Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
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:
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.
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
RDKit: Open-Source Cheminformatics Software
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
►Morgan Fingerprint Generator in RDKit
►What Is Morgan Fingerprint Generator in RDKit
GetMorganFingerprint() Method in RDKit
Impact of 'radius' on GetMorganFingerprint()
Impact of 'useCounts' on GetMorganFingerprint()
Impact of 'invariants' on GetMorganFingerprint()
Impact of 'useBondTypes' on GetMorganFingerprint()
Impact of 'fromAtoms' on GetMorganFingerprint()
GetMorganFingerprintAsBitVect() Method in RDKit
Impact of 'nBits' on GetMorganFingerprintAsBitVect()
GetHashedMorganFingerprint() Method in RDKit
Impact of 'nBits' on GetHashedMorganFingerprint()
GetMorganGenerator() Method in RDKit
Morgan Fingerprint Generator in RDKit for FCFP
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction