Read plumed2 http://www.plumed.org COLVAR files as pandas DataFrames https://pandas.pydata.org

Some codes used in the Advanced Computational Methods (PHY204) course in SNBNCBS, Kolkata

Scripts to convert between PDB to Tinker XYZ files, without using the existing TINKER programs for conversion.

"Deep Generative Modeling": Introductory Examples

Converts an xyz file to an RDKit mol object

MatDeepLearn, package for graph neural networks in materials chemistry

This is a repo that has a collection of codes to parse and train QM data for MLFF training

MDANCE is a flexible n-ary clustering package for all applications.

AAAI 2020: Chemically Interpretable Graph Interaction Network for Prediction of Pharmacokinetic Properties of Drug-like Molecules

a molecular descriptor calculator

Automatic Mutual Information Noise Omission

A public repository collecting links to state of the art QA and evaluation sets for various ML and LLM applications

Visual Interactive Analysis of Molecular Dynamics

ASAP is a package that can quickly analyze and visualize datasets of crystal or molecular structures.

All pdfs of Victor Eijkhout's Art of HPC books and courses

A beautiful, simple, clean, and responsive Jekyll theme for academics

Repository for the 2023 ELLIS Machine Learning for Molecules Discovery workshop

Compressed folder with 10,570 hypothetical zeolite frameworks and scripts to read them

Materials for 0.5-day MDAnalysis workshops

Insert SVG images into matplotlib elements. Can be used to also compose matplotlib plots by nesting them.

Automatic representation based CVs

Tool for finding atomic environments in crystal structures

A community supported Windows build for jax.