Cheminformatics Tutorials - Herong's Tutorial Examples

∟Morgan Fingerprint Generator in RDKit

This chapter provides introductions and tutorial examples on Morgan Fingerprint Generator in RDKit. Topics include introduction of RDKFingerprint(), UnfoldedRDKFingerprintCountBased(), and GetRDKitFPGenerator() methods, impact of radius, useCounts, useBondTypes, and other options.

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

Takeaways:

• RDKit supports options to generate molecular fingerprints using the Morgan algorithm.
• GetMorganFingerprint() method returns fingerprints as collections of identifiers using the Morgan algorithm.
• GetMorganFingerprintAsBitVect() method returns fingerprints as bit strings using the Morgan algorithm.
• GetHashedMorganFingerprint() method returns fingerprints as collections of folded integers using the Morgan algorithm.
• GetRDKitFPGenerator() creates a Daylight generator object, which can generate fingerprints in different formats.

Tutorials given in this chapter are tested with RDKit 2021.09.3.

Table of Contents

 About This Book

 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

 RDKit Performance on Substructure Search

 Introduction to Molecular Fingerprints

 OCSR (Optical Chemical Structure Recognition)

 AlphaFold - Protein Structure Prediction

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB

Morgan Fingerprint Generator in RDKit - Updated in 2024, by Herong Yang