Structural Biology Python Packages

gemmi

macromolecular crystallography library and utilities

biotite

A comprehensive library for computational molecular biology

pdbeccdutils

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

mmcif-pdbx

Yet another version of PDBx/mmCIF Python implementation

hbat

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

cosmolkit

Pure-Rust cheminformatics toolkit and RDKit-compatible alternative for SMILES/SMARTS, SDF, fingerprints, substructure search, ETKDG, UFF/MMFF, and Python workflows.

zsasa

High-performance SASA (Solvent Accessible Surface Area) calculation in Zig with Python bindings

pdbe-mmcif-validator

Real-time VSCode extension and standalone Python script for validating mmCIF/CIF files against the PDBx/mmCIF dictionary or any CIF dictionary.

pdbrust

A Rust library for parsing PDB (Protein Data Bank) files

graphein

Protein Graph Library

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

molecularnodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

mdahole2

An MDAKit implementing a Python interface for the HOLE program.

bioiain

Toolbox for structural analysis of proteins.

pdbecif

A lightweight pure python package for reading, writing and manipulating mmCIF files distributed by the wwPDB"

ipymol

Control PyMOL sessions via IPython

pantometry

Physics for simulated worlds in Rust: a kernel that knows no domain and thirteen that do — heat, mechanics, optics, acoustics, electromagnetism, elasticity, fluids, porous media, molecular dynamics, electrical, quantum, pharmacokinetics, protein folds — plus scene and view layers that know none. Dimensions in the types, conservation audited.

proxide

High-performance protein I/O and physics bridging for JAX, with a Rust backend for structure parsing and force-field parameterization

rnaglib

Toolkit for structure-based deep learning on RNA.

leopard-em

Two-Dimensional Template Matching implemented in Python

pyztraj

High-performance molecular dynamics trajectory analysis library in Zig

dualis

Physics for simulated worlds in Rust: a kernel that knows no domain and thirteen that do — heat, mechanics, optics, acoustics, electromagnetism, elasticity, fluids, porous media, molecular dynamics, electrical, quantum, pharmacokinetics, protein folds — plus scene and view layers that know none. Dimensions in the types, conservation audited.

serd

SERD: Solvent-Exposed Residues Detection