Chemoinformatics Python Packages

scikit-fingerprints

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

marsilea

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

pymol-remote

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

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.

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

lacuna-pockets

Finds cryptic binding pockets that are invisible in a single static structure. Generates a conformational ensemble, detects pockets in every conformer, clusters them into transient sites, and ranks them. Seconds on a CPU, no GPU required. Emits docking-ready Boltz constraints and AutoDock Vina boxes.

fpembed

FPembed - Generalized Molecular Fingerprint Embeddings

chem-mrl

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

bio2bel-chebi

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

grakel-dev

A scikit-learn compatible library for graph kernels

graphkit-learn

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

pytoda

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

magnetstein

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

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.

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.

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

linearscript

A linear script to unfold molecular complexity.

psikit

psi4+RDKit

pykrev

FT-MS data analysis with Python

lindemann

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