantAny

The mathematical operation (sum, difference, product, mean, abs difference) to be applied between the property of the root atom and the respective other atom.

scalebool

Whether to scale the autocorrelation feature at each depth by the number of atoms at that depth.

Returns:

str

The autocorrelation vector as a comma-separated string.

_get_property_vector(dist_vector)

Get the atom property vector for the requested feature to be used in the generation of the autocorrelation features.

This property must be precomputed for every atom in the molecule, requested by the iterable_option input available in the configuration settings of the autocorrelation feature.

Parameters:

dist_vectorNDArray[np.float64]

The vector of the shortest distances in bonds from the root atom to all other atoms in the molecule.

Returns:

Optional[NDArray[np.float64]]

The property vector for the requested feature for all atoms in the molecule or None if an error occurred.

static _kronecker_delta(arr, target_value)

Calculate the Kronecker delta for a given array and target value.

Parameters:

arrNDArray[np.float64]

The input array (i.e., the distance vector of a given atom to all atoms).

target_valueint

The target value (i.e., the current depth).

Returns:

NDArray[np.float64]

The Kronecker delta array, where elements equal to the target value are 1.0, and all other elements are 0.0.

static _mean(num, arr)

Calculate the mean between a number and an array.

Parameters:

numfloat

The number (i.e., the property of the root atom).

arrNDArray[np.float64]

The array (i.e., the property vector of all atoms in the molecule).

Returns:

NDArray[np.float64]

The mean between the number and each element in the array.

depth

iterable_option

run_workflow(operant, scale)

Execute the workflow for calculating an autocorrelation feature vector for a give root atom.

Parameters:

operantAny

The mathematical operation (sum, difference, product, mean, abs difference) to be applied between the property of the root atom and the respective other atom.

scalebool

Whether to scale the autocorrelation feature at each depth by the number of atoms at that depth.

Returns:

None

bonafide.features.constant_feature

Constant values for atoms or bonds as a feature.

class bonafide.features.constant_feature.Bonafide2DAtomConstantFeature

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “constant_feature”, implemented within this package.

The index of this feature is 17 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.constant” in the _feature_config.toml file.

atom_constant

calculate()

Calculate the bonafide2D-atom-constant_feature feature.

class bonafide.features.constant_feature.Bonafide2DBondConstantFeature

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “constant_feature”, implemented within this package.

The index of this feature is 42 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.constant” in the _feature_config.toml file.

bond_constant

calculate()

Calculate the bonafide2D-bond-constant_feature feature.

bonafide.features.dbstep_

Features from DBSTEP.

class bonafide.features.dbstep_.Dbstep3DAtomBuriedVolume

Bases: _Dbstep3DAtom

Feature factory for the 3D atom feature “buried_volume”, calculated with dbstep.

The index of this feature is 90 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “dbstep” in the _feature_config.toml file.

calculate()

Calculate the dbstep3D-atom-buried_volume feature.

class bonafide.features.dbstep_.Dbstep3DAtomFractionBuriedShellVolume

Bases: _Dbstep3DAtom

Feature factory for the 3D atom feature “fraction_buried_shell_volume”, calculated with dbstep.

The index of this feature is 91 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “dbstep” in the _feature_config.toml file.

calculate()

Calculate the dbstep3D-atom-fraction_buried_shell_volume feature.

class bonafide.features.dbstep_.Dbstep3DAtomFractionBuriedVolume

Bases: _Dbstep3DAtom

Feature factory for the 3D atom feature “fraction_buried_volume”, calculated with dbstep.

The index of this feature is 92 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “dbstep” in the _feature_config.toml file.

calculate()

Calculate the dbstep3D-atom-fraction_buried_volume feature.

class bonafide.features.dbstep_._Dbstep3DAtom

Bases: BaseFeaturizer

Parent feature factory for the 3D atom DBSTEP features.

For details, please refer to the DBSTEP repository (https://github.com/patonlab/DBSTEP, last accessed on 09.09.2025).

_run_dbstep()

Run DBSTEP and write the results to the results dictionary.

Returns:

None

_write_input_file()

Write an XYZ file as input for DBSTEP.

Returns:

None

addmetals

exclude

grid

noH

r

scalevdw

scan

vshell

bonafide.features.distance

Bond distance features for atoms and bonds in 2D molecules.

class bonafide.features.distance.Bonafide2DAtomAtomsBeyondXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “atoms_beyond_x_bonds”, implemented within this package.

The index of this feature is 2 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-atoms_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomAtomsWithinXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “atoms_within_x_bonds”, implemented within this package.

The index of this feature is 3 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-atoms_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomAtomsXBondsAway

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “atoms_x_bonds_away”, implemented within this package.

The index of this feature is 4 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-atoms_x_bonds_away feature.

class bonafide.features.distance.Bonafide2DAtomBondsBeyondXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “bonds_beyond_x_bonds”, implemented within this package.

The index of this feature is 15 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-bonds_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomBondsWithinXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “bonds_within_x_bonds”, implemented within this package.

The index of this feature is 16 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-bonds_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomDistanceToAllAtomsMax

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “distance_to_all_atoms_max”, implemented within this package.

The index of this feature is 18 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-distance_to_all_atoms_max feature.

class bonafide.features.distance.Bonafide2DAtomDistanceToAllAtomsMean

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “distance_to_all_atoms_mean”, implemented within this package.

The index of this feature is 19 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-distance_to_all_atoms_mean feature.

class bonafide.features.distance.Bonafide2DAtomDistanceToAllBondsMax

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “distance_to_all_bonds_max”, implemented within this package.

The index of this feature is 20 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-distance_to_all_bonds_max feature.

class bonafide.features.distance.Bonafide2DAtomDistanceToAllBondsMean

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “distance_to_all_bonds_mean”, implemented within this package.

The index of this feature is 21 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-distance_to_all_bonds_mean feature.

class bonafide.features.distance.Bonafide2DAtomFractionAtomsBeyondXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “fraction_atoms_beyond_x_bonds”, implemented within this package.

The index of this feature is 22 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-fraction_atoms_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomFractionAtomsWithinXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “fraction_atoms_within_x_bonds”, implemented within this package.

The index of this feature is 23 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-fraction_atoms_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomFractionAtomsXBondsAway

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “fraction_atoms_x_bonds_away”, implemented within this package.

The index of this feature is 24 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-fraction_atoms_x_bonds_away feature.

class bonafide.features.distance.Bonafide2DAtomFractionBondsBeyondXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “fraction_bonds_beyond_x_bonds”, implemented within this package.

The index of this feature is 25 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-fraction_bonds_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomFractionBondsWithinXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “fraction_bonds_within_x_bonds”, implemented within this package.

The index of this feature is 26 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-fraction_bonds_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomNAtomsBeyondXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “n_atoms_beyond_x_bonds”, implemented within this package.

The index of this feature is 31 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-n_atoms_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomNAtomsWithinXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “n_atoms_within_x_bonds”, implemented within this package.

The index of this feature is 32 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-n_atoms_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomNAtomsXBondsAway

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “n_atoms_x_bonds_away”, implemented within this package.

The index of this feature is 33 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-n_atoms_x_bonds_away feature.

class bonafide.features.distance.Bonafide2DAtomNBondsBeyondXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “n_bonds_beyond_x_bonds”, implemented within this package.

The index of this feature is 34 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-n_bonds_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DAtomNBondsWithinXBonds

Bases: _BonafideAtomDistance

Feature factory for the 2D atom feature “n_bonds_within_x_bonds”, implemented within this package.

The index of this feature is 35 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-n_bonds_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondAtomsBeyondXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “atoms_beyond_x_bonds”, implemented within this package.

The index of this feature is 37 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-atoms_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondAtomsWithinXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “atoms_within_x_bonds”, implemented within this package.

The index of this feature is 38 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-atoms_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondAtomsXBondsAway

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “atoms_x_bonds_away”, implemented within this package.

The index of this feature is 39 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-atoms_x_bonds_away feature.

class bonafide.features.distance.Bonafide2DBondBondsBeyondXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “bonds_beyond_x_bonds”, implemented within this package.

The index of this feature is 40 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-bonds_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondBondsWithinXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “bonds_within_x_bonds”, implemented within this package.

The index of this feature is 41 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-bonds_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondDistanceToAllAtomsMax

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “distance_to_all_atoms_max”, implemented within this package.

The index of this feature is 43 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-distance_to_all_atoms_max feature.

class bonafide.features.distance.Bonafide2DBondDistanceToAllAtomsMean

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “distance_to_all_atoms_mean”, implemented within this package.

The index of this feature is 44 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-distance_to_all_atoms_mean feature.

class bonafide.features.distance.Bonafide2DBondDistanceToAllBondsMax

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “distance_to_all_bonds_max”, implemented within this package.

The index of this feature is 45 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-distance_to_all_bonds_max feature.

class bonafide.features.distance.Bonafide2DBondDistanceToAllBondsMean

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “distance_to_all_bonds_mean”, implemented within this package.

The index of this feature is 46 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-distance_to_all_bonds_mean feature.

class bonafide.features.distance.Bonafide2DBondFractionAtomsBeyondXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “fraction_atoms_beyond_x_bonds”, implemented within this package.

The index of this feature is 47 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-fraction_atoms_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondFractionAtomsWithinXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “fraction_atoms_within_x_bonds”, implemented within this package.

The index of this feature is 48 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-fraction_atoms_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondFractionAtomsXBondsAway

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “fraction_atoms_x_bonds_away”, implemented within this package.

The index of this feature is 49 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-fraction_atoms_x_bonds_away feature.

class bonafide.features.distance.Bonafide2DBondFractionBondsBeyondXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “fraction_bonds_beyond_x_bonds”, implemented within this package.

The index of this feature is 50 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-fraction_bonds_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondFractionBondsWithinXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “fraction_bonds_within_x_bonds”, implemented within this package.

The index of this feature is 51 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-fraction_bonds_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondNAtomsBeyondXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “n_atoms_beyond_x_bonds”, implemented within this package.

The index of this feature is 53 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-n_atoms_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondNAtomsWithinXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “n_atoms_within_x_bonds”, implemented within this package.

The index of this feature is 54 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-n_atoms_within_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondNAtomsXBondsAway

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “n_atoms_x_bonds_away”, implemented within this package.

The index of this feature is 55 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-n_atoms_x_bonds_away feature.

class bonafide.features.distance.Bonafide2DBondNBondsBeyondXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “n_bonds_beyond_x_bonds”, implemented within this package.

The index of this feature is 56 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-n_bonds_beyond_x_bonds feature.

class bonafide.features.distance.Bonafide2DBondNBondsWithinXBonds

Bases: _BonafideBondDistance

Feature factory for the 2D bond feature “n_bonds_within_x_bonds”, implemented within this package.

The index of this feature is 57 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-bond-n_bonds_within_x_bonds feature.

class bonafide.features.distance.Bonafide3DAtomAtomsBeyondXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “atoms_beyond_x_angstrom”, implemented within this package.

The index of this feature is 58 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-atoms_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomAtomsWithinXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “atoms_within_x_angstrom”, implemented within this package.

The index of this feature is 59 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-atoms_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomBondsBeyondXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “bonds_beyond_x_angstrom”, implemented within this package.

The index of this feature is 60 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-bonds_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomBondsWithinXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “bonds_within_x_angstrom”, implemented within this package.

The index of this feature is 61 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-bonds_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomDistanceToAllAtomsMax

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “distance_to_all_atoms_max”, implemented within this package.

The index of this feature is 62 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-distance_to_all_atoms_max feature.

class bonafide.features.distance.Bonafide3DAtomDistanceToAllAtomsMean

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “distance_to_all_atoms_mean”, implemented within this package.

The index of this feature is 63 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-distance_to_all_atoms_mean feature.

class bonafide.features.distance.Bonafide3DAtomDistanceToAllBondsMax

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “distance_to_all_bonds_max”, implemented within this package.

The index of this feature is 64 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-distance_to_all_bonds_max feature.

class bonafide.features.distance.Bonafide3DAtomDistanceToAllBondsMean

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “distance_to_all_bonds_mean”, implemented within this package.

The index of this feature is 65 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-distance_to_all_bonds_mean feature.

class bonafide.features.distance.Bonafide3DAtomFractionAtomsBeyondXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “fraction_atoms_beyond_x_angstrom”, implemented within this package.

The index of this feature is 66 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-fraction_atoms_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomFractionAtomsWithinXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “fraction_atoms_within_x_angstrom”, implemented within this package.

The index of this feature is 67 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-fraction_atoms_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomFractionBondsBeyondXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “fraction_bonds_beyond_x_angstrom”, implemented within this package.

The index of this feature is 68 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-fraction_bonds_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomFractionBondsWithinXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “fraction_bonds_within_x_angstrom”, implemented within this package.

The index of this feature is 69 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-fraction_bonds_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomNAtomsBeyondXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “n_atoms_beyond_x_angstrom”, implemented within this package.

The index of this feature is 70 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-n_atoms_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomNAtomsWithinXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “n_atoms_within_x_angstrom”, implemented within this package.

The index of this feature is 71 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-n_atoms_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomNBondsBeyondXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “n_bonds_beyond_x_angstrom”, implemented within this package.

The index of this feature is 72 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-n_bonds_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DAtomNBondsWithinXAngstrom

Bases: _BonafideAtomDistance

Feature factory for the 3D atom feature “n_bonds_within_x_angstrom”, implemented within this package.

The index of this feature is 73 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-atom-n_bonds_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondAtomsBeyondXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “atoms_beyond_x_angstrom”, implemented within this package.

The index of this feature is 74 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-atoms_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondAtomsWithinXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “atoms_within_x_angstrom”, implemented within this package.

The index of this feature is 75 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-atoms_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondBondsBeyondXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “bonds_beyond_x_angstrom”, implemented within this package.

The index of this feature is 76 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-bonds_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondBondsWithinXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “bonds_within_x_angstrom”, implemented within this package.

The index of this feature is 77 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-bonds_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondDistanceToAllAtomsMax

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “distance_to_all_atoms_max”, implemented within this package.

The index of this feature is 78 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-distance_to_all_atoms_max feature.

class bonafide.features.distance.Bonafide3DBondDistanceToAllAtomsMean

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “distance_to_all_atoms_mean”, implemented within this package.

The index of this feature is 79 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-distance_to_all_atoms_mean feature.

class bonafide.features.distance.Bonafide3DBondDistanceToAllBondsMax

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “distance_to_all_bonds_max”, implemented within this package.

The index of this feature is 80 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-distance_to_all_bonds_max feature.

class bonafide.features.distance.Bonafide3DBondDistanceToAllBondsMean

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “distance_to_all_bonds_mean”, implemented within this package.

The index of this feature is 81 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-distance_to_all_bonds_mean feature.

class bonafide.features.distance.Bonafide3DBondFractionAtomsBeyondXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “fraction_atoms_beyond_x_angstrom”, implemented within this package.

The index of this feature is 82 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-fraction_atoms_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondFractionAtomsWithinXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “fraction_atoms_within_x_angstrom”, implemented within this package.

The index of this feature is 83 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-fraction_atoms_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondFractionBondsBeyondXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “fraction_bonds_beyond_x_angstrom”, implemented within this package.

The index of this feature is 84 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-fraction_bonds_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondFractionBondsWithinXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “fraction_bonds_within_x_angstrom”, implemented within this package.

The index of this feature is 85 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-fraction_bonds_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondNAtomsBeyondXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “n_atoms_beyond_x_angstrom”, implemented within this package.

The index of this feature is 86 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-n_atoms_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondNAtomsWithinXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “n_atoms_within_x_angstrom”, implemented within this package.

The index of this feature is 87 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-n_atoms_within_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondNBondsBeyondXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “n_bonds_beyond_x_angstrom”, implemented within this package.

The index of this feature is 88 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-n_bonds_beyond_x_angstrom feature.

class bonafide.features.distance.Bonafide3DBondNBondsWithinXAngstrom

Bases: _BonafideBondDistance

Feature factory for the 3D bond feature “n_bonds_within_x_angstrom”, implemented within this package.

The index of this feature is 89 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.distance” in the _feature_config.toml file.

calculate()

Calculate the bonafide3D-bond-n_bonds_within_x_angstrom feature.

class bonafide.features.distance._BonafideAtomDistance

Bases: _DistanceMatrixMixin, BaseFeaturizer

Parent feature factory for the 2D and 3D atom distance features.

_run_calculation(dimensionality)

Calculate the distance-based features for a specific atom, either for a 2D molecule (bond distance matrix) or a 3D molecule (spatial distance matrix).

Parameters:

dimensionalitystr

The dimensionality of the molecule (“2D” or “3D”).

Returns:

None

n_bonds_cutoff

radius_cutoff

class bonafide.features.distance._BonafideBondDistance

Bases: _DistanceMatrixMixin, BaseFeaturizer

Parent feature factory for the 2D and 3D bond distance features.

