denoptim-project/AutoCompChem

Tools for automated computational chemistry

Language: Java - Size: 87.7 MB - Last synced at: about 2 hours ago - Pushed at: about 4 hours ago - Stars: 4 - Forks: 0

equinor/acidwatch

AcidWatch is a platform for modeling chemical reactions in CO2 streams, designed for researchers in CCS.

Language: TypeScript - Size: 2.09 MB - Last synced at: about 3 hours ago - Pushed at: about 5 hours ago - Stars: 5 - Forks: 2

SMTG-Bham/easyunfold

Band structure unfolding made easy!

Language: Python - Size: 233 MB - Last synced at: about 13 hours ago - Pushed at: about 15 hours ago - Stars: 55 - Forks: 11

BioinfoMachineLearning/FlowDock

A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)

Language: Python - Size: 32.6 MB - Last synced at: about 16 hours ago - Pushed at: about 18 hours ago - Stars: 104 - Forks: 17

SMTG-Bham/doped

doped is a Python software for the generation, pre-/post-processing and analysis of defect supercell calculations, implementing the defect simulation workflow in an efficient, reproducible, user-friendly yet powerful and fully-customisable manner.

Language: Python - Size: 745 MB - Last synced at: about 10 hours ago - Pushed at: 6 days ago - Stars: 207 - Forks: 36

WSU-Carbon-Lab/dft-learn

Machine Learning from DFT calculations on organic molecules.

Language: Jupyter Notebook - Size: 48.8 MB - Last synced at: about 21 hours ago - Pushed at: about 23 hours ago - Stars: 0 - Forks: 0

grimme-lab/mctc-lib

Modular computation tool chain library

Language: Fortran - Size: 7.89 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 19 - Forks: 20

ml-evs/matador

⚗️ matador is an aggregator, manipulator and runner of first-principles calculations, written with a bent towards battery 🔋 electrode materials.

Language: Python - Size: 40.4 MB - Last synced at: about 8 hours ago - Pushed at: 3 days ago - Stars: 33 - Forks: 20

SidSin0809/vina-batch-docking-windows

High-throughput molecular-docking toolkit for Windows

Language: Perl - Size: 859 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0

caprilesport/scripts

Collection of scripts I use

Language: Python - Size: 128 KB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 2 - Forks: 0

molssi-seamm/lammps_step

A SEAMM plug-in for LAMMPS, a forcefield-based molecular dynamics code.

Language: Python - Size: 13.6 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 2 - Forks: 2

OpenChemistry/avogadrolibs

Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Language: C++ - Size: 76.5 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 552 - Forks: 203

MRChemSoft/mrchem

MultiResolution Chemistry

Language: C++ - Size: 86.1 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 34 - Forks: 25

JaGeo/LobsterPy

Package to perform automatic bonding analysis with the program Lobster in the field of computational materials science and quantum chemistry

Language: Python - Size: 147 MB - Last synced at: about 9 hours ago - Pushed at: 2 days ago - Stars: 101 - Forks: 34

nwchemgit/nwchem

NWChem: Open Source High-Performance Computational Chemistry

Language: Fortran - Size: 341 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 562 - Forks: 178

aaravdave/MSAffect

MSAffect is a computational pipeline to evaluate the robustness of AlphaFold2 protein structure predictions under adversarial MSA perturbations to identify structural sensitivity and confidence shifts in neural-network-based folding.

Language: Python - Size: 654 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 5 - Forks: 0

andizuend/AIOMFAC

Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients (AIOMFAC) model code (used within the online model AIOMFAC-web)

Language: Fortran - Size: 3.94 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 21 - Forks: 6

MDAnalysis/mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Language: Python - Size: 521 MB - Last synced at: 3 days ago - Pushed at: 14 days ago - Stars: 1,456 - Forks: 723

DoNOF/DoNOFsw

Donostia Natural Orbital Functional Software

Language: BASIC - Size: 9.81 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 20 - Forks: 6

grimme-lab/xtb-python

Python API for the extended tight binding program package

Language: Python - Size: 131 KB - Last synced at: 4 days ago - Pushed at: about 1 year ago - Stars: 116 - Forks: 33

GANGTONGH/Discrete-Molecular-Dynamics-Data-Analysis-Toolkit

This GitHub repository contains utility programs for the analysis of simulation data generated by Discrete Molecular Dynamics.

