sailfish009/PyFingerprint

Python tool for generate fingerprints of a molecule

PyFingerprint

There are many types of chemical fingerprint for describing the molecule provided by different tools, such as RDKit, CDK and OpenBabel. This package aims to summarize them all.

Dependencies

1. Anaconda for python 3.6 or later

2. Java SE Development Kit 11

3. jpype

   pip install jpype1
   

4. RDKit

   conda install -c rdkit rdkit
   

5. OpenBabel

   conda install -c conda-forge openbabel
   

Install

pip install git+git://github.com/hcji/PyFingerprint@master

Usage

from PyFingerprint.All_Fingerprint import get_fingerprint
fps = get_fingerprint('CCCCN', fp_type='daylight')

Cite

Predicting Molecular Fingerprint from Electron-Ionization Mass Spectrum with Deep Neural Networks

Support fingerprint types:

**daylight**: Considers paths of a given length. These are hashed fingerprints, with a default length of 1024.
**extended**: Similar to the standard type, but takes rings and atomic properties into account into account.
**graph**: Similar to the standard type by simply considers connectivity.
**hybridization**: Similar to the standard type, but only consider hybridization state.
**estate**: 79 bit fingerprints corresponding to the E-State atom types described by Hall and Kier.
**pubchem**: 881 bit fingerprints defined by PubChem.
**klekota-roth**: 4860 bit fingerprint defined by Klekota and Roth.
**shortestpath**: A fingerprint based on the shortest paths between pairs of atoms and takes into account ring systems, charges etc.
**signature**: A feature,count type of fingerprint, similar in nature to circular fingerprints, but based on the signature descriptor.
**circular**: An implementation of the ECFP6 fingerprint.
**lingo**: An implementation of the LINGO fingerprint.
**rdkit**: Another implementation of a Daylight-like fingerprint by RDKit.
**maccs**: The popular 166 bit MACCS keys described by MDL.
**Avalon**: Substructure or similarity Avalon fingerprint.
**AtomPair**: RDKit Atom-Pair fingerprint.
**TopologicalTorsion**: RDKit Topological-Torsion Fingerprint.
**Morgan**: RDKit Morgan fingerprint.
**FP2**: OpenBabel FP2 fingerprint, which indexes small molecule fragments based on linear segments of up to 7 atoms in length.
**FP3**: OpenBabel FP3 fingerprint, which is a fingerprint method created from a set of SMARTS patterns defining functional groups.
**FP4**: OpenBabel FP4 fingerprint, which is a fingerprint method created from a set of SMARTS patterns defining functional groups.