Chemoinformatics Python Packages

marsilea

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

scikit-fingerprints

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

moleditpy

MoleditPy -- A cross-platform, simple, and intuitive molecular editor built in Python. Please note that these codes are written with the assistance of LLM.

pymol-remote

Send data to and from pymol from a remote server (e.g. a cluster running deep learning workflows)

grakel

A scikit-learn compatible library for graph kernels

pmapper

3D pharmacophore signatures and fingerprints

moleditpy-linux

MoleditPy -- A cross-platform, simple, and intuitive molecular editor built in Python. Please note that these codes are written with the assistance of LLM.

crem

CReM: chemically reasonable mutations framework

linearscript

SCRIPT V3.1: A deterministic, RDKit-independent molecular notation with 100% round-trip stereo parity, materials science extensions, biopolymer support, and formal LALR grammar.

pytoda

pytoda: PaccMann PyTorch Dataset Classes.

xyz2graph

Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

chem-mrl

Chem-MRL: SMILES-based Matryoshka Representation Learning Embedding Model

graphkit-learn

A python package for graph kernels, graph edit distances, and graph pre-image problem.

bio2bel-chebi

A package for converting ChEBI to BEL

grakel-dev

A scikit-learn compatible library for graph kernels

chem-classification

Deep learning in smiles win / loss evaluation.

cremdock

CReM-dock: molecule generation and decoration guided by molecular docking

pykrev

FT-MS data analysis in Python

moleculapy

A command-line application that utilizes the RDKit library to compute molecular descriptors and fingerprints, aiding in the analysis and characterization of chemical structures

chem-ant

Select materials to output molecules similar to the target molecule with MCTS Solver and Genetic Programming.

psikit

psi4+RDKit

ctfile

Parser for chemical table file (CTfile) a family of text-based chemical file formats (e.g. Molfile, SDfile) that describe molecules and chemical reactions.

chelombus

Clustering and visualization of billions of molecules (or other high-dimensional data). 1 billion, 100K clusters, less than 3 hours, one GPU.

lindemann

lindemann is a python package to calculate the Lindemann index of a lammps trajectory