Language: Python - Size: 4.92 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 3 - Forks: 0

dftd3/simple-dftd3

Library first implementation of the D3 dispersion correction

Language: Fortran - Size: 1.68 MB - Last synced at: about 13 hours ago - Pushed at: 10 days ago - Stars: 70 - Forks: 32

ifilot/pyqint

An Educational Hartree-Fock Code in Python: Transparent Implementation of Gaussian-Type Integrals, SCF Procedures, and Geometry Optimization

Language: Python - Size: 6.87 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 33 - Forks: 10

greglandrum/rdkit-blog

RDKit blog

Language: Jupyter Notebook - Size: 104 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 8 - Forks: 2

SMTG-Bham/ShakeNBreak

Defect structure-searching employing chemically-guided bond distortions

Language: Python - Size: 103 MB - Last synced at: 5 days ago - Pushed at: 11 days ago - Stars: 103 - Forks: 21

glotzerlab/freud

Powerful, efficient particle trajectory analysis in scientific Python.

Language: C++ - Size: 82.4 MB - Last synced at: 6 days ago - Pushed at: 28 days ago - Stars: 302 - Forks: 52

popelier-group/ichor

Computational Chemistry Data Management Library for Machine Learning Force Field Development

Language: Python - Size: 86.1 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 20 - Forks: 8

tgraphite/reax_tools

A high performace ReaxFF/AIMD trajectory analysis tool based on graph theory.

Language: Python - Size: 46.9 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 61 - Forks: 4

mzmine/mzmine

mzmine source code repository

Language: Java - Size: 758 MB - Last synced at: about 18 hours ago - Pushed at: 6 days ago - Stars: 237 - Forks: 149

lmmentel/awesome-python-chemistry

A curated list of Python packages related to chemistry

Size: 224 KB - Last synced at: 5 days ago - Pushed at: 11 months ago - Stars: 1,268 - Forks: 225

psi4/psi4

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

Language: C++ - Size: 139 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1,078 - Forks: 465

Avogadro/two.avogadro.cc

Documentation and development website for Avogadro2

Language: Python - Size: 209 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 14 - Forks: 40

apax-hub/apax

A flexible and performant framework for training machine learning potentials.

Language: Python - Size: 6.22 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 28 - Forks: 4

westpa/westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

Language: Python - Size: 34.2 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 203 - Forks: 58

general-molecular-simulations/so3lr

SO3krates and Universal Pairwise Force Field for Molecular Simulation

Language: Python - Size: 15.3 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 110 - Forks: 9

deepmodeling/deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

Language: Python - Size: 70.4 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1,734 - Forks: 569

akensert/molgraph

Graph neural networks for molecular machine learning. Implemented and compatible with TensorFlow and Keras.

Language: Python - Size: 1.73 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 59 - Forks: 5

Qiskit/qiskit-addon-sqd

Sample-based Quantum Diagonalization: Classically postprocess noisy quantum samples to yield more accurate eigenvalue estimations.

Language: Python - Size: 3.05 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 69 - Forks: 23

h-brough/TUNA

A user-friendly quantum chemistry program for diatomics.

Language: Python - Size: 10.3 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 1 - Forks: 0

molssi-seamm/seamm_util

Utility classes and functions that support other MolSSI tools

Language: Python - Size: 5.83 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 1 - Forks: 3

molssi-seamm/seamm_widgets

Custom widgets to support the MolSSI Framework

Language: Python - Size: 5.83 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 2 - Forks: 2

molssi-seamm/seamm

The core of the SEAMM environment and graphical interface.

Language: Python - Size: 9.41 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 14 - Forks: 2

pfloos/QuAcK

QuAcK: a software for emerging quantum electronic structure methods

Language: Fortran - Size: 21 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 28 - Forks: 12

JuliaMolSim/DFTK.jl

Density-functional toolkit

Language: Julia - Size: 94.3 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 486 - Forks: 95

mitkeng/peas

A user-friendly application for precise conformation sampling

Size: 1.76 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 2 - Forks: 0

OpenBioSim/biosimspace

An interoperable Python framework for biomolecular simulation.

Language: Python - Size: 39.4 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 120 - Forks: 18

JDCurry/spatial-needleman-wunsch

A deterministic dynamic programming framework for molecular docking that eliminates stochastic variability while providing complete interpretability

Language: Jupyter Notebook - Size: 568 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

MolSSI/QCElemental

Periodic table, physical constants, and molecule parsing for quantum chemistry.

Language: Python - Size: 35 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 167 - Forks: 71

Dunni3/FlowMol

Mixed continous/categorical flow-matching model for de novo molecule generation.

Language: Python - Size: 3.82 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 123 - Forks: 6

tjira/acorn

Fast and simple way to electronic structure methods.

