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)

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

pmapper

3D pharmacophore signatures and fingerprints

crem

CReM: chemically reasonable mutations framework

pytoda

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

chem-mrl

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

linearscript

A linear script to unfold molecular complexity.

graphkit-learn

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

grakel-dev

A scikit-learn compatible library for graph kernels

chem-classification

Deep learning in smiles win / loss evaluation.

magnetstein

Tools for quantitative analysis of nuclear magnetic resonance (NMR) spectra using the Wasserstein metric.

bio2bel-chebi

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

pykrev

FT-MS data analysis with Python

xyz2graph

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

chem-ant

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

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

metadisassembler

The Metabolic Disassembler

chelombus

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

linchemin

Linked Chemical Information. LinChemIn is a Python toolkit that leverages the native connectivity of Chemical Reaction Data and provides actionable insights. The toolkit provides a program interface to several Computer-Aided Synthesis Prediction tools, allowing users to devise and calculate metrics on predicted Chemical Synthetic Routes.

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.