_run_calculation(dimensionality)

Calculate the distance-based features for a specific bond, either for a 2D molecule (bond distance matrix) or a 3D molecule (spatial distance matrix).

Parameters:

dimensionalitystr

The dimensionality of the molecule (“2D” or “3D”).

Returns:

None

n_bonds_cutoff

radius_cutoff

class bonafide.features.distance._DistanceMatrixMixin

Bases: object

Mixin class to provide methods for calculating and caching distance matrices for 2D and 3D molecules.

_get_distance_matrix_2D()

Get the 2D bond distance matrix for the molecule, either from the cache or by calculating it.

Returns:

NDArray[np.float64]

The 2D bond distance matrix of the molecule.

_get_distance_matrix_3D()

Get the 3D distance matrix for the molecule, either from the cache or by calculating it.

Returns:

NDArray[np.float64]

The 3D distance matrix of the molecule.

conformer_idx

global_feature_cache

mol

bonafide.features.dscribe_

Features from DScribe.

class bonafide.features.dscribe_.Dscribe3DAtomAtomCenteredSymmetryFunction

Bases: _Dscribe3DAtom

Feature factory for the 3D atom feature “atom_centered_symmetry_function”, calculated with dscribe.

The index of this feature is 93 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “dscribe.acsf” in the _feature_config.toml file.

calculate()

Calculate the dscribe3D-atom-atom_centered_symmetry_function feature.

class bonafide.features.dscribe_.Dscribe3DAtomAtomicCoulombVector

Bases: _Dscribe3DAtom

Feature factory for the 3D atom feature “atomic_coulomb_vector”, calculated with dscribe.

The index of this feature is 94 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “dscribe.coulomb_matrix” in the _feature_config.toml file.

calculate()

Calculate the dscribe3D-atom-atomic_coulomb_vector feature.

class bonafide.features.dscribe_.Dscribe3DAtomLocalManyBodyTensorRepresentation

Bases: _Dscribe3DAtom

Feature factory for the 3D atom feature “local_many_body_tensor_representation”, calculated with dscribe.

The index of this feature is 95 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “dscribe.lmbtr” in the _feature_config.toml file.

calculate()

Calculate the dscribe3D-atom-local_many_body_tensor_representation feature.

class bonafide.features.dscribe_.Dscribe3DAtomSmoothOverlapOfAtomicPositions

Bases: _Dscribe3DAtom

Feature factory for the 3D atom feature “smooth_overlap_of_atomic_positions”, calculated with dscribe.

The index of this feature is 96 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “dscribe.soap” in the _feature_config.toml file.

calculate()

Calculate the dscribe3D-atom-smooth_overlap_of_atomic_positions feature.

class bonafide.features.dscribe_._Dscribe3DAtom

Bases: BaseFeaturizer

Parent feature factory for the 3D atom DScribe features.

_write_input_file()

Write an XYZ file as input for DScribe.

Returns:

None

average

g2_params

g3_params

g4_params

g5_params

geometry_function

grid_max

grid_min

grid_n

grid_sigma

l_max

n_max

normalization

normalize_gaussians

r_cut

rbf

scaling_exponent

sigma

species

weighting_function

weighting_scale

weighting_threshold

bonafide.features.functional_group

Functional group match feature based on predefined SMARTS patterns.

class bonafide.features.functional_group.Bonafide2DAtomFunctionalGroupMatch

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “functional_group_match”, implemented within this package.

The index of this feature is 27 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.functional_group” in the _feature_config.toml file.

_add_custom_functional_groups(df)

Add custom functional groups to the functional groups SMARTS DataFrame.

Returns:

Optional[pd.DataFrame]

The updated functional groups SMARTS DataFrame, or None if a custom functional group name was provided that already exists in the original SMARTS DataFrame.

_functional_groups_smarts

_read_functional_group_smarts()

Read the functional groups SMARTS patterns and store them in a hierarchical dictionary.

The SMARTS patterns are only read and processed if not already done, i.e. if the _functional_groups_smarts attribute is not empty.

Returns:

None

_validate_and_format_smarts_df(df)

Generate RDKit mol objects from the SMARTS patterns and format the SMARTS DataFrame into a hierarchical dictionary.

Returns:

None

calculate()

Calculate the bonafide2D-atom-functional_group_match feature.

custom_groups

key_level

bonafide.features.kallisto_

Features from kallisto.

class bonafide.features.kallisto_.Kallisto3DAtomCoordinationNumber

Bases: _Kallisto3DAtom

Feature factory for the 3D atom feature “coordination_number”, calculated with kallisto.

The index of this feature is 97 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “kallisto” in the _feature_config.toml file.

calculate()

Calculate the kallisto3D-atom-coordination_number feature.

class bonafide.features.kallisto_.Kallisto3DAtomPartialCharge

Bases: _Kallisto3DAtom

Feature factory for the 3D atom feature “partial_charge”, calculated with kallisto.

The index of this feature is 98 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “kallisto” in the _feature_config.toml file.

calculate()

Calculate the kallisto3D-atom-partial_charge feature.

class bonafide.features.kallisto_.Kallisto3DAtomPolarizability

Bases: _Kallisto3DAtom

Feature factory for the 3D atom feature “polarizability”, calculated with kallisto.

The index of this feature is 99 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “kallisto” in the _feature_config.toml file.

calculate()

Calculate the kallisto3D-atom-polarizability feature.

class bonafide.features.kallisto_.Kallisto3DAtomProximityShell

Bases: _Kallisto3DAtom

Feature factory for the 3D atom feature “proximity_shell”, calculated with kallisto.

The index of this feature is 100 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “kallisto” in the _feature_config.toml file.

calculate()

Calculate the kallisto3D-atom-proximity_shell feature.

class bonafide.features.kallisto_.Kallisto3DAtomRelativePolarizability

Bases: _Kallisto3DAtom

Feature factory for the 3D atom feature “relative_polarizability”, calculated with kallisto.

The index of this feature is 101 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “kallisto” in the _feature_config.toml file.

calculate()

Calculate the kallisto3D-atom-relative_polarizability feature.

class bonafide.features.kallisto_.Kallisto3DAtomVdwRadius

Bases: _Kallisto3DAtom

Feature factory for the 3D atom feature “vdw_radius”, calculated with kallisto.

The index of this feature is 102 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “kallisto” in the _feature_config.toml file.

calculate()

Calculate the kallisto3D-atom-vdw_radius feature.

class bonafide.features.kallisto_._Kallisto3DAtom

Bases: BaseFeaturizer

Parent feature factory for the 3D atom kallisto features.

For further details, please refer to the Kallisto documentation (https://ehjc.gitbook.io/kallisto/, last accessed on 09.09.2025).

_read_output_file(normalize=False)

Read the output file from kallisto and write the results to the results dictionary.

Parameters:

normalizebool, optional

Whether to normalize the feature values to sum up to 1, by default False.

Returns:

None

_run_kallisto(input_section)

Run kallisto.

Parameters:

input_sectionList[str]

The feature-specific arguments passed to kallisto.

Returns:

None

_write_input_file()

Write an XYZ file as input for kallisto.

Returns:

None

angstrom

charge

cntype

coordinates

elements

size

vdwtype

bonafide.features.mendeleev_

Features from mendeleev.

class bonafide.features.mendeleev_.Mendeleev2DAtomAtomicRadius

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “atomic_radius”, calculated with mendeleev.

The index of this feature is 103 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-atomic_radius feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomAtomicRadiusRahm

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “atomic_radius_rahm”, calculated with mendeleev.

The index of this feature is 104 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-atomic_radius_rahm feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomAtomicVolume

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “atomic_volume”, calculated with mendeleev.

The index of this feature is 105 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-atomic_volume feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomAtomicWeight

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “atomic_weight”, calculated with mendeleev.

The index of this feature is 106 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-atomic_weight feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomBlock

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “block”, calculated with mendeleev.

The index of this feature is 107 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-block feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomC6

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “c6”, calculated with mendeleev.

The index of this feature is 108 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-c6 feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomC6Gb

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “c6_gb”, calculated with mendeleev.

The index of this feature is 109 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-c6_gb feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomCas

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “cas”, calculated with mendeleev.

The index of this feature is 110 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-cas feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusBragg

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “covalent_radius_bragg”, calculated with mendeleev.

The index of this feature is 111 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-covalent_radius_bragg feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusCordero

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “covalent_radius_cordero”, calculated with mendeleev.

The index of this feature is 112 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-covalent_radius_cordero feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusPyykko

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “covalent_radius_pyykko”, calculated with mendeleev.

The index of this feature is 113 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-covalent_radius_pyykko feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusPyykkoDouble

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “covalent_radius_pyykko_double”, calculated with mendeleev.

The index of this feature is 114 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-covalent_radius_pyykko_double feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusPyykkoTriple

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “covalent_radius_pyykko_triple”, calculated with mendeleev.

The index of this feature is 115 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-covalent_radius_pyykko_triple feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomDensity

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “density”, calculated with mendeleev.

The index of this feature is 116 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-density feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomDipolePolarizability

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “dipole_polarizability”, calculated with mendeleev.

The index of this feature is 117 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-dipole_polarizability feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEconf

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “econf”, calculated with mendeleev.

The index of this feature is 118 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-econf feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomElectronAffinity

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “electron_affinity”, calculated with mendeleev.

The index of this feature is 119 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-electron_affinity feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomElectrophilicity

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “electrophilicity”, calculated with mendeleev.

The index of this feature is 120 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-electrophilicity feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnAllen

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_allen”, calculated with mendeleev.

The index of this feature is 121 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_allen feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnAllredRochow

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_allred_rochow”, calculated with mendeleev.

The index of this feature is 122 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_allred_rochow feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnCottrellSutton

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_cottrell_sutton”, calculated with mendeleev.

The index of this feature is 123 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_cottrell_sutton feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnGhosh

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_ghosh”, calculated with mendeleev.

The index of this feature is 124 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_ghosh feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnGordy

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_gordy”, calculated with mendeleev.

The index of this feature is 125 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_gordy feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnMartynovBatsanov

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_martynov_batsanov”, calculated with mendeleev.

The index of this feature is 126 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_martynov_batsanov feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnMiedema

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_miedema”, calculated with mendeleev.

The index of this feature is 127 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_miedema feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnMulliken

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_mulliken”, calculated with mendeleev.

The index of this feature is 128 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_mulliken feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnNagle

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_nagle”, calculated with mendeleev.

The index of this feature is 129 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_nagle feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnPauling

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_pauling”, calculated with mendeleev.

The index of this feature is 130 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_pauling feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEnSanderson

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “en_sanderson”, calculated with mendeleev.

The index of this feature is 131 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-en_sanderson feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomEvaporationHeat

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “evaporation_heat”, calculated with mendeleev.

The index of this feature is 132 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-evaporation_heat feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomFirstIonizationEnergy

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “first_ionization_energy”, calculated with mendeleev.

The index of this feature is 133 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-first_ionization_energy feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomFusionHeat

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “fusion_heat”, calculated with mendeleev.

The index of this feature is 134 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-fusion_heat feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomGasBasicity

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “gas_basicity”, calculated with mendeleev.

The index of this feature is 135 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-gas_basicity feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomGroupId

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “group_id”, calculated with mendeleev.

The index of this feature is 136 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-group_id feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomHardness

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “hardness”, calculated with mendeleev.

The index of this feature is 137 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-hardness feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomHeatOfFormation

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “heat_of_formation”, calculated with mendeleev.

The index of this feature is 138 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-heat_of_formation feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomInchi

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “inchi”, calculated with mendeleev.

The index of this feature is 139 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-inchi feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomIsMonoisotopic

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “is_monoisotopic”, calculated with mendeleev.

The index of this feature is 140 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-is_monoisotopic feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomIsRadioactive

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “is_radioactive”, calculated with mendeleev.

The index of this feature is 141 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-is_radioactive feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomLatticeConstant

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “lattice_constant”, calculated with mendeleev.

The index of this feature is 142 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-lattice_constant feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomLatticeStructure

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “lattice_structure”, calculated with mendeleev.

The index of this feature is 143 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-lattice_structure feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomMeltingPoint

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “melting_point”, calculated with mendeleev.

The index of this feature is 144 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-melting_point feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomMetallicRadius

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “metallic_radius”, calculated with mendeleev.

The index of this feature is 145 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-metallic_radius feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomMetallicRadiusC12

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “metallic_radius_c12”, calculated with mendeleev.

The index of this feature is 146 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-metallic_radius_c12 feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomMiedemaElectronDensity

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “miedema_electron_density”, calculated with mendeleev.

The index of this feature is 147 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-miedema_electron_density feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomMiedemaMolarVolume

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “miedema_molar_volume”, calculated with mendeleev.

The index of this feature is 148 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-miedema_molar_volume feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomMolarHeatCapacity

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “molar_heat_capacity”, calculated with mendeleev.

The index of this feature is 149 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-molar_heat_capacity feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomNValenceElectrons

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “n_valence_electrons”, calculated with mendeleev.

The index of this feature is 150 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-n_valence_electrons feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomName

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “name”, calculated with mendeleev.

The index of this feature is 151 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-name feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomPeriod

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “period”, calculated with mendeleev.

The index of this feature is 152 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-period feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomPettiforNumber

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “pettifor_number”, calculated with mendeleev.

The index of this feature is 153 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-pettifor_number feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomProtonAffinity

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “proton_affinity”, calculated with mendeleev.

The index of this feature is 154 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-proton_affinity feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomSoftness

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “softness”, calculated with mendeleev.

The index of this feature is 155 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-softness feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomSpecificHeatCapacity

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “specific_heat_capacity”, calculated with mendeleev.

The index of this feature is 156 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-specific_heat_capacity feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomThermalConductivity

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “thermal_conductivity”, calculated with mendeleev.

The index of this feature is 157 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-thermal_conductivity feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadius

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “vdw_radius”, calculated with mendeleev.

The index of this feature is 158 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-vdw_radius feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusAlvarez

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “vdw_radius_alvarez”, calculated with mendeleev.

The index of this feature is 159 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-vdw_radius_alvarez feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusBatsanov

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “vdw_radius_batsanov”, calculated with mendeleev.

The index of this feature is 160 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-vdw_radius_batsanov feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusBondi

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “vdw_radius_bondi”, calculated with mendeleev.

The index of this feature is 161 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-vdw_radius_bondi feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusDreiding

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “vdw_radius_dreiding”, calculated with mendeleev.

The index of this feature is 162 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-vdw_radius_dreiding feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusMm3

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “vdw_radius_mm3”, calculated with mendeleev.

The index of this feature is 163 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-vdw_radius_mm3 feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusRt

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “vdw_radius_rt”, calculated with mendeleev.

The index of this feature is 164 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-vdw_radius_rt feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusUff

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “vdw_radius_uff”, calculated with mendeleev.

The index of this feature is 165 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

calculate()

Calculate the mendeleev2D-atom-vdw_radius_uff feature.

class bonafide.features.mendeleev_.Mendeleev2DAtomZeff

Bases: _Mendeleev2DAtom

Feature factory for the 2D atom feature “zeff”, calculated with mendeleev.

The index of this feature is 166 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “mendeleev” in the _feature_config.toml file.

alle

calculate()

Calculate the mendeleev2D-atom-zeff feature.

method

class bonafide.features.mendeleev_._Mendeleev2DAtom

Bases: BaseFeaturizer

Parent feature factory for the 2D atom mendeleev features.

For details, please refer to the Mendeleev documentation (https://mendeleev.readthedocs.io/en/stable/, last accessed on 09.09.2025).

_get_attribute_data(none_to_false=False)

Get an atom property as an attribute from the mendeleev element object and write it to the results dictionary.

Parameters:

none_to_falsebool, optional

Whether to convert None values to False, by default False.

Returns:

None

_get_en_data(**kwargs)

Get the electronegativity data from the mendeleev element object and write it to the results dictionary.

Parameters:

**kwargs: Union[str, int]

Optional keyword arguments to pass to the electronegativity() method of the mendeleev element object.

Returns:

None

_periodic_table

_pull_from_periodic_table()

Get the element data from the periodic table.

Returns:

element

The mendeleev element object for the atom of interest.

bonafide.features.morfeus_bv

Buried volume features from MORFEUS.

class bonafide.features.morfeus_bv.Morfeus3DAtomBuriedVolume

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “buried_volume”, calculated with morfeus.

The index of this feature is 167 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-buried_volume feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomBuriedVolumeOctants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “buried_volume_octants”, calculated with morfeus.

The index of this feature is 168 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-buried_volume_octants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomBuriedVolumeQuadrants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “buried_volume_quadrants”, calculated with morfeus.

The index of this feature is 169 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-buried_volume_quadrants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomDistalVolume

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “distal_volume”, calculated with morfeus.

The index of this feature is 174 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-distal_volume feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomDistalVolumeOctants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “distal_volume_octants”, calculated with morfeus.

