schrodinger.rdkit.fingerprints module

class schrodinger.rdkit.fingerprints.RDKitPathFingerprinter(ignored_smarts: str = '', *, max_path: int = 3, num_bits_per_feature: int = 1)

Bases: object

Generate sparse-count RDKit path fingerprints.

When ignored_smarts is provided, paths containing a bond whose endpoints are both in the first SMARTS match are excluded. Other paths may include matched atoms, including attachment bonds and paths through a single matched atom. Consequently, a single-atom match masks no paths. If the SMARTS does not match, the fingerprint is unmasked.

Only the first match is used, so the pattern should uniquely identify the intended core.

Parameters:

  • ignored_smarts – Optional SMARTS identifying the core.

  • max_path – Positive maximum number of bonds in a fingerprint path.

  • num_bits_per_feature – Positive number of bits set for each path feature.

__init__(ignored_smarts: str = '', *, max_path: int = 3, num_bits_per_feature: int = 1)
fingerprint(mol: Mol) → ULongSparseIntVect

Generate a sparse-count fingerprint for mol.

Parameters:

mol – Molecule to fingerprint.

Returns:

Sparse-count RDKit path fingerprint.