Cheminformatics Tutorials - Herong's Tutorial Examples

∟Daylight Fingerprint Generator in RDKit

This chapter provides introductions and tutorial examples on Daylight Fingerprint Generator in RDKit. Topics include introduction of RDKFingerprint(), UnfoldedRDKFingerprintCountBased(), and GetRDKitFPGenerator() methods, impact of maxPath, fpSize, branchedPaths, and other options.

What Is Daylight Fingerprint Generator in RDKit

RDKFingerprint() Method in RDKit

Impact of 'useBondOrder' on RDKFingerprint()

Impact of 'branchedPaths' on RDKFingerprint()

Impact of 'maxPath' on RDKFingerprint()

Impact of 'fpSize' on RDKFingerprint()

Impact of 'tgtDensity' on RDKFingerprint()

Impact of 'nBitsPerHash' on RDKFingerprint()

UnfoldedRDKFingerprintCountBased() Method in RDKit

GetRDKitFPGenerator() Method in RDKit

Takeaways:

• RDKit supports options to generate molecular fingerprints using the Daylight method.
• RDKFingerprint() returns fingerprints as bit strings using the Daylight method.
• UnfoldedRDKFingerprintCountBased() returns fingerprints as collections of identifiers using the Daylight method.
• 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

Daylight Fingerprint Generator in RDKit - Updated in 2023, by Herong Yang