thompat

bio-diffusion

A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization (Nature CommsChem)

depthcharge

A deep learning toolkit for mass spectrometry

CRANK-MS

Classification and Ranking Analysis using Neural network generates Knowledge from Mass Spectrometry

massformer

Tandem Mass Spectrum Prediction with Graph Transformers

GoodScientificCodeWorkshop

A workshop on writing good scientific code.

nablaDFT

nablaDFT: Large-Scale Conformational Energy and Hamiltonian Prediction benchmark and dataset

xyz2tab

Convert XYZ data to bond lengths & angles, calculate contacts, planes and dihedral angles and print tables

xyzoverlay

Python 3 script for overlaying or superimposing two or more molecules. The overlayed / superimposed molecules can be displayed and the modified coordinates can be saved as xyz files. Coloring by atom or molecule is possible.

EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

PodPals

A Graphical User Interface (GUI) designed to streamline the creation and analysis of files generated by the ORCA computational chemistry package.

getdoi

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

cheat-sheets

General compchem "cheat sheets".

fix-achemso-refs

A BASH script for abbreviating journal titles in a bib file using CASSI abbreviations.

Exphormer

Exphormer: Sparse Transformer for Graphs

rdkit-scripts

rdkit scripts making life easier

rdkit-scripts

A collection of cheminformatics scripts that use rdkit

practical_cheminformatics_tutorials

Practical Cheminformatics Tutorials

FullMonte

Automated Monte Carlo Conformational Searching with Python

dotfiles

My current dotfiles

chem_laqa

Efficient search for energetically favorable molecular conformations via gray-box optimization

MoleGuLAR

Repository for MoleGuLAR: Molecule generation using Reinforcement Learning and Alternating Rewards

MolGen

awesome-graph-generation

marimo

A reactive notebook for Python — run reproducible experiments, execute as a script, deploy as an app, and version with git.

MobCal-MPI

Parallelization of the commonly used MobCal suite to calculate ion mobilities and collision cross sections

lazy-ml

ML algorithms implementations that are good for learning the underlying principles

pytorch-transformer

Attention is all you need implementation

secdpy

SECD machine and Lispkit Lisp compiler, in Python

lambdalisp

A Lisp interpreter written in untyped lambda calculus