The index of this feature is 175 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-distal_volume_octants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomDistalVolumeQuadrants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “distal_volume_quadrants”, calculated with morfeus.

The index of this feature is 176 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-distal_volume_quadrants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomFractionBuriedVolume

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “fraction_buried_volume”, calculated with morfeus.

The index of this feature is 177 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-fraction_buried_volume feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomFractionBuriedVolumeOctants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “fraction_buried_volume_octants”, calculated with morfeus.

The index of this feature is 178 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-fraction_buried_volume_octants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomFractionBuriedVolumeQuadrants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “fraction_buried_volume_quadrants”, calculated with morfeus.

The index of this feature is 179 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-fraction_buried_volume_quadrants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomFractionFreeVolume

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “fraction_free_volume”, calculated with morfeus.

The index of this feature is 180 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-fraction_free_volume feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomFractionFreeVolumeOctants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “fraction_free_volume_octants”, calculated with morfeus.

The index of this feature is 181 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-fraction_free_volume_octants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomFractionFreeVolumeQuadrants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “fraction_free_volume_quadrants”, calculated with morfeus.

The index of this feature is 182 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-fraction_free_volume_quadrants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomFreeVolume

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “free_volume”, calculated with morfeus.

The index of this feature is 183 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-free_volume feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomFreeVolumeOctants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “free_volume_octants”, calculated with morfeus.

The index of this feature is 184 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-free_volume_octants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomFreeVolumeQuadrants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “free_volume_quadrants”, calculated with morfeus.

The index of this feature is 185 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-free_volume_quadrants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomMolecularVolumeOctants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “molecular_volume_octants”, calculated with morfeus.

The index of this feature is 186 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-molecular_volume_octants feature.

class bonafide.features.morfeus_bv.Morfeus3DAtomMolecularVolumeQuadrants

Bases: _Morfeus3DAtomBV

Feature factory for the 3D atom feature “molecular_volume_quadrants”, calculated with morfeus.

The index of this feature is 187 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.buried_volume” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-molecular_volume_quadrants feature.

class bonafide.features.morfeus_bv._Morfeus3DAtomBV

Bases: BaseFeaturizer

Parent feature factory for the 3D atom MORFEUS buried volume features.

For details, please refer to the MORFEUS documentation (https://digital-chemistry-laboratory.github.io/morfeus/index.html, last accessed on 09.09.2025).

_run_morfeus(do_octant_analysis=False)

Run MORFEUS and populate the buried volume attribute (bv_).

Parameters:

do_octant_analysisbool, optional

Whether to calculate the decomposition of the buried-volume features in octants and quadrants, by default False.

Returns:

bool

Whether morfeus ran (successfully).

_validate_atom_indices(atom_indices_list, parameter_name, all_indices)

Validate user-provided atom indices.

Parameters:

atom_indices_listList[int]

The list of atom indices to be validated.

parameter_namestr

The name of the parameter being validated (for error messages).

all_indicesList[int]

A list of all valid atom indices.

Returns:

Optional[List[int]]

Returns the validated list of atom indices (converted to 1-indexed) or None if validation fails.

bv_

density

distal_volume_method

distal_volume_sasa_density

excluded_atoms

include_hs

radii

radii_scale

radii_type

radius

xz_plane_atoms

z_axis_atoms

bonafide.features.morfeus_dispersion

Dispersion features from MORFEUS.

class bonafide.features.morfeus_dispersion.Morfeus3DAtomPInt

Bases: _Morfeus3DAtomDispersion

Feature factory for the 3D atom feature “p_int”, calculated with morfeus.

The index of this feature is 188 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.dispersion” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-p_int feature.

class bonafide.features.morfeus_dispersion.Morfeus3DAtomPMax

Bases: _Morfeus3DAtomDispersion

Feature factory for the 3D atom feature “p_max”, calculated with morfeus.

The index of this feature is 189 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.dispersion” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-p_max feature.

class bonafide.features.morfeus_dispersion.Morfeus3DAtomPMin

Bases: _Morfeus3DAtomDispersion

Feature factory for the 3D atom feature “p_min”, calculated with morfeus.

The index of this feature is 190 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.dispersion” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-p_min feature.

class bonafide.features.morfeus_dispersion._Morfeus3DAtomDispersion

Bases: BaseFeaturizer

Parent feature factory for the 3D atom MORFEUS dispersion features.

For details, please refer to the MORFEUS documentation (https://digital-chemistry-laboratory.github.io/morfeus/index.html, last accessed on 09.09.2025).

_run_morfeus()

Run MORFEUS and populate the dispersion attribute (dispersion_).

Returns:

bool

Whether MORFEUS ran (successfully).

_validate_atom_indices(atom_indices_list, parameter_name, all_indices)

Validate user-provided atom indices.

Parameters:

atom_indices_listList[int]

The list of atom indices to be validated.

parameter_namestr

The name of the parameter being validated (for error messages).

all_indicesList[int]

A list of all valid atom indices.

Returns:

Optional[List[int]]

Returns the validated list of atom indices (converted to 1-indexed) or None if validation fails.

density

dispersion_

excluded_atoms

included_atoms

radii

radii_type

bonafide.features.morfeus_local_force

Local force constant features from MORFEUS.

class bonafide.features.morfeus_local_force.Morfeus3DBondLocalForceConstant

Bases: _Morfeus3DBondLocalForce

Feature factory for the 3D bond feature “local_force_constant”, calculated with morfeus.

The index of this feature is 198 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.local_force” in the _feature_config.toml file.

class bonafide.features.morfeus_local_force.Morfeus3DBondLocalFrequency

Bases: _Morfeus3DBondLocalForce

Feature factory for the 3D bond feature “local_frequency”, calculated with morfeus.

The index of this feature is 199 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.local_force” in the _feature_config.toml file.

class bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce

Bases: BaseFeaturizer

Parent feature factory for the 3D bond MORFEUS local force features.

For details, please refer to the MORFEUS documentation (https://digital-chemistry-laboratory.github.io/morfeus/index.html, last accessed on 09.09.2025).

_get_program_filetype()

Determine the program and file type based on the electronic structure file extension.

Returns:

Tuple[Optional[str], Optional[str]]

A tuple containing the program name and file type. If the file type is invalid, returns (None, None).

_save_values()

Loop over all bonds and get the local force constant and frequency.

Returns:

None

calculate()

Calculate the morfeus3D-bond-local_force_constant and morfeus3D-bond-local_frequency feature.

electronic_struc_type_n

imag_cutoff

local_force_

method

project_imag

save_hessian

bonafide.features.morfeus_sasa

Solvent-accessible surface features from MORFEUS.

class bonafide.features.morfeus_sasa.Morfeus3DAtomSasAtomArea

Bases: _Morfeus3DAtomSASA

Feature factory for the 3D atom feature “sas_atom_area”, calculated with morfeus.

The index of this feature is 196 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.sasa” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-sas_atom_area feature.

class bonafide.features.morfeus_sasa.Morfeus3DAtomSasFractionAtomArea

Bases: _Morfeus3DAtomSASA

Feature factory for the 3D atom feature “sas_fraction_atom_area”, calculated with morfeus.

The index of this feature is 197 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “morfeus.sasa” in the _feature_config.toml file.

calculate()

Calculate the morfeus3D-atom-sas_fraction_atom_area feature.

class bonafide.features.morfeus_sasa._Morfeus3DAtomSASA

Bases: BaseFeaturizer

Parent feature factory for the 3D atom MORFEUS SASA features.

For details, please refer to the MORFEUS documentation (https://digital-chemistry-laboratory.github.io/morfeus/index.html, last accessed on 09.09.2025).

_run_morfeus()

Run MORFEUS and populate the solvent-accessible surface area attribute (sasa_).

Returns:

None

density

probe_radius

radii

radii_type

sasa_

bonafide.features.multiwfn_bond

Bond order features from Multiwfn.

class bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderFuzzy

Bases: _Multiwfn3DBondOrder

Feature factory for the 3D bond feature “bond_order_fuzzy”, calculated with multiwfn.

The index of this feature is 427 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.bond_analysis” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-bond_order_fuzzy feature.

class bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderLaplacian

Bases: _Multiwfn3DBondOrder

Feature factory for the 3D bond feature “bond_order_laplacian”, calculated with multiwfn.

The index of this feature is 428 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.bond_analysis” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-bond_order_laplacian feature.

class bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderMayer

Bases: _Multiwfn3DBondOrder

Feature factory for the 3D bond feature “bond_order_mayer”, calculated with multiwfn.

The index of this feature is 429 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.bond_analysis” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-bond_order_mayer feature.

class bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderMulliken

Bases: _Multiwfn3DBondOrder

Feature factory for the 3D bond feature “bond_order_mulliken”, calculated with multiwfn.

The index of this feature is 430 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.bond_analysis” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-bond_order_mulliken feature.

class bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderWiberg

Bases: _Multiwfn3DBondOrder

Feature factory for the 3D bond feature “bond_order_wiberg”, calculated with multiwfn.

The index of this feature is 431 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.bond_analysis” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-bond_order_wiberg feature.

class bonafide.features.multiwfn_bond.Multiwfn3DBondIntrinsicBondStrengthIndex

Bases: _Multiwfn3DBondOrder

Feature factory for the 3D bond feature “intrinsic_bond_strength_index”, calculated with multiwfn.

The index of this feature is 445 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.bond_analysis” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-intrinsic_bond_strength_index feature.

ibis_igm_type

ibsi_grid

class bonafide.features.multiwfn_bond._Multiwfn3DBondOrder

Bases: BaseFeaturizer

Parent feature factory for the 3D bond order Multiwfn features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_read_output_file(start_string, skip_n_lines=1)

Read the output file from Multiwfn and write the results to the results dictionary.

Parameters:

start_stringstr

The string that marks the beginning of the relevant section in the output file.

skip_n_linesint, optional

How many lines to skip after the line starting with start_string before reading the actual data, by default 1.

Returns:

None

_run_multiwfn(command_list)

Run Multiwfn.

Parameters:

command_listList[Union[int, str, float]]

List of commands to be passed to Multiwfn to select the respective bond order analysis method and potential settings.

Returns:

None

bonafide.features.multiwfn_bond_misc

Miscellaneous bond features from Multiwfn.

class bonafide.features.multiwfn_bond_misc.Multiwfn3DBondCoordinatesCenterOfMass

Bases: _Multiwfn3DBond

Feature factory for the 3D bond feature “coordinates_center_of_mass”, calculated with multiwfn.

The index of this feature is 432 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

class bonafide.features.multiwfn_bond_misc.Multiwfn3DBondCoordinatesCenterOfNuclearCharges

Bases: _Multiwfn3DBond

Feature factory for the 3D bond feature “coordinates_center_of_nuclear_charges”, calculated with multiwfn.

The index of this feature is 433 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

class bonafide.features.multiwfn_bond_misc.Multiwfn3DBondElectrostaticInteractionEnergyNuclearCharges

Bases: _Multiwfn3DBond

Feature factory for the 3D bond feature “electrostatic_interaction_energy_nuclear_charges”, calculated with multiwfn.

The index of this feature is 434 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

class bonafide.features.multiwfn_bond_misc.Multiwfn3DBondGyrationRadius

Bases: _Multiwfn3DBond

Feature factory for the 3D bond feature “gyration_radius”, calculated with multiwfn.

The index of this feature is 439 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

class bonafide.features.multiwfn_bond_misc._Multiwfn3DBond

Bases: BaseFeaturizer

Parent feature factory for the 3D bond Multiwfn features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_read_output_file()

Read the output file from Multiwfn and write the results to the results dictionary.

Returns:

None

_run_multiwfn()

Run Multiwfn.

Returns:

None

_write_input_file()

Write an XYZ file as input for Multiwfn.

Returns:

None

calculate()

Calculate the Multiwfn bond features.

bonafide.features.multiwfn_cdft

Condensed C-DFT features from Multiwfn.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalElectrophilicityFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_electrophilicity_fmo”, calculated with multiwfn.

The index of this feature is 208 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_electrophilicity_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalElectrophilicityRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_electrophilicity_redox”, calculated with multiwfn.

The index of this feature is 209 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_electrophilicity_redox feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessMinusFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_minus_fmo”, calculated with multiwfn.

The index of this feature is 210 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hardness_minus_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessMinusRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_minus_redox”, calculated with multiwfn.

The index of this feature is 211 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hardness_minus_redox feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessPlusFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_plus_fmo”, calculated with multiwfn.

The index of this feature is 212 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hardness_plus_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessPlusRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_plus_redox”, calculated with multiwfn.

The index of this feature is 213 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hardness_plus_redox feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessZeroFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_zero_fmo”, calculated with multiwfn.

The index of this feature is 214 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hardness_zero_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessZeroRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_zero_redox”, calculated with multiwfn.

The index of this feature is 215 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hardness_zero_redox feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHyperhardnessFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hyperhardness_fmo”, calculated with multiwfn.

The index of this feature is 216 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hyperhardness_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHyperhardnessRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hyperhardness_redox”, calculated with multiwfn.

The index of this feature is 217 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hyperhardness_redox feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHypersoftnessFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hypersoftness_fmo”, calculated with multiwfn.

The index of this feature is 218 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hypersoftness_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHypersoftnessRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hypersoftness_redox”, calculated with multiwfn.

The index of this feature is 219 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_hypersoftness_redox feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalNucleophilicityFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_nucleophilicity_fmo”, calculated with multiwfn.

The index of this feature is 220 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_nucleophilicity_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalNucleophilicityRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_nucleophilicity_redox”, calculated with multiwfn.

The index of this feature is 221 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_nucleophilicity_redox feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalRelativeElectrophilicity

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_relative_electrophilicity”, calculated with multiwfn.

The index of this feature is 222 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_relative_electrophilicity feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalRelativeNucleophilicity

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_relative_nucleophilicity”, calculated with multiwfn.

The index of this feature is 223 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_relative_nucleophilicity feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessMinusFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_minus_fmo”, calculated with multiwfn.

The index of this feature is 224 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_softness_minus_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessMinusRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_minus_redox”, calculated with multiwfn.

The index of this feature is 225 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_softness_minus_redox feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessPlusFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_plus_fmo”, calculated with multiwfn.

The index of this feature is 226 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_softness_plus_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessPlusRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_plus_redox”, calculated with multiwfn.

The index of this feature is 227 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_softness_plus_redox feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessZeroFmo

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_zero_fmo”, calculated with multiwfn.

The index of this feature is 228 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_softness_zero_fmo feature.

class bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessZeroRedox

Bases: _Multiwfn3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_zero_redox”, calculated with multiwfn.

The index of this feature is 229 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_local_softness_zero_redox feature.

class bonafide.features.multiwfn_cdft._Multiwfn3DAtomCdftLocal

Bases: BaseFeaturizer, CdftLocalRedoxMixin

Parent feature factory for the 3D atom C-DFT Multiwfn features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_calculate_global_descriptors_fmo()

Calculate molecule-level descriptors from the electronic structure data, that is from the frontier molecular orbital energies (HOMO and LUMO).

The included descriptors are:

• HOMO energy

• LUMO energy

• HOMO-LUMO gap

• Chemical potential

• Hardness

• Softness

• Electrophilicity

• Nucleophilicity

Returns:

Optional[str]

The error messages of the subroutines for calculating the global descriptors. None if everything worked as expected or if the data is already in the global feature cache.

_check_electronic_structure_data(el_struc_data, data_name)

Check if the required electronic structure data is available.

Parameters:

el_struc_dataOptional[str]

The electronic structure data to check. It is either None (not available) or the path to the electronic structure data file.

data_namestr

The identification string of the electronic structure data to check (used for logging).

Returns:

Optional[str]

The error message if the required electronic structure data is not available, None if the required electronic structure data is available.

_wrap_fukui_dual()

Calculate the condensed dual descriptor with Multiwfn.

Returns:

Tuple[Optional[Union[int, float, bool, str]], Optional[str]]

The condensed dual descriptor and an error message, which is None if everything worked as expected.

_wrap_fukui_minus()

Calculate the condensed Fukui minus coefficient with Multiwfn.

Returns:

Tuple[Optional[Union[int, float, bool, str]], Optional[str]]

The condensed Fukui minus coefficient and an error message, which is None if everything worked as expected.

_wrap_fukui_plus()

Calculate the condensed Fukui plus coefficient with Multiwfn.

Returns:

Tuple[Optional[Union[int, float, bool, str]], Optional[str]]

The condensed Fukui plus coefficient and an error message, which is None if everything worked as expected.

_wrap_fukui_zero()

Calculate the condensed Fukui zero coefficient with Multiwfn.

Returns:

Tuple[Optional[Union[int, float, bool, str]], Optional[str]]

The condensed Fukui zero coefficient and an error message, which is None if everything worked as expected.

iterable_option

bonafide.features.multiwfn_connectivity

Atom connectivity features from Multiwfn.

class bonafide.features.multiwfn_connectivity.Multiwfn3DAtomConnectivityIndex

Bases: _Multiwfn3DAtomConnectivity

Feature factory for the 3D atom feature “connectivity_index”, calculated with multiwfn.

