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)

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.

grakel

A scikit-learn compatible library for graph kernels

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. Read the docs: https://paccmann.github.io/paccmann_datasets/

grakel-dev

A scikit-learn compatible library for graph kernels

graphkit-learn

A Python library for graph kernels, graph edit distances, and graph pre-images

chem-mrl

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

xyz2graph

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

pykrev

FT-MS data analysis with Python

chelombus

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

bio2bel-chebi

A Bio2BEL package for converting Chemical Entities of Biological Interest (ChEBI) to BEL

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

cremdock

CReM-dock: generation of chemically reasonable molecules guided by molecular docking

chem-ant

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

pymopac

a python wrapper to interact with the semiempirical quantum chemistry program MOPAC

psikit

A thin wrapper library for Psi4 and RDKit

lindemann

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

metadisassembler

The Metabolic Disassembler