fraggle_distance#

skfp.distances.fraggle_distance(mol_query: Mol, mol_ref: Mol, tversky_threshold: float = 0.8) → float#

Fraggle distance between molecules.

Computes the Fraggle distance [1] [2] between two RDKit Mol objects by subtracting similarity value from 1, using the formula:

\[dist(a, b) = 1 - sim(a, b)\]

See also fraggle_binary_similarity(). The calculated distance falls within the range \([0, 1]\). Passing all-zero vectors to this function results in a distance of 0. Note that this measure is asymmetric, and order of query and reference molecules matters.

Parameters:

  • mol_query (RDKit Mol object) – Query molecule.

  • mol_ref (RDKit Mol object) – Reference molecule.

  • tversky_threshold (float, default=0.8) – Required minimal Tversky similarity [3] between a fragment and the reference molecule.

Returns:

similarity – Fraggle similarity between mol_query and mol_ref.

Return type:

float

References

Examples

>>> from rdkit.Chem import MolFromSmiles
>>> from skfp.distances import fraggle_distance
>>> mol_query = MolFromSmiles("COc1cc(CN2CCC(NC(=O)c3cncc(C)c3)CC2)c(OC)c2ccccc12")
>>> mol_ref = MolFromSmiles("COc1ccccc1")
>>> dist = fraggle_distance(mol_query, mol_ref)
>>> dist
0.8359375
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