The index of this feature is 230 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.bond_analysis” in the _feature_config.toml file.

class bonafide.features.multiwfn_connectivity.Multiwfn3DAtomConnectivityIndexInteger

Bases: _Multiwfn3DAtomConnectivity

Feature factory for the 3D atom feature “connectivity_index_integer”, calculated with multiwfn.

The index of this feature is 231 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.bond_analysis” in the _feature_config.toml file.

class bonafide.features.multiwfn_connectivity._Multiwfn3DAtomConnectivity

Bases: BaseFeaturizer

Parent feature factory for the 3D atom connectivity Multiwfn features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_read_output_file()

Read the output file from Multiwfn and write the results to the results dictionary.

Returns:

None

_run_multiwfn()

Run Multiwfn.

Returns:

None

_write_input_file()

Write an XYZ file as input for Multiwfn.

Returns:

None

calculate()

Calculate the Multiwfn connectivity features.

connectivity_index_threshold

bonafide.features.multiwfn_forces

Hellmann-Feynman force features from Multiwfn.

class bonafide.features.multiwfn_forces.Multiwfn3DAtomForceHellmannFeynman

Bases: _Multiwfn3DAtomForce

Feature factory for the 3D atom feature “force_hellmann_feynman”, calculated with multiwfn.

The index of this feature is 233 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

class bonafide.features.multiwfn_forces.Multiwfn3DAtomForceHellmannFeynmanElectrons

Bases: _Multiwfn3DAtomForce

Feature factory for the 3D atom feature “force_hellmann_feynman_electrons”, calculated with multiwfn.

The index of this feature is 234 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

class bonafide.features.multiwfn_forces.Multiwfn3DAtomForceHellmannFeynmanNuclearCharges

Bases: _Multiwfn3DAtomForce

Feature factory for the 3D atom feature “force_hellmann_feynman_nuclear_charges”, calculated with multiwfn.

The index of this feature is 235 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

class bonafide.features.multiwfn_forces._Multiwfn3DAtomForce

Bases: BaseFeaturizer

Parent feature factory for the 3D atom Multiwfn Hellmann-Feynman force features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_read_output_file()

Read the output file from Multiwfn and write the results to the results dictionary.

Returns:

None

_run_multiwfn()

Run Multiwfn.

Returns:

None

calculate()

Calculate the Multiwfn Hellmann-Feynman force features.

bonafide.features.multiwfn_fukui

Fukui indices calculated with Multiwfn.

class bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedFukuiDual

Bases: _Multiwfn3DAtomCdftCondensedFukui

Feature factory for the 3D atom feature “cdft_condensed_fukui_dual”, calculated with multiwfn.

The index of this feature is 200 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_condensed_fukui_dual feature.

class bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedFukuiMinus

Bases: _Multiwfn3DAtomCdftCondensedFukui

Feature factory for the 3D atom feature “cdft_condensed_fukui_minus”, calculated with multiwfn.

The index of this feature is 201 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_condensed_fukui_minus feature.

class bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedFukuiPlus

Bases: _Multiwfn3DAtomCdftCondensedFukui

Feature factory for the 3D atom feature “cdft_condensed_fukui_plus”, calculated with multiwfn.

The index of this feature is 202 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_condensed_fukui_plus feature.

class bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedFukuiZero

Bases: _Multiwfn3DAtomCdftCondensedFukui

Feature factory for the 3D atom feature “cdft_condensed_fukui_zero”, calculated with multiwfn.

The index of this feature is 203 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_condensed_fukui_zero feature.

class bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiDual

Bases: _Multiwfn3DAtomCdftCondensedOrbitalWeightedFukui

Feature factory for the 3D atom feature “cdft_condensed_orbital_weighted_fukui_dual”, calculated with multiwfn.

The index of this feature is 204 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_condensed_orbital_weighted_fukui_dual feature.

class bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiMinus

Bases: _Multiwfn3DAtomCdftCondensedOrbitalWeightedFukui

Feature factory for the 3D atom feature “cdft_condensed_orbital_weighted_fukui_minus”, calculated with multiwfn.

The index of this feature is 205 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_condensed_orbital_weighted_fukui_minus feature.

class bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiPlus

Bases: _Multiwfn3DAtomCdftCondensedOrbitalWeightedFukui

Feature factory for the 3D atom feature “cdft_condensed_orbital_weighted_fukui_plus”, calculated with multiwfn.

The index of this feature is 206 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_condensed_orbital_weighted_fukui_plus feature.

class bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiZero

Bases: _Multiwfn3DAtomCdftCondensedOrbitalWeightedFukui

Feature factory for the 3D atom feature “cdft_condensed_orbital_weighted_fukui_zero”, calculated with multiwfn.

The index of this feature is 207 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.cdft” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-cdft_condensed_orbital_weighted_fukui_zero feature.

class bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui

Bases: BaseFeaturizer

Parent feature factory for the 3D atom Multiwfn Fukui index features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

NUM_THREADS

OMP_STACKSIZE

_check_electronic_structure_data(el_struc_data, data_name)

Check if the required electronic structure data is available.

Parameters:

el_struc_dataOptional[str]

The electronic structure data to check. It is either None (not available) or the path to the electronic structure data file.

data_namestr

The identification string of the electronic structure data to check (used for logging).

Returns:

None

_run_calculation(**kwargs)

Run Multiwfn to calculate the atomic partial charges required to calculate the Fukui indices.

This is done by initializing a “child” feature calculation pipeline as for all other features. After this is completed, the Fukui indices are calculated.

Parameters:

**kwargsAny

Additional keyword arguments passed to the calculate() method of the feature factory for calculating the partial charges. These parameters are set as attributes of the “child” feature factory instance.

Returns:

Tuple[Optional[Union[int, float, bool, str]], Optional[str]]

The calculated partial charge and the error message from the “child” feature factory call. The error message is None if the “child” feature factory did not encounter an error.

_save_output_files2()

Save the generated output files of the “child” feature factory.

Returns:

None

ensemble_dimensionality

feature_cache_n_minus1

feature_cache_n_plus1

feature_dimensionality

iterable_option

multiplicity

class bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedOrbitalWeightedFukui

Bases: BaseFeaturizer

Parent feature factory for the 3D atom Multiwfn condensed orbital-weighted Fukui index features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_read_output_file()

Read the output file from Multiwfn and write the results to the results dictionary.

Returns:

None

_run_multiwfn()

Run Multiwfn.

Returns:

None

ow_delta

bonafide.features.multiwfn_fuzzy_space

Fuzzy space features from Multiwfn.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceAtomicElectronicSpatialExtent

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_atomic_electronic_spatial_extent”, calculated with multiwfn.

The index of this feature is 236 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_atomic_electronic_spatial_extent feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceAtomicValence

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_atomic_valence”, calculated with multiwfn.

The index of this feature is 237 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_atomic_valence feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceAtomicValenceAlpha

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_atomic_valence_alpha”, calculated with multiwfn.

The index of this feature is 238 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_atomic_valence_alpha feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceAtomicValenceBeta

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_atomic_valence_beta”, calculated with multiwfn.

The index of this feature is 239 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_atomic_valence_beta feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceCondensedLinearResponseKernelMatrixElement

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_condensed_linear_response_kernel_matrix_element”, calculated with multiwfn.

The index of this feature is 240 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_condensed_linear_response_kernel_matrix_element feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceContributionToSystemDipoleMoment

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_contribution_to_system_dipole_moment”, calculated with multiwfn.

The index of this feature is 241 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_contribution_to_system_dipole_moment feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceContributionToSystemDipoleMomentNorm

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_contribution_to_system_dipole_moment_norm”, calculated with multiwfn.

The index of this feature is 242 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_contribution_to_system_dipole_moment_norm feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceDipoleMoment

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_dipole_moment”, calculated with multiwfn.

The index of this feature is 243 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_dipole_moment feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceDipoleMomentNorm

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_dipole_moment_norm”, calculated with multiwfn.

The index of this feature is 244 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_dipole_moment_norm feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceIntegrationDescriptor

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_integration_descriptor”, calculated with multiwfn.

The index of this feature is 245 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_integration_descriptor feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceIntegrationDescriptorAbsRelative

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_integration_descriptor_abs_relative”, calculated with multiwfn.

The index of this feature is 246 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_integration_descriptor_abs_relative feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceIntegrationDescriptorRelative

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_integration_descriptor_relative”, calculated with multiwfn.

The index of this feature is 247 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_integration_descriptor_relative feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceLocalizationIndex

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_localization_index”, calculated with multiwfn.

The index of this feature is 248 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_localization_index feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceLocalizationIndexAlpha

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_localization_index_alpha”, calculated with multiwfn.

The index of this feature is 249 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_localization_index_alpha feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceLocalizationIndexBeta

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_localization_index_beta”, calculated with multiwfn.

The index of this feature is 250 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_localization_index_beta feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceMonopoleMoment

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_monopole_moment”, calculated with multiwfn.

The index of this feature is 251 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_monopole_moment feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceOctopoleMomentMagnitude

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_octopole_moment_magnitude”, calculated with multiwfn.

The index of this feature is 252 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_octopole_moment_magnitude feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceQuadrupoleMomentMagnitude

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_quadrupole_moment_magnitude”, calculated with multiwfn.

The index of this feature is 253 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_quadrupole_moment_magnitude feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceTracelessQuadrupoleMomentTensorMagnitude

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D atom feature “fuzzy_space_traceless_quadrupole_moment_tensor_magnitude”, calculated with multiwfn.

The index of this feature is 254 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-fuzzy_space_traceless_quadrupole_moment_tensor_magnitude feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DBondFuzzySpaceCondensedLinearResponseKernelMatrixElement

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D bond feature “fuzzy_space_condensed_linear_response_kernel_matrix_element”, calculated with multiwfn.

The index of this feature is 435 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-fuzzy_space_condensed_linear_response_kernel_matrix_element feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DBondFuzzySpaceOverlapIntegrationDescriptor

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D bond feature “fuzzy_space_overlap_integration_descriptor”, calculated with multiwfn.

The index of this feature is 436 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-fuzzy_space_overlap_integration_descriptor feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DBondFuzzySpaceOverlapIntegrationDescriptorNegative

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D bond feature “fuzzy_space_overlap_integration_descriptor_negative”, calculated with multiwfn.

The index of this feature is 437 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-fuzzy_space_overlap_integration_descriptor_negative feature.

class bonafide.features.multiwfn_fuzzy_space.Multiwfn3DBondFuzzySpaceOverlapIntegrationDescriptorPositive

Bases: _Multiwfn3DFuzzySpace

Feature factory for the 3D bond feature “fuzzy_space_overlap_integration_descriptor_positive”, calculated with multiwfn.

The index of this feature is 438 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.fuzzy” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-fuzzy_space_overlap_integration_descriptor_positive feature.

class bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace

Bases: BaseFeaturizer

Parent feature factory for the 3D atom and bond Multiwfn fuzzy space features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_clrk_exists()

Check if the CLRK output file already exists.

If it already exists, it is moved to the current working directory.

Returns:

bool

Whether the CLRK output file already exists.

_parse_delocalization_matrix(files_lines, loc, feature_name)

Extract the delocalization matrix data from the file format and write it to the results dictionary.

Parameters:

files_linesList[str]

The lines of the file containing the delocalization matrix.

locstr

The location (name of the calling method) for error messages.

feature_namestr

The name of the feature.

Returns:

None

_parse_localization_index_block(files_lines, feature_name)

Extract the localization index data from the file format and write it to the results dictionary.

Parameters:

files_linesList[str]

The lines of the file containing the localization indices.

feature_namestr

The name of the feature.

Returns:

None

_read_output_file_atom()

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used read the data for the integration descriptor features.

Returns:

None

_read_output_file_atom2(is_open_shell)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used read the data for the atomic valence and localization index features.

Parameters:

is_open_shellbool

Whether the calculation was performed for an open-shell molecule.

Returns:

None

_read_output_file_atom3()

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used to read the data for all fuzzy space features that are not covered by the other methods (_read_output_file_atom(), _read_output_file_bond(), and _read_output_file_clrk()).

Returns:

None

_read_output_file_bond()

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used read the data for all fuzzy space bond features.

Returns:

None

_read_output_file_clrk(feature_type)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used read the data for the condensed linear response kernel matrix element features, both for atoms and bonds.

Parameters:

feature_typestr

The type of the feature to calculate, either “atom” or “bond”.

Returns:

None

_run_multiwfn(command_list, output_file_prefix=None, select_scheme=True, enforce_closed_shell=None, enforce_open_shell=False)

Run Multiwfn.

Parameters:

command_listList[Union[int, float, str]]

List of commands to be passed to Multiwfn to select the respective fuzzy space analysis method.

output_file_prefixOptional[str], optional

Prefix to be added to the output file name, by default None. If None, the prefix is automatically constructed from the name of the class.

select_schemebool, optional

Whether to select a partitioning scheme for the fuzzy space analysis, by default True.

enforce_closed_shellOptional[str], optional

Whether to enforce closed-shell electronic structure for the calculation, by default None. If set to a string value, the calculation is only run if the molecule is closed-shell.

enforce_open_shellbool, optional

Whether to enforce open-shell electronic structure for the calculation, by default False. If set to True, the calculation is only run if the molecule is open-shell.

Returns:

bool

Returns False if a feature only defined for closed-shell molecules is requested for an open-shell molecule. If the input is correct and Multiwfn is executed, True is returned.

exclude_atoms

integration_grid

n_iterations_becke_partition

partitioning_scheme

radius_becke_partition

real_space_function

bonafide.features.multiwfn_hilbert_space

Hilbert space features from Multiwfn.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMoment

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D atom feature “hilbert_space_contribution_to_system_dipole_moment”, calculated with multiwfn.

The index of this feature is 255 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-hilbert_space_contribution_to_system_dipole_moment feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentElectrons

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D atom feature “hilbert_space_contribution_to_system_dipole_moment_electrons”, calculated with multiwfn.

The index of this feature is 256 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-hilbert_space_contribution_to_system_dipole_moment_electrons feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentElectronsNorm

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D atom feature “hilbert_space_contribution_to_system_dipole_moment_electrons_norm”, calculated with multiwfn.

The index of this feature is 257 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-hilbert_space_contribution_to_system_dipole_moment_electrons_norm feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentNorm

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D atom feature “hilbert_space_contribution_to_system_dipole_moment_norm”, calculated with multiwfn.

The index of this feature is 258 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-hilbert_space_contribution_to_system_dipole_moment_norm feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentNuclearCharge

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D atom feature “hilbert_space_contribution_to_system_dipole_moment_nuclear_charge”, calculated with multiwfn.

The index of this feature is 259 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-hilbert_space_contribution_to_system_dipole_moment_nuclear_charge feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentNuclearChargeNorm

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D atom feature “hilbert_space_contribution_to_system_dipole_moment_nuclear_charge_norm”, calculated with multiwfn.

The index of this feature is 260 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-hilbert_space_contribution_to_system_dipole_moment_nuclear_charge_norm feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceDipoleMoment

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D atom feature “hilbert_space_dipole_moment”, calculated with multiwfn.

The index of this feature is 261 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-hilbert_space_dipole_moment feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceDipoleMomentNorm

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D atom feature “hilbert_space_dipole_moment_norm”, calculated with multiwfn.

The index of this feature is 262 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-hilbert_space_dipole_moment_norm feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceLocalPopulationNumber

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D atom feature “hilbert_space_local_population_number”, calculated with multiwfn.

The index of this feature is 263 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-hilbert_space_local_population_number feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceContributionToSystemDipoleMoment

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D bond feature “hilbert_space_contribution_to_system_dipole_moment”, calculated with multiwfn.

The index of this feature is 440 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-hilbert_space_contribution_to_system_dipole_moment feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceContributionToSystemDipoleMomentNorm

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D bond feature “hilbert_space_contribution_to_system_dipole_moment_norm”, calculated with multiwfn.

The index of this feature is 441 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-hilbert_space_contribution_to_system_dipole_moment_norm feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceDipoleMoment

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D bond feature “hilbert_space_dipole_moment”, calculated with multiwfn.

The index of this feature is 442 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-hilbert_space_dipole_moment feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceDipoleMomentNorm

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D bond feature “hilbert_space_dipole_moment_norm”, calculated with multiwfn.

The index of this feature is 443 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-hilbert_space_dipole_moment_norm feature.

class bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceOverlapPopulation

Bases: _Multiwfn3DHilbertSpace

Feature factory for the 3D bond feature “hilbert_space_overlap_population”, calculated with multiwfn.

