What Is Morgan Fingerprint Generator in RDKit

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∟What Is Morgan Fingerprint Generator in RDKit

This section provides a quick introduction on the Morgan Fingerprint Generator provided in the RDKit library.

What Is Morgan Fingerprint Generator in RDKit? - Morgan Fingerprint Generator in RDKit allows you to generate molecular fingerprints using the Morgan algorithm.

Main features of the Morgan Fingerprint Generator:

Capable to generate ECFP (Extended Connectivity Fingerprints).
Capable to generate FCFP (Functional-Class Fingerprints).
Capable to generate fingerprints with your owns initial identifiers.
Capable to output fingerprints as a collection of identifiers.
Capable to output fingerprints as a fixed-length bit string.

There are several ways to access the Morgan Fingerprint Generator in the RDKit library.

1. Calling the rdkit.Chem.rdMolDescriptors.GetMorganFingerprint(mol, radius) method, which returns a fingerprint as a collection of identifiers representing local structures within the given radius for a given molecule.

2. Calling the rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect(mol, radius, nBits) method, which returns a fingerprint as a bit string of length nBits representing combined local structures within the given radius for a given molecule.

3. Calling the rdkit.Chem.rdMolDescriptors.GetHashedMorganFingerprint(mol, radius, nBits) method, which returns a fingerprint as a collection of integers smaller than a given limit nBits, representing local structures for a given molecule.

4. Use gen = rdkit.Chem.rdFingerprintGenerator.GetMorganGenerator(radius, fpSize) to create a Morgan generator object of a given radius and size fpSize. Then call gen.GetFingerprint(mol), gen.GetCountFingerprint(mol), gen.GetSparseFingerprint(mol), or gen.GetSparseCountFingerprint(mol) to generate a Morgan fingerprint in different output formats for a given molecule.