Rafal Wiewiora's repositories
autoprotocol-python
Python library for generating Autoprotocol
BetterMedTime
A tool for optimizing when to take multiple drugs to reduce side effects
biopython
Official git repository for Biopython (converted from CVS)
cardsReader
CARDS-Reader: Methods to analyze CARDS data
cbang
C! (cbang) is a library of cross-platform C++ utilities.
cdk
CDK2/CDK4 Folding@home simulations
covid
MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store
deeptime
Deep learning meets molecular dynamics.
ensembler
Software pipeline for automating omics-scale protein modeling and simulation setup.
enspara
Modeling molecular ensembles with scalable data structures and parallel computing
erk_reconstruction
ERK ancestral reconstruction
FAHMunge
Tools for Munging Folding@Home datasets
FFConv
Amber --> OpenMM ffxml conversion
keras
Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano and TensorFlow.
mdtraj
A modern, open library for the analysis of molecular dynamics trajectories
MolProbity
Protein and nucleic acid validation service
msmbuilder
Statistical models for biomolecular dynamics
mta
Scrape & analyze MTA arrival times
nglview
IPython widget to interactively view molecular structures and trajectories
notes
For making notes and storing some asap code for my current work
openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
openmmexampleplugin
An example of how to write a plugin for OpenMM
openmoltools
An open set of tools for automating tasks relating to small molecules
ParmEd
Parameter/topology editor and molecular simulator
PyEMMA
Emma's Markov Model Algorithms
pytraj
Interactive data analysis for molecular dynamics simulations
stuff
Various useful scripts
tensorflow
Computation using data flow graphs for scalable machine learning