The index of this feature is 444 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-bond-hilbert_space_overlap_population feature.

class bonafide.features.multiwfn_hilbert_space._Multiwfn3DHilbertSpace

Bases: BaseFeaturizer

Parent feature factory for the 3D atom and bond Multiwfn Hilbert space features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_read_output_file_atom()

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used to process the atom features.

Returns:

None

_read_output_file_bond()

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used to process the bond features.

Returns:

None

_run_multiwfn(feature_type)

Run Multiwfn.

Parameters:

feature_typestr

The type of the feature to calculate, either “atom” or “bond”.

Returns:

None

bonafide.features.multiwfn_misc

Energy index atom feature from Multiwfn.

class bonafide.features.multiwfn_misc.Multiwfn3DAtomEnergyIndex

Bases: BaseFeaturizer

Feature factory for the 3D atom feature “energy_index”, calculated with multiwfn.

The index of this feature is 232 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.misc” in the _feature_config.toml file.

_read_output_file()

Read the output file from Multiwfn and write the results to the results dictionary.

Returns:

None

_run_multiwfn()

Run Multiwfn.

Returns:

None

calculate()

Calculate the multiwfn3D-atom-energy_index feature.

bonafide.features.multiwfn_orbital

Orbital features from Multiwfn.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMulliken

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_occupied_mulliken”, calculated with multiwfn.

The index of this feature is 264 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_occupied_mulliken feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenAlpha

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_occupied_mulliken_alpha”, calculated with multiwfn.

The index of this feature is 265 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_occupied_mulliken_alpha feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenBeta

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_occupied_mulliken_beta”, calculated with multiwfn.

The index of this feature is 266 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_occupied_mulliken_beta feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenRosSchuit

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_occupied_mulliken_ros_schuit”, calculated with multiwfn.

The index of this feature is 267 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_occupied_mulliken_ros_schuit feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenRosSchuitAlpha

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_occupied_mulliken_ros_schuit_alpha”, calculated with multiwfn.

The index of this feature is 268 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_occupied_mulliken_ros_schuit_alpha feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenRosSchuitBeta

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_occupied_mulliken_ros_schuit_beta”, calculated with multiwfn.

The index of this feature is 269 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_occupied_mulliken_ros_schuit_beta feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenStoutPolitzer

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_occupied_mulliken_stout_politzer”, calculated with multiwfn.

The index of this feature is 270 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_occupied_mulliken_stout_politzer feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenStoutPolitzerAlpha

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_occupied_mulliken_stout_politzer_alpha”, calculated with multiwfn.

The index of this feature is 271 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_occupied_mulliken_stout_politzer_alpha feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenStoutPolitzerBeta

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_occupied_mulliken_stout_politzer_beta”, calculated with multiwfn.

The index of this feature is 272 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_occupied_mulliken_stout_politzer_beta feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMulliken

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_unoccupied_mulliken”, calculated with multiwfn.

The index of this feature is 273 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_unoccupied_mulliken feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenAlpha

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_unoccupied_mulliken_alpha”, calculated with multiwfn.

The index of this feature is 274 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_unoccupied_mulliken_alpha feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenBeta

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_unoccupied_mulliken_beta”, calculated with multiwfn.

The index of this feature is 275 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_unoccupied_mulliken_beta feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenRosSchuit

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_unoccupied_mulliken_ros_schuit”, calculated with multiwfn.

The index of this feature is 276 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_unoccupied_mulliken_ros_schuit feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenRosSchuitAlpha

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_unoccupied_mulliken_ros_schuit_alpha”, calculated with multiwfn.

The index of this feature is 277 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_unoccupied_mulliken_ros_schuit_alpha feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenRosSchuitBeta

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_unoccupied_mulliken_ros_schuit_beta”, calculated with multiwfn.

The index of this feature is 278 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_unoccupied_mulliken_ros_schuit_beta feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenStoutPolitzer

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_unoccupied_mulliken_stout_politzer”, calculated with multiwfn.

The index of this feature is 279 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_unoccupied_mulliken_stout_politzer feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenStoutPolitzerAlpha

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_unoccupied_mulliken_stout_politzer_alpha”, calculated with multiwfn.

The index of this feature is 280 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_unoccupied_mulliken_stout_politzer_alpha feature.

class bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenStoutPolitzerBeta

Bases: _Multiwfn3DAtomMoContribution

Feature factory for the 3D atom feature “mo_contribution_unoccupied_mulliken_stout_politzer_beta”, calculated with multiwfn.

The index of this feature is 281 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.orbital” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-mo_contribution_unoccupied_mulliken_stout_politzer_beta feature.

class bonafide.features.multiwfn_orbital._Multiwfn3DAtomMoContribution

Bases: BaseFeaturizer

Parent feature factory for the 3D atom orbital Multiwfn features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_format_orbital_idx(mo_type, orbital_idx, open_shell)

Format the orbital index to the format required by Multiwfn.

Parameters:

mo_typestr

The type of orbital to consider, either “occupied” or “unoccupied”.

orbital_idxint

The index of the orbital defined by the distance (in orbital counts) to the highest occupied and lowest unoccupied molecular orbital, respectively (HOMO and LUMO).

open_shellUnion[bool, str]

Whether the molecule has an open- or closed-shell electronic structure. This influences input formatting and output processing. This is False for closed-shell cases and either alpha or beta for open-shell cases.

Returns:

str

_description_

_read_output_file()

Read the output file from Multiwfn and write the results to the results dictionary.

Returns:

None

_run_multiwfn(mo_type, orbital_idx, charge_scheme, open_shell)

Run Multiwfn.

Parameters:

mo_typestr

The type of orbital to consider, either “occupied” or “unoccupied”.

orbital_idxint

The index of the orbital defined by the distance (in orbital counts) to the highest occupied and lowest unoccupied molecular orbital, respectively (HOMO and LUMO).

charge_schemestr

The name of the population analysis.

open_shellUnion[bool, str]

Whether the molecule has an open- or closed-shell electronic structure. This influences input formatting and output processing. This is False for closed-shell cases and either alpha or beta for open-shell cases.

Returns:

bool

Returns False if alpha/beta features are requested for closed-shell molecules or the total features for open-shell molecules. If the input is correct and Multiwfn is executed, True is returned.

homo_minus

lumo_plus

bonafide.features.multiwfn_partial_charge

Partial charge features from Multiwfn.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeBecke

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_becke”, calculated with multiwfn.

The index of this feature is 273 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_becke feature.

n_iterations_becke_partition

radius_becke_partition

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeChelpg

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_chelpg”, calculated with multiwfn.

The index of this feature is 283 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

atomic_radii

box_extension_chelpg

calculate()

Calculate the multiwfn3D-atom-partial_charge_chelpg feature.

esp_type

exclude_atoms

grid_spacing_chelpg

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeCm5

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_cm5”, calculated with multiwfn.

The index of this feature is 284 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_cm5 feature.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeCm5Scaled1point2

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_cm5_scaled_1point2”, calculated with multiwfn.

The index of this feature is 285 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_cm5_scaled_1point2 feature.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeCorrectedHirshfeld

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_corrected_hirshfeld”, calculated with multiwfn.

The index of this feature is 286 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_corrected_hirshfeld feature.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeEem

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_eem”, calculated with multiwfn.

The index of this feature is 287 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_eem feature.

eem_parameters

electronic_struc_n

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeHirshfeld

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_hirshfeld”, calculated with multiwfn.

The index of this feature is 288 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_hirshfeld feature.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeLowdin

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_lowdin”, calculated with multiwfn.

The index of this feature is 289 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_lowdin feature.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMerzKollmann

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_merz_kollmann”, calculated with multiwfn.

The index of this feature is 290 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

atomic_radii

calculate()

Calculate the multiwfn3D-atom-partial_charge_merz_kollmann feature.

esp_type

exclude_atoms

fitting_points_settings_merz_kollmann

n_points_angstrom2_merz_kollmann

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMulliken

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_mulliken”, calculated with multiwfn.

The index of this feature is 291 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_mulliken feature.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMullikenBickelhaupt

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_mulliken_bickelhaupt”, calculated with multiwfn.

The index of this feature is 292 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_mulliken_bickelhaupt feature.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMullikenRosSchuit

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_mulliken_ros_schuit”, calculated with multiwfn.

The index of this feature is 293 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_mulliken_ros_schuit feature.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMullikenStoutPolitzer

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_mulliken_stout_politzer”, calculated with multiwfn.

The index of this feature is 294 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_mulliken_stout_politzer feature.

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_resp_chelpg_one_stage”, calculated with multiwfn.

The index of this feature is 295 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

atomic_radii

box_extension_chelpg

calculate()

Calculate the multiwfn3D-atom-partial_charge_resp_chelpg_one_stage feature.

ch_equivalence_constraint_resp

convergence_threshold_resp

esp_type

grid_spacing_chelpg

n_iterations_resp

restraint_one_stage_resp

restraint_stage1_resp

restraint_stage2_resp

tightness_resp

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_resp_chelpg_two_stage”, calculated with multiwfn.

The index of this feature is 296 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

atomic_radii

box_extension_chelpg

calculate()

Calculate the multiwfn3D-atom-partial_charge_resp_chelpg_two_stage feature.

ch_equivalence_constraint_resp

convergence_threshold_resp

esp_type

grid_spacing_chelpg

n_iterations_resp

restraint_one_stage_resp

restraint_stage1_resp

restraint_stage2_resp

tightness_resp

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_resp_merz_kollmann_one_stage”, calculated with multiwfn.

The index of this feature is 297 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

atomic_radii

calculate()

Calculate the multiwfn3D-atom-partial_charge_resp_merz_kollmann_one_stage feature.

ch_equivalence_constraint_resp

convergence_threshold_resp

esp_type

fitting_points_settings_merz_kollmann

n_iterations_resp

n_points_angstrom2_merz_kollmann

restraint_one_stage_resp

restraint_stage1_resp

restraint_stage2_resp

tightness_resp

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_resp_merz_kollmann_two_stage”, calculated with multiwfn.

The index of this feature is 298 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

atomic_radii

calculate()

Calculate the multiwfn3D-atom-partial_charge_resp_merz_kollmann_two_stage feature.

ch_equivalence_constraint_resp

convergence_threshold_resp

esp_type

fitting_points_settings_merz_kollmann

n_iterations_resp

n_points_angstrom2_merz_kollmann

restraint_one_stage_resp

restraint_stage1_resp

restraint_stage2_resp

tightness_resp

class bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeVdd

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “partial_charge_vdd”, calculated with multiwfn.

The index of this feature is 299 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-partial_charge_vdd feature.

bonafide.features.multiwfn_population

Atom and orbital population features from Multiwfn.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdin

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_lowdin”, calculated with multiwfn.

The index of this feature is 300 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_lowdin feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_alpha”, calculated with multiwfn.

The index of this feature is 301 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_beta”, calculated with multiwfn.

The index of this feature is 302 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinD

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_lowdin_d”, calculated with multiwfn.

The index of this feature is 303 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_lowdin_d feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinDAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_d_alpha”, calculated with multiwfn.

The index of this feature is 304 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinDBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_d_beta”, calculated with multiwfn.

The index of this feature is 305 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinF

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_lowdin_f”, calculated with multiwfn.

The index of this feature is 306 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_lowdin_f feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinFAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_f_alpha”, calculated with multiwfn.

The index of this feature is 307 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinFBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_f_beta”, calculated with multiwfn.

The index of this feature is 308 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinG

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_lowdin_g”, calculated with multiwfn.

The index of this feature is 309 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_lowdin_g feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinGAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_g_alpha”, calculated with multiwfn.

The index of this feature is 310 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinGBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_g_beta”, calculated with multiwfn.

The index of this feature is 311 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinH

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_lowdin_h”, calculated with multiwfn.

The index of this feature is 312 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_lowdin_h feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinHAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_h_alpha”, calculated with multiwfn.

The index of this feature is 313 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinHBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_h_beta”, calculated with multiwfn.

The index of this feature is 314 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinP

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_lowdin_p”, calculated with multiwfn.

The index of this feature is 315 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_lowdin_p feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinPAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_p_alpha”, calculated with multiwfn.

The index of this feature is 316 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinPBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_p_beta”, calculated with multiwfn.

The index of this feature is 317 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinS

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_lowdin_s”, calculated with multiwfn.

The index of this feature is 318 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_lowdin_s feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinSAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_s_alpha”, calculated with multiwfn.

The index of this feature is 319 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinSBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinAlphaBetaMixin

Feature factory for the 3D atom feature “population_lowdin_s_beta”, calculated with multiwfn.

The index of this feature is 320 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMulliken

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken”, calculated with multiwfn.

The index of this feature is 321 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_alpha”, calculated with multiwfn.

The index of this feature is 322 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_beta”, calculated with multiwfn.

The index of this feature is 323 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenBickelhaupt

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken_bickelhaupt”, calculated with multiwfn.

The index of this feature is 324 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken_bickelhaupt feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenBickelhauptAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenBickelhauptAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_bickelhaupt_alpha”, calculated with multiwfn.

The index of this feature is 325 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenBickelhauptBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenBickelhauptAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_bickelhaupt_beta”, calculated with multiwfn.

The index of this feature is 326 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenD

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken_d”, calculated with multiwfn.

The index of this feature is 327 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken_d feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenDAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_d_alpha”, calculated with multiwfn.

The index of this feature is 328 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenDBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_d_beta”, calculated with multiwfn.

The index of this feature is 329 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenF

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken_f”, calculated with multiwfn.

The index of this feature is 330 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken_f feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenFAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_f_alpha”, calculated with multiwfn.

The index of this feature is 331 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenFBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_f_beta”, calculated with multiwfn.

The index of this feature is 332 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenG

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken_g”, calculated with multiwfn.

The index of this feature is 333 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken_g feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenGAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_g_alpha”, calculated with multiwfn.

The index of this feature is 334 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenGBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_g_beta”, calculated with multiwfn.

The index of this feature is 335 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenH

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken_h”, calculated with multiwfn.

The index of this feature is 336 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken_h feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenHAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_h_alpha”, calculated with multiwfn.

The index of this feature is 337 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenHBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_h_beta”, calculated with multiwfn.

The index of this feature is 338 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenP

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken_p”, calculated with multiwfn.

The index of this feature is 339 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken_p feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenPAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_p_alpha”, calculated with multiwfn.

The index of this feature is 340 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenPBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_p_beta”, calculated with multiwfn.

The index of this feature is 341 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenRosSchuit

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken_ros_schuit”, calculated with multiwfn.

The index of this feature is 342 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken_ros_schuit feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenRosSchuitAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenRosSchuitAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_ros_schuit_alpha”, calculated with multiwfn.

The index of this feature is 343 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenRosSchuitBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenRosSchuitAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_ros_schuit_beta”, calculated with multiwfn.

The index of this feature is 344 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenS

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken_s”, calculated with multiwfn.

The index of this feature is 345 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken_s feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenSAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_s_alpha”, calculated with multiwfn.

The index of this feature is 346 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenSBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_s_beta”, calculated with multiwfn.

The index of this feature is 347 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenStoutPolitzer

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “population_mulliken_stout_politzer”, calculated with multiwfn.

The index of this feature is 348 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-population_mulliken_stout_politzer feature.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenStoutPolitzerAlpha

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenStoutPolitzerAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_stout_politzer_alpha”, calculated with multiwfn.

The index of this feature is 349 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenStoutPolitzerBeta

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenStoutPolitzerAlphaBetaMixin

Feature factory for the 3D atom feature “population_mulliken_stout_politzer_beta”, calculated with multiwfn.

The index of this feature is 350 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_population._LowdinAlphaBetaMixin

Bases: object

Mixin class for the Lowdin alpha and beta atom population features.

calculate()

Calculate the features.

class bonafide.features.multiwfn_population._MullikenAlphaBetaMixin

Bases: object

Mixin class for the Mulliken alpha and beta atom population features.

calculate()

Calculate the features.

class bonafide.features.multiwfn_population._MullikenBickelhauptAlphaBetaMixin

Bases: object

Mixin class for the Mulliken-Bickelhaupt alpha and beta atom population features.

calculate()

Calculate the features.

class bonafide.features.multiwfn_population._MullikenRosSchuitAlphaBetaMixin

Bases: object

Mixin class for the Mulliken-Ros-Schuit alpha and beta atom population features.

calculate()

Calculate the features.

class bonafide.features.multiwfn_population._MullikenStoutPolitzerAlphaBetaMixin

Bases: object

Mixin class for the Mulliken-Stout-Politzer alpha and beta atom population features.

calculate()

Calculate the features.

bonafide.features.multiwfn_population_analysis

Base class for all population analyses features from Multiwfn.

class bonafide.features.multiwfn_population_analysis._Multiwfn3DAtomPopulationAnalysis

Bases: BaseFeaturizer

Parent feature factory for the 3D atom population analysis Multiwfn features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_read_output_file(feature_name)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used to read the data for the Becke, CM5, scaled CM5, Hirsheld, corrected Hirshfeld, and Voronoi deformation density charges.

