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alphafold

Open source code for AlphaFold.

biochem-notebooks

Python notebooks with biochem related topics

cctbx-notebooks

cctbx_project

Computational Crystallography Toolbox

cif-assembly

cod_tools

A set of scripts to filter the COD database for use as a molecular training set

colabfolds

cryoem-rerefine-ligands

dual_quaternions_ros

Basic Dual Quaternion functionality and conversions from/to ROS messages

espaloma

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

fragmentml

geostd

geostd_mol

A subset of molecule structures which appear in the Phenix geostd library. Here, they have been converted to .mol file format.

harmonic-oscillator

Simple harmonic oscillator using godot

hexamer_measurements

A place to store scripts for measuring hexamer structural properties for HBV capsid

molstar-testing

ndual_quaternion

notebooks

A location to store and organize personal notebooks

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

pdbmodule

phenix_fragments

An experimental toolbox for working with molecular fragments and generating chemical restraints for the Phenix project

phenixml

A framework for doing classification and regression tasks on molecular fragments

pyquaternion

A fully featured, pythonic library for representing and using quaternions

qscore_standalone

An implementation of the cryo-EM validation metric Q-score using cctbx/numpy/scipy

qtconsole_pyside2

Jupyter Qt Console using pyside2

relionnotebooks

s3ql

a full featured file system for online data storage

stario

Simple Input/Output between .star files from the Relion EM software and Pandas dataframes

transformer

Transformer seq2seq model, program that can build a language translator from parallel corpus

trimerssa