Chemistry Python Packages

pubchempy

Python wrapper for the PubChem PUG REST API.

pybaselines

A Python library of algorithms for the baseline correction of experimental data.

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

thermo

Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)

mendeleev

A python package for accessing various properties of elements, ions and isotopes in the periodic table of elements.

chematic

A pure-Rust cheminformatics library targeting RDKit feature parity — zero C/C++ by default.

epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

chemprop

Message Passing Neural Networks for Molecule Property Prediction

meeko

Interface for AutoDock, molecule parameterization

mmcif-pdbx

Yet another version of PDBx/mmCIF Python implementation

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

readcon

Oxidized rewrite of readCon

scikit-fingerprints

Scikit-learn compatible library for molecular fingerprints and chemoinformatics

openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

molmass

Molecular mass calculations.

sella

A Python software package for saddle point optimization and minimization of atomic systems.

qcelemental

Periodic table, physical constants, and molecule parsing for quantum chemistry.

readcon-chemfiles

Oxidized rewrite of readCon

chempy

⚗ A package useful for chemistry written in Python

reaction-network

Reaction Network is a Python package for predicting likely inorganic chemical reaction pathways using graph theoretical methods. Project led by @mattmcdermott (formerly at Berkeley Lab).

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures https://hbat-web.abhishek-tiwari.com

phreeqpython

Object-oriented python wrapper for the VIPhreeqc module

mandacaru

Everything you need for fermionic quantum simulation

structuregraph-helpers

Helpers for working with pymatgen structure graphs.