Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
What Is Daylight Fingerprint Generator in RDKit
This section provides a quick introduction on the Daylight Fingerprint Generator provided in the RDKit library.
What Is Daylight Fingerprint Generator in RDKit? - Daylight Fingerprint Generator in RDKit allows you to generate molecular fingerprints using the Daylight fingerprint method developed by Daylight Chemical Information Systems Inc.. For more details, see "Daylight Fingerprint Method - 1987" section in this book.
Main features of the Daylight Fingerprint Generator:
Daylight fingerprint generator in RDKit library is referred as RDK fingerprint generator. There are several ways to access the Daylight Fingerprint Generator in the RDKit library.
1. Calling the rdkit.Chem.rdmolops.RDKFingerprint(mol, fpSize) method, which returns a fingerprint as a bit string of length fpSize representing combined subgraphs for a given molecule.
2. Calling the rdkit.Chem.rdmolops.UnfoldedRDKFingerprintCountBased(mol) method, which returns a fingerprint as a collection of identifiers representing subgraphs for a given molecule.
3. Use gen = rdkit.Chem.rdFingerprintGenerator.GetRDKitFPGenerator(fpSize) to create a Daylight generator object of a size fpSize. Then call gen.GetFingerprint(mol), gen.GetCountFingerprint(mol), gen.GetSparseFingerprint(mol), or gen.GetSparseCountFingerprint(mol) to generate a Daylight 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
►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
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction