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aariam

alds

Algorithms and data structures implemented in Python

arminariam.github.io

array_storage_benchmark

Compare some methods of array storage in Python (numpy)

biopandas

Working with molecular structures in pandas DataFrames

biopython

Official git repository for Biopython (originally converted from CVS)

biotite

A comprehensive library for computational molecular biology

caviar

// PROJECT PAUSED FOR NOW (lack of capacity) // Protein cavity identification and automatic subpocket decomposition

chessy

A chess engine in Python, using different AI methods.

cookiecutter-python-project-repo

Cookiecutter template for Python project repositories

duq

DUQ is a python package for working with physical Dimensions, Units, and Quantities.

funpy

Short & fun projects in Python with tutorials in Jupyter notebook

griddataformats

GridDataFormats is a pure Python library to handle data on a regular grid using commonly used file formats in molecular simulations.

hydride

Adding hydrogens to molecular models

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

mdforce

Implementation of different force-fields for molecular dynamics simulations

mdsim

Python package for molecular dynamics simulations

mdtraj

An open library for the analysis of molecular dynamics trajectories

mmtf-python

The python implementation of the MMTF API, decoder and encoder.

mrcfile

A Python implementation of the MRC2014 file format

ngl

WebGL protein viewer

nglview

Jupyter widget to interactively view molecular structures and trajectories

numintegrator

A python package providing numerical integrators for solving differential equations

openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

opencadd

A Python library for structural cheminformatics

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

pdb-tools_haddocking

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

pdbecif

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

pdbfixer

PDBFixer fixes problems in PDB files