# PyFingerprint

**Repository Path**: fullstackqa/PyFingerprint

## Basic Information

- **Project Name**: PyFingerprint
- **Description**: Python tool for generate fingerprints of a molecule
- **Primary Language**: Python
- **License**: AGPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 2
- **Created**: 2019-04-15
- **Last Updated**: 2020-12-19

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

## 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
 2. Java Runtime Environment 8.0
 3. jpype
 
        pip install jpype1

 4. RDKit

        conda install libboost=1.65.1
        conda install boost=1.65.1
        conda install boost-cpp=1.65.1
        conda install -c rdkit rdkit
 5. [Pybel](https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html) (Optional, only for OpenBabel fingerprints)
 
### 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')

### 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.