wutobias

Apollo-11

Original Apollo 11 Guidance Computer (AGC) source code for the command and lunar modules.

ray

Ray is a unified framework for scaling AI and Python applications. Ray consists of a core distributed runtime and a set of AI Libraries for accelerating ML workloads.

numpy

The fundamental package for scientific computing with Python.

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

virtualagc

Virtual Apollo Guidance Computer (AGC) software

nlopt

library for nonlinear optimization, wrapping many algorithms for global and local, constrained or unconstrained, optimization

mdtraj

An open library for the analysis of molecular dynamics trajectories

propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

xyz2mol

Converts an xyz file to an RDKit mol object

gemmi

macromolecular crystallography library and utilities

WriteTeX

An Inkscape extension: Latex/Tex editor for Inkscape

QCEngine

Quantum chemistry program executor and IO standardizer (QCSchema).

geomeTRIC

Geometry optimization code that includes the TRIC coordinate system

accupy

:dart: Accurate sums and dot products for Python.

openff-interchange

A project (and object) for storing, manipulating, and converting molecular mechanics data.

openff-bespokefit

Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.

ligpargen

UGM_2023

Materials from the 2023 RDKit UGM

blues

Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling

pAPRika

Advanced toolkit for binding free energy calculations

de-forcefields

Transferable Double Exponential non-bonded potential for condensed phase simulations of small molecules

chemper

Repository for Chemical Perception Sampling Tools

openff-nagl

OpenFF NAGL

aimmd

asyncmd

asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.

random-scripts

A collection of useful scripts (pre- and post-processing) because I keep forgetting where I kept them

besmarts

A toolkit for data-driven force field design based on binary-encoded SMARTS

notebooks

Miscellaneous preliminary notebooks

HG-GBSA-Optimization

Example for running GBSA optimization targeting host-guest binding data with OpenFF-Evaluator and ForceBalance