Parameters:

feature_namestr

The name of the feature.

Returns:

None

_read_output_file2(scheme_name)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is only used for closed-shell molecules (multiplicity = 1). The respective method for open-shell molecules is _read_output_file3(). _read_output_file2() is used to read the data for the Lowdin, Mulliken and its respective modified versions partial charges as well as for the data for the individual Lowdin and Mulliken orbital population features.

Parameters:

scheme_namestr

The name of the population analysis method.

Returns:

None

_read_output_file3(scheme_name)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is only used for open-shell molecules (multiplicity != 1). The respective method for closed-shell molecules is _read_output_file2(). _read_output_file3() is used to read the data for the Lowdin, Mulliken and its respective modified versions partial charges as well as for the data for the individual Lowdin and Mulliken orbital population features. Additionally, it is used to read the spin population data.

Parameters:

scheme_namestr

The name of the population analysis method.

Returns:

None

_read_output_file4(feature_name)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used to read the data for the CHELPG, Merz-Kollmann, and RESP charges.

Parameters:

feature_namestr

The name of the feature.

Returns:

None

_read_output_file5(feature_name)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used to read the data for the EEM charges.

Parameters:

feature_namestr

The name of the feature.

Returns:

None

_run_multiwfn(command_list, from_eem=False, from_resp_chelpg=False)

Run Multiwfn.

Parameters:

command_listList[Union[int, float, str]]

The list of commands to be passed to Multiwfn to select the respective population analysis method and options.

from_eembool, optional

Whether the Multiwfn run is for EEM charges. Default is False.

from_resp_chelpgbool, optional

Whether the Multiwfn run is for RESP charges. Default is False.

Returns:

None

bonafide.features.multiwfn_spin_population

Atom and orbital spin population features from Multiwfn.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationLowdin

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinMixin

Feature factory for the 3D atom feature “spin_population_lowdin”, calculated with multiwfn.

The index of this feature is 351 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationLowdinD

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinMixin

Feature factory for the 3D atom feature “spin_population_lowdin_d”, calculated with multiwfn.

The index of this feature is 352 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationLowdinF

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinMixin

Feature factory for the 3D atom feature “spin_population_lowdin_f”, calculated with multiwfn.

The index of this feature is 353 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationLowdinG

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinMixin

Feature factory for the 3D atom feature “spin_population_lowdin_g”, calculated with multiwfn.

The index of this feature is 354 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationLowdinH

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinMixin

Feature factory for the 3D atom feature “spin_population_lowdin_h”, calculated with multiwfn.

The index of this feature is 355 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationLowdinP

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinMixin

Feature factory for the 3D atom feature “spin_population_lowdin_p”, calculated with multiwfn.

The index of this feature is 356 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationLowdinS

Bases: _Multiwfn3DAtomPopulationAnalysis, _LowdinMixin

Feature factory for the 3D atom feature “spin_population_lowdin_s”, calculated with multiwfn.

The index of this feature is 357 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMulliken

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenMixin

Feature factory for the 3D atom feature “spin_population_mulliken”, calculated with multiwfn.

The index of this feature is 358 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenBickelhaupt

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “spin_population_mulliken_bickelhaupt”, calculated with multiwfn.

The index of this feature is 359 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-spin_population_mulliken_bickelhaupt feature.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenD

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenMixin

Feature factory for the 3D atom feature “spin_population_mulliken_d”, calculated with multiwfn.

The index of this feature is 360 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenF

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenMixin

Feature factory for the 3D atom feature “spin_population_mulliken_f”, calculated with multiwfn.

The index of this feature is 361 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenG

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenMixin

Feature factory for the 3D atom feature “spin_population_mulliken_g”, calculated with multiwfn.

The index of this feature is 362 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenH

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenMixin

Feature factory for the 3D atom feature “spin_population_mulliken_h”, calculated with multiwfn.

The index of this feature is 363 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenP

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenMixin

Feature factory for the 3D atom feature “spin_population_mulliken_p”, calculated with multiwfn.

The index of this feature is 364 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenRosSchuit

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “spin_population_mulliken_ros_schuit”, calculated with multiwfn.

The index of this feature is 365 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-spin_population_mulliken_ros_schuit feature.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenS

Bases: _Multiwfn3DAtomPopulationAnalysis, _MullikenMixin

Feature factory for the 3D atom feature “spin_population_mulliken_s”, calculated with multiwfn.

The index of this feature is 366 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

class bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenStoutPolitzer

Bases: _Multiwfn3DAtomPopulationAnalysis

Feature factory for the 3D atom feature “spin_population_mulliken_stout_politzer”, calculated with multiwfn.

The index of this feature is 367 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.population” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-spin_population_mulliken_stout_politzer feature.

class bonafide.features.multiwfn_spin_population._LowdinMixin

Bases: object

Mixin class for the Lowdin atom spin population features.

calculate()

Calculate the features.

class bonafide.features.multiwfn_spin_population._MullikenMixin

Bases: object

Mixin class for the Mulliken atom spin population features.

calculate()

Calculate the features.

bonafide.features.multiwfn_surface

Molecular surface features from Multiwfn.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceAverageLocalIonizationEnergyMax

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_average_local_ionization_energy_max”, calculated with multiwfn.

The index of this feature is 368 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_average_local_ionization_energy_max feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceAverageLocalIonizationEnergyMean

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_average_local_ionization_energy_mean”, calculated with multiwfn.

The index of this feature is 369 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_average_local_ionization_energy_mean feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceAverageLocalIonizationEnergyMin

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_average_local_ionization_energy_min”, calculated with multiwfn.

The index of this feature is 370 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_average_local_ionization_energy_min feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMax

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electron_delocalization_range_function_max”, calculated with multiwfn.

The index of this feature is 371 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electron_delocalization_range_function_max feature.

length_scale

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMean

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electron_delocalization_range_function_mean”, calculated with multiwfn.

The index of this feature is 372 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electron_delocalization_range_function_mean feature.

length_scale

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMin

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electron_delocalization_range_function_min”, calculated with multiwfn.

The index of this feature is 373 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electron_delocalization_range_function_min feature.

length_scale

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDensityMax

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electron_density_max”, calculated with multiwfn.

The index of this feature is 374 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electron_density_max feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDensityMean

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electron_density_mean”, calculated with multiwfn.

The index of this feature is 375 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electron_density_mean feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDensityMin

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electron_density_min”, calculated with multiwfn.

The index of this feature is 376 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electron_density_min feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialBalanceOfCharges

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electrostatic_potential_balance_of_charges”, calculated with multiwfn.

The index of this feature is 377 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electrostatic_potential_balance_of_charges feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialBalanceOfChargesTimesVariance

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electrostatic_potential_balance_of_charges_times_variance”, calculated with multiwfn.

The index of this feature is 378 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electrostatic_potential_balance_of_charges_times_variance feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialInternalChargeSeparation

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electrostatic_potential_internal_charge_separation”, calculated with multiwfn.

The index of this feature is 379 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electrostatic_potential_internal_charge_separation feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialMax

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electrostatic_potential_max”, calculated with multiwfn.

The index of this feature is 380 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electrostatic_potential_max feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialMean

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electrostatic_potential_mean”, calculated with multiwfn.

The index of this feature is 381 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electrostatic_potential_mean feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialMin

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_electrostatic_potential_min”, calculated with multiwfn.

The index of this feature is 382 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_electrostatic_potential_min feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAffinityMax

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_local_electron_affinity_max”, calculated with multiwfn.

The index of this feature is 383 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_local_electron_affinity_max feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAffinityMean

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_local_electron_affinity_mean”, calculated with multiwfn.

The index of this feature is 384 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_local_electron_affinity_mean feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAffinityMin

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_local_electron_affinity_min”, calculated with multiwfn.

The index of this feature is 385 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_local_electron_affinity_min feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAttachmentEnergyMax

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_local_electron_attachment_energy_max”, calculated with multiwfn.

The index of this feature is 386 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_local_electron_attachment_energy_max feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAttachmentEnergyMean

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_local_electron_attachment_energy_mean”, calculated with multiwfn.

The index of this feature is 387 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_local_electron_attachment_energy_mean feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAttachmentEnergyMin

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_local_electron_attachment_energy_min”, calculated with multiwfn.

The index of this feature is 388 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_local_electron_attachment_energy_min feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMax

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_orbital_overlap_length_function_max”, calculated with multiwfn.

The index of this feature is 389 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_orbital_overlap_length_function_max feature.

orbital_overlap_edr_option

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMean

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_orbital_overlap_length_function_mean”, calculated with multiwfn.

The index of this feature is 390 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_orbital_overlap_length_function_mean feature.

orbital_overlap_edr_option

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMin

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_orbital_overlap_length_function_min”, calculated with multiwfn.

The index of this feature is 391 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_orbital_overlap_length_function_min feature.

orbital_overlap_edr_option

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceSignSecondLargestEigenvalueElectronDensityHessianMax

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_sign_second_largest_eigenvalue_electron_density_hessian_max”, calculated with multiwfn.

The index of this feature is 392 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_sign_second_largest_eigenvalue_electron_density_hessian_max feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceSignSecondLargestEigenvalueElectronDensityHessianMean

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_sign_second_largest_eigenvalue_electron_density_hessian_mean”, calculated with multiwfn.

The index of this feature is 393 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_sign_second_largest_eigenvalue_electron_density_hessian_mean feature.

class bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceSignSecondLargestEigenvalueElectronDensityHessianMin

Bases: _Multiwfn3DAtomSurface

Feature factory for the 3D atom feature “surface_sign_second_largest_eigenvalue_electron_density_hessian_min”, calculated with multiwfn.

The index of this feature is 394 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.surface” in the _feature_config.toml file.

calculate()

Calculate the multiwfn3D-atom-surface_sign_second_largest_eigenvalue_electron_density_hessian_min feature.

class bonafide.features.multiwfn_surface._Multiwfn3DAtomSurface

Bases: BaseFeaturizer

Parent feature factory for the 3D atom surface Multiwfn features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_read_output_file(id_string, feature_name)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used to read the data for the average local ionization energy features.

Parameters:

id_stringstr

A feature-specific identifier string to distinguish the output files of different features.

feature_namestr

The name of the feature.

Returns:

None

_read_output_file2(id_string, feature_name)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used to read the data for all surface features except for the average local ionization energy and the electrostatic potential features.

Parameters:

id_stringstr

A feature-specific identifier string to distinguish the output files of different features.

feature_namestr

The name of the feature.

Returns:

None

_read_output_file3(id_string, feature_name)

Read the output file from Multiwfn and write the results to the results dictionary.

This method is used to read the data for the electrostatic potential features.

Parameters:

id_stringstr

A feature-specific identifier string to distinguish the output files of different features.

feature_namestr

The name of the feature.

Returns:

None

_run_multiwfn(mapping_function_idx, id_string)

Run Multiwfn.

Parameters:

mapping_function_idxUnion[int, str]

The Multiwfn option(s) to select the real space function requested by the user along with additional input if required.

id_stringstr

A feature-specific identifier string to distinguish the output files of different features.

Returns:

None

grid_point_spacing

surface_definition

surface_iso_value

bonafide.features.multiwfn_topology_atom

Atom topology features from Multiwfn.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyAverageLocalIonizationEnergy

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_average_local_ionization_energy”, calculated with multiwfn.

The index of this feature is 395 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyDeltaGHirshfeld

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_delta_g_hirshfeld”, calculated with multiwfn.

The index of this feature is 396 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyDeltaGPromolecular

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_delta_g_promolecular”, calculated with multiwfn.

The index of this feature is 397 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyElectronDensity

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_electron_density”, calculated with multiwfn.

The index of this feature is 398 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyElectronDensityAlpha

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_electron_density_alpha”, calculated with multiwfn.

The index of this feature is 399 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyElectronDensityBeta

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_electron_density_beta”, calculated with multiwfn.

The index of this feature is 400 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyElectronDensityEllipticity

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_electron_density_ellipticity”, calculated with multiwfn.

The index of this feature is 401 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyElectronLocalizationFunction

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_electron_localization_function”, calculated with multiwfn.

The index of this feature is 402 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyElectrostaticPotential

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_electrostatic_potential”, calculated with multiwfn.

The index of this feature is 403 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyElectrostaticPotentialElectrons

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_electrostatic_potential_electrons”, calculated with multiwfn.

The index of this feature is 404 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyElectrostaticPotentialNuclearCharges

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_electrostatic_potential_nuclear_charges”, calculated with multiwfn.

The index of this feature is 405 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyEnergyDensity

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_energy_density”, calculated with multiwfn.

The index of this feature is 406 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyEtaIndex

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_eta_index”, calculated with multiwfn.

The index of this feature is 407 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyGradientComponentsXYZ

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_gradient_components_x_y_z”, calculated with multiwfn.

The index of this feature is 408 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyGradientNorm

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_gradient_norm”, calculated with multiwfn.

The index of this feature is 409 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyHamiltonianKineticEnergy

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_hamiltonian_kinetic_energy”, calculated with multiwfn.

The index of this feature is 410 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyHessianDeterminant

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_hessian_determinant”, calculated with multiwfn.

The index of this feature is 411 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyHessianEigenvalues

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_hessian_eigenvalues”, calculated with multiwfn.

The index of this feature is 412 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyInteractionRegionIndicator

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_interaction_region_indicator”, calculated with multiwfn.

The index of this feature is 413 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyLagrangianKineticEnergy

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_lagrangian_kinetic_energy”, calculated with multiwfn.

The index of this feature is 414 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyLaplacianComponentsXYZ

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_laplacian_components_x_y_z”, calculated with multiwfn.

The index of this feature is 415 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyLaplacianOfElectronDensity

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_laplacian_of_electron_density”, calculated with multiwfn.

The index of this feature is 416 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyLaplacianTotal

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_laplacian_total”, calculated with multiwfn.

The index of this feature is 417 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyLocalInformationEntropy

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_local_information_entropy”, calculated with multiwfn.

The index of this feature is 418 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyLocalizedOrbitalLocator

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_localized_orbital_locator”, calculated with multiwfn.

The index of this feature is 419 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyPotentialEnergyDensity

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_potential_energy_density”, calculated with multiwfn.

The index of this feature is 420 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyReducedDensityGradient

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_reduced_density_gradient”, calculated with multiwfn.

The index of this feature is 421 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyReducedDensityGradientPromolecular

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_reduced_density_gradient_promolecular”, calculated with multiwfn.

The index of this feature is 422 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologySignSecondLargestEigenvalueElectronDensityHessian

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_sign_second_largest_eigenvalue_electron_density_hessian”, calculated with multiwfn.

The index of this feature is 423 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologySignSecondLargestEigenvalueElectronDensityHessianPromolecular

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_sign_second_largest_eigenvalue_electron_density_hessian_promolecular”, calculated with multiwfn.

The index of this feature is 424 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologySpinDensity

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_spin_density”, calculated with multiwfn.

The index of this feature is 425 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom.Multiwfn3DAtomTopologyVdwPotential

Bases: _Multiwfn3DAtomTopology

Feature factory for the 3D atom feature “topology_vdw_potential”, calculated with multiwfn.

The index of this feature is 426 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_atom._Multiwfn3DAtomTopology

Bases: BaseFeaturizer

Parent feature factory for the 3D atom topology Multiwfn features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

_read_atom_prop_file()

Read the output file from Multiwfn and write the results to the results dictionary.

Returns:

None

_run_multiwfn()

Run Multiwfn.

Returns:

None

calculate()

Calculate the Multiwfn atom topology features.

bonafide.features.multiwfn_topology_bond

Bond topology features from Multiwfn.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpAverageLocalIonizationEnergy

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_average_local_ionization_energy”, calculated with multiwfn.

The index of this feature is 446 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpCoordinates

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_coordinates”, calculated with multiwfn.

The index of this feature is 447 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpDeltaGHirshfeld

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_delta_g_hirshfeld”, calculated with multiwfn.

The index of this feature is 448 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpDeltaGPromolecular

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_delta_g_promolecular”, calculated with multiwfn.

The index of this feature is 449 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpDistanceEndAtom

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_distance_end_atom”, calculated with multiwfn.

The index of this feature is 450 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpDistanceStartAtom

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_distance_start_atom”, calculated with multiwfn.

The index of this feature is 451 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpElectronDensity

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_electron_density”, calculated with multiwfn.

The index of this feature is 452 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpElectronDensityAlpha

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_electron_density_alpha”, calculated with multiwfn.

The index of this feature is 453 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpElectronDensityBeta

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_electron_density_beta”, calculated with multiwfn.

The index of this feature is 454 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpElectronDensityEllipticity

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_electron_density_ellipticity”, calculated with multiwfn.