Language: Zig - Size: 47.1 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 0

Nix-QChem/NixOS-QChem

Nix expressions for HPC/Quantum chemistry software packages

Language: Nix - Size: 7.01 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 95 - Forks: 16

tensorcircuit/TenCirChem-NG

Quantum computational chemistry based on TensorCircuit

Language: Python - Size: 3.52 MB - Last synced at: 3 days ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 4

grimme-lab/CENSO

CENSO - Commandline ENergetic SOrting of Conformer Rotamer Ensembles

Language: Python - Size: 1.56 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 29 - Forks: 13

MDAnalysis/mdacli

Command line interface for MDAnalysis

Language: Python - Size: 7.15 MB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 20 - Forks: 7

soilqualitylab/soilqualitylab.github.io Fork of MarkBruns/PKE

Curated Portfolio For A 100-Module Graduate Curriculum in ML/AI Ops Engineering Development of Soil Quality Laboratory Foundation Models Using A Set Of 100 Foundational Model Concepts

Language: HTML - Size: 187 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

WMD-group/SMACT

Python package to aid materials design and informatics

Language: Python - Size: 43.2 MB - Last synced at: about 3 hours ago - Pushed at: 2 days ago - Stars: 121 - Forks: 29

qcserenity/serenity

The release-only repository of the subsystem focused quantum chemistry code Serenity

Language: C++ - Size: 35.8 MB - Last synced at: 10 days ago - Pushed at: 4 months ago - Stars: 37 - Forks: 9

JuaoSea/Chemistry

Language: Jupyter Notebook - Size: 4.27 MB - Last synced at: 11 days ago - Pushed at: 12 days ago - Stars: 1 - Forks: 0

JuDFTteam/best-of-atomistic-machine-learning

🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.

Size: 5.8 MB - Last synced at: 12 days ago - Pushed at: 14 days ago - Stars: 533 - Forks: 45

rk-lindsey/chimes_lsq

Tools to develop ChIMES parameter sets

Language: DIGITAL Command Language - Size: 2.26 GB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 2 - Forks: 25

cesoie44/numerical-methods-physical-chemistry

Fortran implementations of numerical algorithms for computational chemistry

Language: Fortran - Size: 12.7 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

mir-group/nequip

NequIP is a code for building E(3)-equivariant interatomic potentials

Language: Python - Size: 4.25 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 768 - Forks: 170

OpenFreeEnergy/openfe

The Open Free Energy toolkit

Language: Python - Size: 74.1 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 190 - Forks: 30

Theozeud/AtomicKohnSham

Solver to compute the groundstate of atoms and ions formulated in the Extended-Kohn-Sham framework.

Language: Julia - Size: 18.5 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 2 - Forks: 0

Dirac4pi/TRESC

Thomas Relativistic Electronic Structure Calculation

Language: Fortran - Size: 74.4 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 6 - Forks: 0

gph82/mdciao

mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data

Language: Python - Size: 76.6 MB - Last synced at: 12 days ago - Pushed at: about 2 months ago - Stars: 35 - Forks: 6

mitkeng/SEER

Gas phase molecular charge state predictor

Language: Jupyter Notebook - Size: 1.04 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 2 - Forks: 0

MolSSI/QCFractal

A distributed compute and database platform for quantum chemistry.

Language: Python - Size: 77.6 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 154 - Forks: 52

ajz34/libcint-rs

Rust FFI and wrapper of libcint, a GTO electronic integral engine (C language).

Language: C - Size: 1.24 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 4 - Forks: 0

huymanhnguyen0811/Arson

This repo is a demonstration of the workflow of the paper: An open-access computational fingerprinting workflow for source classifications of neat gasoline using GC×GC-TOFMS and Machine Learning

Language: R - Size: 7.82 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

berquist/personal_scripts

Personal scripts, mostly for computational chemistry analysis.

Language: Python - Size: 639 KB - Last synced at: 5 days ago - Pushed at: 15 days ago - Stars: 7 - Forks: 3

WMD-group/PDynA

Python package to analyse the structural dynamics of perovskites

Language: Python - Size: 106 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 44 - Forks: 4

dralgroup/mlatom

AI-enhanced computational chemistry

Language: Python - Size: 196 MB - Last synced at: 12 days ago - Pushed at: 16 days ago - Stars: 105 - Forks: 15

hbar-team/SPyCCI

The Simple Python Computational Chemistry Interface (SPyCCI) provides a simple interface to run calculation and analysis using a wide range of computational chemistry softwares.

Language: Python - Size: 49.4 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 2 - Forks: 3

JCelestial/molFrame

For when you are tired of writing new scripts for every Molecular Simulation

Language: Fortran - Size: 229 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0

grimme-lab/dxtb

Efficient And Fully Differentiable Extended Tight-Binding

Language: Python - Size: 3.34 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 100 - Forks: 20

ChiCheng45/Gaussium

A Quantum Chemistry program written in Python 3 supporting RHF, UHF, TDHF, CIS, MP2, DFT, CCSD and CCSD(T) methods.

