Structural Bioinformatics Python Packages

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 https://hbat-web.abhishek-tiwari.com

protein-design-tools

A library of tools for protein design

py-packman

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

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..

buildamol

A fragment-based molecular assembly toolkit

diff-biophys

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

dlpdb

collect statistics from the entire PDB library

old-pdb

Convert between PDB and CIF formats

frustration-gpu

Pure-PyTorch LAMMPS-AWSEM frustration analysis. 14-53x faster than frustrapy on a single GPU. Byte-comparable to frustratometeR.

zmpy3d

Python implementation of 3D Zernike moments with NumPy

intermap

Accelerated Detection of Interaction Fingerprints on Large-Scale Molecular Ensembles

zmpy3d-cp

Python implementation of 3D Zernike moments with CuPy

zmpy3d-tf

Python implementation of 3D Zernike moments with Tensorflow

go2pdb

Extract PDB entries annotated with specific GO codes

zmpy3d-pt

Python implementation of 3D Zernike moments with PyTorch

biobuild

A fragment-based molecular assembly toolkit