The index of this feature is 455 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpElectronLocalizationFunction

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_electron_localization_function”, calculated with multiwfn.

The index of this feature is 456 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpElectrostaticPotential

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_electrostatic_potential”, calculated with multiwfn.

The index of this feature is 457 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpElectrostaticPotentialElectrons

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_electrostatic_potential_electrons”, calculated with multiwfn.

The index of this feature is 458 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpElectrostaticPotentialNuclearCharges

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_electrostatic_potential_nuclear_charges”, calculated with multiwfn.

The index of this feature is 459 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpEnergyDensity

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_energy_density”, calculated with multiwfn.

The index of this feature is 460 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpEtaIndex

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_eta_index”, calculated with multiwfn.

The index of this feature is 461 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpGradientComponentsXYZ

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_gradient_components_x_y_z”, calculated with multiwfn.

The index of this feature is 462 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpGradientNorm

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_gradient_norm”, calculated with multiwfn.

The index of this feature is 463 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpHamiltonianKineticEnergy

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_hamiltonian_kinetic_energy”, calculated with multiwfn.

The index of this feature is 464 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpHessianDeterminant

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_hessian_determinant”, calculated with multiwfn.

The index of this feature is 465 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpHessianEigenvalues

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_hessian_eigenvalues”, calculated with multiwfn.

The index of this feature is 466 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpInteractionRegionIndicator

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_interaction_region_indicator”, calculated with multiwfn.

The index of this feature is 467 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpLagrangianKineticEnergy

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_lagrangian_kinetic_energy”, calculated with multiwfn.

The index of this feature is 468 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpLaplacianComponentsXYZ

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_laplacian_components_x_y_z”, calculated with multiwfn.

The index of this feature is 469 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpLaplacianOfElectronDensity

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_laplacian_of_electron_density”, calculated with multiwfn.

The index of this feature is 470 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpLaplacianTotal

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_laplacian_total”, calculated with multiwfn.

The index of this feature is 471 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpLocalInformationEntropy

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_local_information_entropy”, calculated with multiwfn.

The index of this feature is 472 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpLocalizedOrbitalLocator

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_localized_orbital_locator”, calculated with multiwfn.

The index of this feature is 473 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpPotentialEnergyDensity

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_potential_energy_density”, calculated with multiwfn.

The index of this feature is 474 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpReducedDensityGradient

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_reduced_density_gradient”, calculated with multiwfn.

The index of this feature is 475 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpReducedDensityGradientPromolecular

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_reduced_density_gradient_promolecular”, calculated with multiwfn.

The index of this feature is 476 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpRelativeBondPosition

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_relative_bond_position”, calculated with multiwfn.

The index of this feature is 477 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpSignSecondLargestEigenvalueElectronDensityHessian

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_sign_second_largest_eigenvalue_electron_density_hessian”, calculated with multiwfn.

The index of this feature is 478 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpSignSecondLargestEigenvalueElectronDensityHessianPromolecular

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_sign_second_largest_eigenvalue_electron_density_hessian_promolecular”, calculated with multiwfn.

The index of this feature is 479 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpSpinDensity

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_spin_density”, calculated with multiwfn.

The index of this feature is 480 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyBcpVdwPotential

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_bcp_vdw_potential”, calculated with multiwfn.

The index of this feature is 481 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyCpIndex

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_cp_index”, calculated with multiwfn.

The index of this feature is 482 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond.Multiwfn3DBondTopologyCpType

Bases: _Multiwfn3DBondTopology

Feature factory for the 3D bond feature “topology_cp_type”, calculated with multiwfn.

The index of this feature is 483 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “multiwfn.topology” in the _feature_config.toml file.

class bonafide.features.multiwfn_topology_bond._Multiwfn3DBondTopology

Bases: BaseFeaturizer

Parent feature factory for the 3D bond topology Multiwfn features.

For details, please refer to the Multiwfn manual (http://sobereva.com/multiwfn/, last accessed on 12.09.2025).

static _get_distance(data, to, bond_obj, mol_obj)

Calculate the distance of a bond critical point to one of the atoms forming the bond.

Parameters:

dataDict[str, Any]

The dictionary containing the coordinates of the bond critical point.

tostr

Whether to calculate the distance to the “start” or “end” atom of the bond.

bond_objChem.rdchem.Bond

The RDKit bond object.

mol_objChem.rdchem.Mol

The RDKit molecule object.

Returns:

Tuple[float, NDArray[np.float64]]

The distance of the bond critical point to the respective atom and that atom’s cartesian coordinates.

static _get_relative_bond_position(start_atom_coordinates, end_atom_coordinates, distance_start_atom)

Calculate the relative position of a bond critical point along its respective bond.

Parameters:

start_atom_coordinatesNDArray[np.float64]

The cartesian coordinates of the start atom of the bond.

end_atom_coordinatesNDArray[np.float64]

The cartesian coordinates of the end atom of the bond.

distance_start_atomfloat

The distance of the bond critical point to the start atom of the bond.

Returns:

float

The ratio between the bond length and the distance of the bond critical point to the start atom of the bond.

_read_cp_prop_file()

Read the output file from Multiwfn and write the results to the results dictionary.

Returns:

None

_run_multiwfn()

Run Multiwfn.

Returns:

None

calculate()

Calculate the Multiwfn bond topology features.

neighbor_distance_cutoff

step_size

bonafide.features.oxidation_state

Oxidation state feature.

class bonafide.features.oxidation_state.Bonafide2DAtomOxidationState

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “oxidation_state”, implemented within this package.

The index of this feature is 36 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.oxidation_state” in the _feature_config.toml file.

_periodic_table

calculate()

Calculate the bonafide2D-atom-oxidation_state feature.

en_scale

bonafide.features.qmdesc_

Atom and bond features from qmdesc.

class bonafide.features.qmdesc_.Qmdesc2DAtomFukuiDual

Bases: _Qmdesc2DAtom

Feature factory for the 2D atom feature “fukui_dual”, calculated with qmdesc.

The index of this feature is 484 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “qmdesc” in the _feature_config.toml file.

class bonafide.features.qmdesc_.Qmdesc2DAtomFukuiMinus

Bases: _Qmdesc2DAtom

Feature factory for the 2D atom feature “fukui_minus”, calculated with qmdesc.

The index of this feature is 485 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “qmdesc” in the _feature_config.toml file.

class bonafide.features.qmdesc_.Qmdesc2DAtomFukuiPlus

Bases: _Qmdesc2DAtom

Feature factory for the 2D atom feature “fukui_plus”, calculated with qmdesc.

The index of this feature is 486 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “qmdesc” in the _feature_config.toml file.

class bonafide.features.qmdesc_.Qmdesc2DAtomNmrChemicalShift

Bases: _Qmdesc2DAtom

Feature factory for the 2D atom feature “nmr_chemical_shift”, calculated with qmdesc.

The index of this feature is 487 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “qmdesc” in the _feature_config.toml file.

class bonafide.features.qmdesc_.Qmdesc2DAtomPartialCharge

Bases: _Qmdesc2DAtom

Feature factory for the 2D atom feature “partial_charge”, calculated with qmdesc.

The index of this feature is 488 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “qmdesc” in the _feature_config.toml file.

class bonafide.features.qmdesc_.Qmdesc2DBondBondLength

Bases: _Qmdesc2DBond

Feature factory for the 2D bond feature “bond_length”, calculated with qmdesc.

The index of this feature is 489 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “qmdesc” in the _feature_config.toml file.

class bonafide.features.qmdesc_.Qmdesc2DBondBondOrder

Bases: _Qmdesc2DBond

Feature factory for the 2D bond feature “bond_order”, calculated with qmdesc.

The index of this feature is 490 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “qmdesc” in the _feature_config.toml file.

class bonafide.features.qmdesc_._Qmdesc2DAtom

Bases: BaseFeaturizer

Parent feature factory for the 2D atom qmdesc features.

_run_qmdesc()

Run qmdesc and write the atom features to the results dictionary.

Returns:

None

calculate()

Calculate the qmdesc atom features.

class bonafide.features.qmdesc_._Qmdesc2DBond

Bases: BaseFeaturizer

Parent feature factory for qmdesc’s bond features.

_run_qmdesc()

Run qmdesc and write the bond features to the results dictionary.

Returns:

None

calculate()

Calculate the qmdesc bond features.

bonafide.features.rdkit_atom

RDKit features for atoms.

class bonafide.features.rdkit_atom.Rdkit2DAtomAtomMapNumber

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “atom_map_number”, calculated with rdkit.

The index of this feature is 491 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-atom_map_number feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomAtomicNumber

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “atomic_number”, calculated with rdkit.

The index of this feature is 492 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-atomic_number feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomChiralTag

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “chiral_tag”, calculated with rdkit.

The index of this feature is 493 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-chiral_tag feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomDegree

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “degree”, calculated with rdkit.

The index of this feature is 494 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-degree feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomEstate

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “estate”, calculated with rdkit.

The index of this feature is 495 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-estate feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomExplicitValence

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “explicit_valence”, calculated with rdkit.

The index of this feature is 496 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-explicit_valence feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomFormalCharge

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “formal_charge”, calculated with rdkit.

The index of this feature is 497 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-formal_charge feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomGasteigerCharge

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “gasteiger_charge”, calculated with rdkit.

The index of this feature is 498 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-gasteiger_charge and rdkit2D-atom-gasteiger_h_charge feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomGasteigerHCharge

Bases: Rdkit2DAtomGasteigerCharge

Feature factory for the 2D atom feature “gasteiger_h_charge”, calculated with rdkit.

The index of this feature is 499 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

class bonafide.features.rdkit_atom.Rdkit2DAtomHybridization

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “hybridization”, calculated with rdkit.

The index of this feature is 500 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-hybridization feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomImplicitValence

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “implicit_valence”, calculated with rdkit.

The index of this feature is 501 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-implicit_valence feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomIsAromatic

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “is_aromatic”, calculated with rdkit.

The index of this feature is 502 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-is_aromatic feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomIsotope

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “isotope”, calculated with rdkit.

The index of this feature is 503 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-isotope feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomLabuteAsaContribution

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “labute_asa_contribution”, calculated with rdkit.

The index of this feature is 504 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-labute_asa_contribution feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomMass

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “mass”, calculated with rdkit.

The index of this feature is 505 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-mass feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomNExplicitH

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “n_explicit_h”, calculated with rdkit.

The index of this feature is 506 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-n_explicit_h feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomNImplicitH

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “n_implicit_h”, calculated with rdkit.

The index of this feature is 507 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-n_implicit_h feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomNNeighbors

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “n_neighbors”, calculated with rdkit.

The index of this feature is 508 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-n_neighbors feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomNRadicalElectrons

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “n_radical_electrons”, calculated with rdkit.

The index of this feature is 509 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-n_radical_electrons feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomNeighboringAtomsIndices

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “neighboring_atoms_indices”, calculated with rdkit.

The index of this feature is 510 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-neighboring_atoms_indices feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomNeighboringAtomsMapNumbers

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “neighboring_atoms_map_numbers”, calculated with rdkit.

The index of this feature is 511 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-neighboring_atoms_map_numbers feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomNeighboringBondsIndices

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “neighboring_bonds_indices”, calculated with rdkit.

The index of this feature is 512 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-neighboring_bonds_indices feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomNoImplicit

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “no_implicit”, calculated with rdkit.

The index of this feature is 513 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-no_implicit feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomRingInfo

Bases: _Rdkit2DAtomRingInfo

Feature factory for the 2D atom feature “ring_info”, calculated with rdkit.

The index of this feature is 514 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-ring_info feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomRingInfoAromaticCarbocycle

Bases: _Rdkit2DAtomRingInfo

Feature factory for the 2D atom feature “ring_info_aromatic_carbocycle”, calculated with rdkit.

The index of this feature is 515 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-ring_info_aromatic_carbocycle feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomRingInfoAromaticHeterocycle

Bases: _Rdkit2DAtomRingInfo

Feature factory for the 2D atom feature “ring_info_aromatic_heterocycle”, calculated with rdkit.

The index of this feature is 516 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-ring_info_aromatic_heterocycle feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomRingInfoNonaromaticCarbocycle

Bases: _Rdkit2DAtomRingInfo

Feature factory for the 2D atom feature “ring_info_nonaromatic_carbocycle”, calculated with rdkit.

The index of this feature is 517 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-ring_info_nonaromatic_carbocycle feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomRingInfoNonaromaticHeterocycle

Bases: _Rdkit2DAtomRingInfo

Feature factory for the 2D atom feature “ring_info_nonaromatic_heterocycle”, calculated with rdkit.

The index of this feature is 518 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-ring_info_nonaromatic_heterocycle feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomSymbol

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “symbol”, calculated with rdkit.

The index of this feature is 529 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-symbol feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomTotalDegree

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “total_degree”, calculated with rdkit.

The index of this feature is 530 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-total_degree feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomTotalNH

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “total_n_h”, calculated with rdkit.

The index of this feature is 531 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-total_n_h feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomTotalValence

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “total_valence”, calculated with rdkit.

The index of this feature is 532 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-total_valence feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomTpsaContribution

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “tpsa_contribution”, calculated with rdkit.

The index of this feature is 533 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-tpsa_contribution feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomWildmanCrippenLogpContribution

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “wildman_crippen_logp_contribution”, calculated with rdkit.

The index of this feature is 534 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-wildman_crippen_logp_contribution and wildman_crippen_mr_contribution feature.

class bonafide.features.rdkit_atom.Rdkit2DAtomWildmanCrippenMrContribution

Bases: Rdkit2DAtomWildmanCrippenLogpContribution

Feature factory for the 2D atom feature “wildman_crippen_mr_contribution”, calculated with rdkit.

The index of this feature is 535 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

class bonafide.features.rdkit_atom.Rdkit3DAtomCoordinates

Bases: BaseFeaturizer

Feature factory for the 3D atom feature “coordinates”, calculated with rdkit.

The index of this feature is 556 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit3D-atom-coordinates feature.

class bonafide.features.rdkit_atom._Rdkit2DAtomRingInfo

Bases: BaseFeaturizer

Parent feature factory for the 2D atom features calculated based on RDKit’s GetRingInfo().

_analyze_rings()

Get the RDKit ring information atom features.

Returns:

None

bonafide.features.rdkit_bond

RDKit features for bonds.

class bonafide.features.rdkit_bond.Rdkit2DBondBeginAtomIndex

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “begin_atom_index”, calculated with rdkit.

The index of this feature is 536 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-begin_atom_index feature.

class bonafide.features.rdkit_bond.Rdkit2DBondBeginAtomMapNumber

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “begin_atom_map_number”, calculated with rdkit.

The index of this feature is 537 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-begin_atom_map_number feature.

class bonafide.features.rdkit_bond.Rdkit2DBondBondOrder

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “bond_order”, calculated with rdkit.

The index of this feature is 538 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-bond_order feature.

class bonafide.features.rdkit_bond.Rdkit2DBondBondType

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “bond_type”, calculated with rdkit.

The index of this feature is 539 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-bond_type feature.

class bonafide.features.rdkit_bond.Rdkit2DBondEndAtomIndex

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “end_atom_index”, calculated with rdkit.

The index of this feature is 540 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-end_atom_index feature.

class bonafide.features.rdkit_bond.Rdkit2DBondEndAtomMapNumber

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “end_atom_map_number”, calculated with rdkit.

The index of this feature is 541 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-end_atom_map_number feature.

class bonafide.features.rdkit_bond.Rdkit2DBondIsAromatic

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “is_aromatic”, calculated with rdkit.

The index of this feature is 542 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-is_aromatic feature.

class bonafide.features.rdkit_bond.Rdkit2DBondIsConjugated

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “is_conjugated”, calculated with rdkit.

The index of this feature is 543 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-is_conjugated feature.

class bonafide.features.rdkit_bond.Rdkit2DBondNNeighbors

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “n_neighbors”, calculated with rdkit.

The index of this feature is 544 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-n_neighbors feature.

class bonafide.features.rdkit_bond.Rdkit2DBondNeighboringAtomsIndices

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “neighboring_atoms_indices”, calculated with rdkit.

The index of this feature is 545 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-neighboring_atoms_indices feature.

class bonafide.features.rdkit_bond.Rdkit2DBondNeighboringAtomsMapNumbers

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “neighboring_atoms_map_numbers”, calculated with rdkit.

The index of this feature is 546 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-neighboring_atoms_map_numbers feature.

class bonafide.features.rdkit_bond.Rdkit2DBondNeighboringBondsIndices

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “neighboring_bonds_indices”, calculated with rdkit.

The index of this feature is 547 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-neighboring_bonds_indices feature.

class bonafide.features.rdkit_bond.Rdkit2DBondRingInfo

Bases: _Rdkit2DBondRingInfo

Feature factory for the 2D bond feature “ring_info”, calculated with rdkit.

