Structural Biology Python Packages

biotite

A comprehensive library for computational molecular biology

gemmi

macromolecular crystallography library and utilities

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

mmcif-pdbx

Yet another version of PDBx/mmCIF Python implementation

pdb-tools

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

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

mdahole2

An MDAKit implementing a Python interface for the HOLE program.

diff-biophys

Differentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.

zsasa

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

synth-nmr

NMR spectroscopy calculations for protein structures. Jupyter Notebook tutorials are available to visualize the concepts.

synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

ipymol

Control PyMOL sessions via IPython

pdbecif

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

graphein

Protein Graph Library

sidechainnet

An all-atom protein structure dataset for machine learning.

pyztraj

High-performance molecular dynamics trajectory analysis library in Zig

molforge

A forge for protein workflows. One Python script, every tool in your stack.

rnaglib

Toolkit for structure-based deep learning on RNA.

molecularnodes

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

diff-em

Differentiable Cryo-EM map fitting in JAX

pdbe-arpeggio

Calculation of interatomic interactions in molecular structures

diff-epr

Differentiable EPR/DEER distance distribution modeling in JAX

fandango-aria

Client library for interacting with ARIA APIs for data deposition.