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

ipymol

Control PyMOL sessions via IPython

zsasa

Fast SASA calculation using Zig

mdahole2

An MDAKit implementing a Python interface for the HOLE program.

pyztraj

High-performance molecular dynamics trajectory analysis library in Zig

synth-nmr

NMR spectroscopy calculations for protein structures

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development

graphein

Protein Graph Library

pdbecif

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

rnaglib

RNAglib: Tools for learning on the structure of RNA using 2.5D geometric representations

squarna

RNA secondary structure prediction tool

sidechainnet

An all-atom protein structure dataset for machine learning.

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.

glycontact

GlyContact: a Python package for retrieving, processing, and analyzing 3D glycan structures.

pycapsid

A set of computational tools written in python for the analysis of viral capsids

molecularnodes

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

mdciao

mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data

pdbe-arpeggio

Calculation of interatomic interactions in molecular structures