The index of this feature is 548 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-ring_info feature.

class bonafide.features.rdkit_bond.Rdkit2DBondRingInfoAromaticCarbocycle

Bases: _Rdkit2DBondRingInfo

Feature factory for the 2D bond feature “ring_info_aromatic_carbocycle”, calculated with rdkit.

The index of this feature is 549 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-ring_info_aromatic_carbocycle feature.

class bonafide.features.rdkit_bond.Rdkit2DBondRingInfoAromaticHeterocycle

Bases: _Rdkit2DBondRingInfo

Feature factory for the 2D bond feature “ring_info_aromatic_heterocycle”, calculated with rdkit.

The index of this feature is 550 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-ring_info_aromatic_heterocycle feature.

class bonafide.features.rdkit_bond.Rdkit2DBondRingInfoNonaromaticCarbocycle

Bases: _Rdkit2DBondRingInfo

Feature factory for the 2D bond feature “ring_info_nonaromatic_carbocycle”, calculated with rdkit.

The index of this feature is 551 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-ring_info_nonaromatic_carbocycle feature.

class bonafide.features.rdkit_bond.Rdkit2DBondRingInfoNonaromaticHeterocycle

Bases: _Rdkit2DBondRingInfo

Feature factory for the 2D bond feature “ring_info_nonaromatic_heterocycle”, calculated with rdkit.

The index of this feature is 552 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-ring_info_nonaromatic_heterocycle feature.

class bonafide.features.rdkit_bond.Rdkit2DBondStereo

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “stereo”, calculated with rdkit.

The index of this feature is 553 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-stereo feature.

class bonafide.features.rdkit_bond.Rdkit2DBondValenceContributionBeginAtom

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “valence_contribution_begin_atom”, calculated with rdkit.

The index of this feature is 554 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-valence_contribution_begin_atom feature.

class bonafide.features.rdkit_bond.Rdkit2DBondValenceContributionEndAtom

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “valence_contribution_end_atom”, calculated with rdkit.

The index of this feature is 555 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-bond-valence_contribution_end_atom feature.

class bonafide.features.rdkit_bond.Rdkit3DBondBondLength

Bases: BaseFeaturizer

Feature factory for the 3D bond feature “bond_length”, calculated with rdkit.

The index of this feature is 557 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit3D-bond-bond_length feature.

class bonafide.features.rdkit_bond.Rdkit3DBondCoordinatesBeginAtom

Bases: BaseFeaturizer

Feature factory for the 3D bond feature “coordinates_begin_atom”, calculated with rdkit.

The index of this feature is 558 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit3D-bond-coordinates_begin_atom feature.

class bonafide.features.rdkit_bond.Rdkit3DBondCoordinatesCenter

Bases: BaseFeaturizer

Feature factory for the 3D bond feature “coordinates_center”, calculated with rdkit.

The index of this feature is 559 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit3D-bond-coordinates_center feature.

class bonafide.features.rdkit_bond.Rdkit3DBondCoordinatesEndAtom

Bases: BaseFeaturizer

Feature factory for the 3D bond feature “coordinates_end_atom”, calculated with rdkit.

The index of this feature is 560 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.misc” in the _feature_config.toml file.

calculate()

Calculate the rdkit3D-bond-coordinates_end_atom feature.

class bonafide.features.rdkit_bond._Rdkit2DBondRingInfo

Bases: BaseFeaturizer

Parent feature factory for the 2D bond features calculated based on RDKit’s GetRingInfo().

_analyze_rings()

Get the RDKit ring information bond features.

Returns:

None

bonafide.features.rdkit_fingerprint

RDKit fingerprint features.

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintAtomPair

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_count_fingerprint_atom_pair”, calculated with rdkit.

The index of this feature is 519 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-rooted_count_fingerprint_atom_pair feature.

countBounds

countSimulation

fpSize

includeChirality

maxDistance

minDistance

use2D

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintFeatureMorgan

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_count_fingerprint_feature_morgan”, calculated with rdkit.

The index of this feature is 520 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-rooted_count_fingerprint_feature_morgan feature.

countBounds

countSimulation

fpSize

includeChirality

radius

useBondTypes

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintMorgan

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_count_fingerprint_morgan”, calculated with rdkit.

The index of this feature is 521 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-rooted_count_fingerprint_morgan feature.

countBounds

countSimulation

fpSize

includeChirality

radius

useBondTypes

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_count_fingerprint_rdkit”, calculated with rdkit.

The index of this feature is 522 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

branchedPaths

calculate()

Calculate the rdkit2D-atom-rooted_count_fingerprint_rdkit feature.

countBounds

countSimulation

fpSize

maxPath

minPath

numBitsPerFeature

useBondOrder

useHs

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintTopologicalTorsion

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_count_fingerprint_topological_torsion”, calculated with rdkit.

The index of this feature is 523 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-rooted_count_fingerprint_topological_torsion feature.

countBounds

countSimulation

fpSize

includeChirality

torsionAtomCount

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintAtomPair

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_fingerprint_atom_pair”, calculated with rdkit.

The index of this feature is 524 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-rooted_fingerprint_atom_pair feature.

countBounds

countSimulation

fpSize

includeChirality

maxDistance

minDistance

use2D

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintFeatureMorgan

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_fingerprint_feature_morgan”, calculated with rdkit.

The index of this feature is 525 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-rooted_fingerprint_feature_morgan feature.

countBounds

countSimulation

fpSize

includeChirality

radius

useBondTypes

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintMorgan

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_fingerprint_morgan”, calculated with rdkit.

The index of this feature is 526 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-rooted_fingerprint_morgan feature.

countBounds

countSimulation

fpSize

includeChirality

radius

useBondTypes

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_fingerprint_rdkit”, calculated with rdkit.

The index of this feature is 527 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

branchedPaths

calculate()

Calculate the rdkit2D-atom-rooted_fingerprint_rdkit feature.

countBounds

countSimulation

fpSize

maxPath

minPath

numBitsPerFeature

useBondOrder

useHs

class bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintTopologicalTorsion

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “rooted_fingerprint_topological_torsion”, calculated with rdkit.

The index of this feature is 528 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “rdkit.fingerprint” in the _feature_config.toml file.

calculate()

Calculate the rdkit2D-atom-rooted_fingerprint_topological_torsion feature.

countBounds

countSimulation

fpSize

includeChirality

torsionAtomCount

bonafide.features.spiro_bridgehead

Features for spiro and bridgehead atoms.

class bonafide.features.spiro_bridgehead.Bonafide2DAtomIsBridgehead

Bases: _Bonafide2DAtomIsSpiroBridgehead

Feature factory for the 2D atom feature “is_bridgehead”, implemented within this package.

The index of this feature is 28 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.misc” in the _feature_config.toml file.

class bonafide.features.spiro_bridgehead.Bonafide2DAtomIsSpiro

Bases: _Bonafide2DAtomIsSpiroBridgehead

Feature factory for the 2D atom feature “is_spiro”, implemented within this package.

The index of this feature is 29 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.misc” in the _feature_config.toml file.

class bonafide.features.spiro_bridgehead._Bonafide2DAtomIsSpiroBridgehead

Bases: BaseFeaturizer

Parent feature factory for the 2D atom features “is_spiro” and “is_bridgehead”.

_get_spiro_bridgehead()

Get the atom indices of spiro and bridgehead atoms in a molecule.

This is done based on the following heuristics:

1. If two rings share exactly one atom, then that atom is a spiro atom.

2. If two rings share more than one atom (intersecting ring), then the shared atoms are classified as bridgehead atoms if a given atom of the shared atoms has at least 3 explicit neighbors that are part of the intersecting rings under consideration.

Returns:

Tuple[Set[int], Set[int]]

A tuple containing two sets: the atom indices of spiro and bridgehead atoms.

calculate()

Calculate the bonafide2D-atom-is_spiro and bonafide2D-atom-is_bridgehead feature.

bonafide.features.symmetric_sites

Identification of symmetry equivalent positions in 2D mol objects.

class bonafide.features.symmetric_sites.Bonafide2DAtomIsSymmetricTo

Bases: BaseFeaturizer

Feature factory for the 2D atom feature “is_symmetric_to”, implemented within this package.

The index of this feature is 30 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.symmetry” in the _feature_config.toml file.

calculate()

Calculate the bonafide2D-atom-is_symmetric_to feature.

includeAtomMaps

includeChiralPresence

includeChirality

includeIsotopes

reduce_to_canonical

class bonafide.features.symmetric_sites.Bonafide2DBondIsSymmetricTo

Bases: BaseFeaturizer

Feature factory for the 2D bond feature “is_symmetric_to”, implemented within this package.

The index of this feature is 52 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “bonafide.symmetry” in the _feature_config.toml file.

static _get_rank_idx(rank_dict, idx)

Get the rank index for a given atom index from the rank dictionary.

Parameters:

rank_dictDict[int, List[int]]

The rank dictionary mapping rank indices to lists of atom indices.

idxint

The atom index for which to find the rank index.

Returns:

int

The rank index corresponding to the given atom index.

calculate()

Calculate the bonafide2D-bond-is_symmetric_to feature.

includeAtomMaps

includeChiralPresence

includeChirality

includeIsotopes

reduce_to_canonical

bonafide.features.xtb_cdft

C-DFT features based on condensed Fukui indices calculated with xtb.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalElectrophilicityFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_electrophilicity_fmo”, calculated with xtb.

The index of this feature is 566 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_electrophilicity_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalElectrophilicityRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_electrophilicity_redox”, calculated with xtb.

The index of this feature is 567 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_electrophilicity_redox feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessMinusFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_minus_fmo”, calculated with xtb.

The index of this feature is 568 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hardness_minus_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessMinusRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_minus_redox”, calculated with xtb.

The index of this feature is 569 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hardness_minus_redox feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessPlusFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_plus_fmo”, calculated with xtb.

The index of this feature is 570 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hardness_plus_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessPlusRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_plus_redox”, calculated with xtb.

The index of this feature is 571 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hardness_plus_redox feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessZeroFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_zero_fmo”, calculated with xtb.

The index of this feature is 572 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hardness_zero_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessZeroRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hardness_zero_redox”, calculated with xtb.

The index of this feature is 573 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hardness_zero_redox feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHyperhardnessFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hyperhardness_fmo”, calculated with xtb.

The index of this feature is 574 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hyperhardness_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHyperhardnessRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hyperhardness_redox”, calculated with xtb.

The index of this feature is 575 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hyperhardness_redox feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHypersoftnessFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hypersoftness_fmo”, calculated with xtb.

The index of this feature is 576 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hypersoftness_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHypersoftnessRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_hypersoftness_redox”, calculated with xtb.

The index of this feature is 577 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_hypersoftness_redox feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalNucleophilicityFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_nucleophilicity_fmo”, calculated with xtb.

The index of this feature is 578 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_nucleophilicity_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalNucleophilicityRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_nucleophilicity_redox”, calculated with xtb.

The index of this feature is 579 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_nucleophilicity_redox feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalRelativeElectrophilicity

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_relative_electrophilicity”, calculated with xtb.

The index of this feature is 580 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_relative_electrophilicity feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalRelativeNucleophilicity

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_relative_nucleophilicity”, calculated with xtb.

The index of this feature is 581 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_relative_nucleophilicity feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessMinusFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_minus_fmo”, calculated with xtb.

The index of this feature is 582 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_softness_minus_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessMinusRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_minus_redox”, calculated with xtb.

The index of this feature is 583 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_softness_minus_redox feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessPlusFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_plus_fmo”, calculated with xtb.

The index of this feature is 584 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_softness_plus_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessPlusRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_plus_redox”, calculated with xtb.

The index of this feature is 585 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_softness_plus_redox feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessZeroFmo

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_zero_fmo”, calculated with xtb.

The index of this feature is 586 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_softness_zero_fmo feature.

class bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessZeroRedox

Bases: _Xtb3DAtomCdftLocal

Feature factory for the 3D atom feature “cdft_local_softness_zero_redox”, calculated with xtb.

The index of this feature is 587 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_local_softness_zero_redox feature.

class bonafide.features.xtb_cdft._Xtb3DAtomCdftLocal

Bases: BaseFeaturizer, CdftLocalRedoxMixin

Parent feature factory for calculating C-DFT descriptors based on condensed Fukui indices calculated with xtb.

_wrap_fukui(factory, fukui_feature_name)

Calculate the condensed Fukui indices with xtb.

The calculation is performed with the feature factory class of the respective Fukui coefficient.

Parameters:

factorytype

The feature factory class to be used for the Fukui calculation.

fukui_feature_namestr

The name of the Fukui feature to be calculated.

Returns:

Tuple[Optional[float], Optional[str]]

The calculated Fukui value and an error message.

bonafide.features.xtb_fukui_misc

Condensed Fukui coefficients and some additional features from the semi-empirical quantum chemistry package xtb.

class bonafide.features.xtb_fukui_misc.Xtb3DAtomC6DispersionCoefficient

Bases: _Xtb3DAtomFukuiMisc

Feature factory for the 3D atom feature “c6_dispersion_coefficient”, calculated with xtb.

The index of this feature is 561 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-c6_dispersion_coefficient feature.

class bonafide.features.xtb_fukui_misc.Xtb3DAtomCdftCondensedFukuiDual

Bases: _Xtb3DAtomFukuiMisc

Feature factory for the 3D atom feature “cdft_condensed_fukui_dual”, calculated with xtb.

The index of this feature is 562 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_condensed_fukui_dual feature.

class bonafide.features.xtb_fukui_misc.Xtb3DAtomCdftCondensedFukuiMinus

Bases: _Xtb3DAtomFukuiMisc

Feature factory for the 3D atom feature “cdft_condensed_fukui_minus”, calculated with xtb.

The index of this feature is 563 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_condensed_fukui_minus feature.

class bonafide.features.xtb_fukui_misc.Xtb3DAtomCdftCondensedFukuiPlus

Bases: _Xtb3DAtomFukuiMisc

Feature factory for the 3D atom feature “cdft_condensed_fukui_plus”, calculated with xtb.

The index of this feature is 564 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_condensed_fukui_plus feature.

class bonafide.features.xtb_fukui_misc.Xtb3DAtomCdftCondensedFukuiZero

Bases: _Xtb3DAtomFukuiMisc

Feature factory for the 3D atom feature “cdft_condensed_fukui_zero”, calculated with xtb.

The index of this feature is 565 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-cdft_condensed_fukui_zero feature.

class bonafide.features.xtb_fukui_misc.Xtb3DAtomPartialChargeHueckel

Bases: _Xtb3DAtomFukuiMisc

Feature factory for the 3D atom feature “partial_charge_hueckel”, calculated with xtb.

The index of this feature is 588 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-partial_charge_hueckel feature.

class bonafide.features.xtb_fukui_misc.Xtb3DAtomPolarizability

Bases: _Xtb3DAtomFukuiMisc

Feature factory for the 3D atom feature “polarizability”, calculated with xtb.

The index of this feature is 589 (see the list_atom_features() and list_bond_features() method). The corresponding configuration settings can be found under “xtb” in the _feature_config.toml file.

calculate()

Calculate the xtb3D-atom-polarizability feature.

class bonafide.features.xtb_fukui_misc._Xtb3DAtomFukuiMisc

Bases: BaseFeaturizer

Parent feature factory for the 3D atom Fukui and miscellaneous features calculated with xtb.

_calculate_global_descriptors_fmo(homo_energy, lumo_energy)

Calculate molecule-level descriptors from the HOMO and LUMO energy.

The included descriptors are:

• HOMO-LUMO gap

• Chemical potential

• Hardness

• Softness

• Electrophilicity

• Nucleophilicity

Parameters:

homo_energyfloat

The energy of the highest occupied molecular orbital of the molecule in eV.

lumo_energyfloat

The energy of the lowest unoccupied molecular orbital of the molecule in eV.

Returns:

Optional[str]

Returns an error message if the calculation of the C-DFT descriptors failed or None if everything worked as expected.

_check_xtb_method(allowed_method)

Check if the selected xtb method is allowed for the specific feature.

Parameters:

allowed_methodstr

The name of the allowed xtb method.

Returns:

None

_get_fukuis()

Calculate the condensed Fukui indices using xtb and read them from the output file.

Returns:

None

_read_output_file(enforce, out_file_prefix)

Read the output file, extract the respective data and write it to results.

This method is used to extract Fukui indices or other atomic properties from an xtb output file.

Parameters:

enforcestr

Whether to enforce extraction of “fukui” or “misc” data.

out_file_prefixstr

Prefix of the output file name.

Returns:

None

_read_output_file2()

Read the output file, extract the respective data and write it to results.

This method is used to extract Hueckel charges from an xtb ceh.charges file.

Returns:

None

_run_xtb(calc_fukui, calc_ceh, out_file_prefix)

Run an xtb single-point energy calculation.

Parameters:

calc_fukuibool

Whether to calculate Fukui indices.

calc_cehbool

Whether to calculate Hueckel charges.

out_file_prefixstr

The prefix for the output file name.

Returns:

None

method