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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

pyztraj

High-performance molecular dynamics trajectory analysis library in Zig

zsasa

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

mdahole2

An MDAKit implementing a Python interface for the HOLE program.

synth-nmr

NMR spectroscopy calculations for protein structures

graphein

Protein Graph Library

synth-pdb

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

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

pycapsid

Python package to extract quasi-rigid domains in protein shells and other macromolecular complexes.

pdbecif

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

rnaglib

Toolkit for structure-based deep learning on RNA.

pdbe-arpeggio

Arpeggio calculates interatomic contacts based on the rules defined in CREDO.

pdbe-mmcif-validator

Validate mmCIF/CIF files against the PDBx/mmCIF dictionary or any CIF dictionary

sidechainnet

An all-atom protein structure dataset for machine learning.

pdbrust

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

py-packman

Python package built around protein structure and dynamics. OpenBabel-inspired objects.

molecularnodes

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

leopard-em

Location & Orientation of Particles found using Two-Dimensional Template Matching