Language: Python - Size: 787 KB - Last synced at: 11 days ago - Pushed at: over 4 years ago - Stars: 69 - Forks: 22

qcscine/chemoton

Language: Python - Size: 1.19 MB - Last synced at: 13 days ago - Pushed at: about 1 year ago - Stars: 51 - Forks: 6

ecrl/padelpy

A Python wrapper for PaDEL-Descriptor software

Language: Python - Size: 19.5 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 211 - Forks: 39

zotko/xyz2graph

Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

Language: Python - Size: 7.5 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 86 - Forks: 22

mminotaki/ml_dacs

A machine learning workflow for assessing the stability of Dual-Atom Catalysts with respect to aggregation.

Language: Jupyter Notebook - Size: 31.6 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0

rangsimanketkaew/AWS-HPC

AWS resources for high-performance scientific computing

Language: Shell - Size: 297 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0

WMD-group/ElementEmbeddings

Python package to interact with high-dimensional representations of the chemical elements

Language: Python - Size: 43.6 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 44 - Forks: 4

grimme-lab/multicharge

Electronegativity equilibration model for atomic partial charges

Language: Fortran - Size: 138 KB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 19 - Forks: 16

junxia97/awesome-pretrain-on-molecules

[IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models

Size: 565 KB - Last synced at: about 16 hours ago - Pushed at: about 2 years ago - Stars: 531 - Forks: 59

ma3ke/molly

Read xtc files, fast.

Language: Rust - Size: 171 MB - Last synced at: 18 days ago - Pushed at: 24 days ago - Stars: 5 - Forks: 1

dftd4/dftd4

Generally Applicable Atomic-Charge Dependent London Dispersion Correction

Language: Fortran - Size: 2.13 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 194 - Forks: 54

SUNCAT-Center/CatLearn

A machine learning environment for atomic-scale modeling in surface science and catalysis.

Language: Python - Size: 89.9 MB - Last synced at: 19 days ago - Pushed at: about 1 year ago - Stars: 114 - Forks: 67

3dmol/3Dmol.js

WebGL accelerated JavaScript molecular graphics library

Language: Jupyter Notebook - Size: 1.01 GB - Last synced at: 17 days ago - Pushed at: about 1 month ago - Stars: 888 - Forks: 211

RMeli/spyrmsd

📐 Symmetry-corrected RMSD in Python

Language: Python - Size: 787 KB - Last synced at: about 2 hours ago - Pushed at: 17 days ago - Stars: 101 - Forks: 9

Eipgen/Neural-Network-Models-for-Chemistry

A collection of Nerual Network Models for chemistry

Size: 271 KB - Last synced at: 12 days ago - Pushed at: 22 days ago - Stars: 154 - Forks: 24

SMTG-Bham/sumo

Heavyweight plotting tools for ab initio calculations

Language: Python - Size: 315 MB - Last synced at: about 3 hours ago - Pushed at: 4 months ago - Stars: 227 - Forks: 86

duartegroup/autodE

automated reaction profile generation

Language: Python - Size: 71.6 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 186 - Forks: 62

Edinburgh-Chemistry-Teaching/MD_ResearchTechniques

Materials for the "Introduction to Computational Chemistry Techniques" course at the University of Edinburgh

Language: HTML - Size: 277 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 2 - Forks: 3

pfloos/QUESTDB

QUESTDB: A Database of Highly-Accurate Excitation Energies

Language: TeX - Size: 49.7 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 16 - Forks: 2

OSU-NLP-Group/AutoSDT

AutoSDT is a fully automatic pipeline to collect data-driven scientific coding tasks to train co-scientist models.

Language: Python - Size: 4.25 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 10 - Forks: 0

Atomic-Samplers/quansino

`quansino` is a modular package based on the Atomic Simulation Environment (ASE) for quickly building custom Monte Carlo algorithms

Language: Python - Size: 3.27 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 28 - Forks: 1

phatdatnguyen/HCMUTE_Cheminformatics

Cheminformatics course at [Ho Chi Minh City University of Technology and Education (HCMUTE)

Language: Jupyter Notebook - Size: 61.4 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 1 - Forks: 0

markovmodel/deeptime

Deep learning meets molecular dynamics.

Language: Jupyter Notebook - Size: 2.57 MB - Last synced at: 21 days ago - Pushed at: over 6 years ago - Stars: 182 - Forks: 41

cclib/cclib

Parsers and algorithms for computational chemistry logfiles

Language: Python - Size: 81.8 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 370 - Forks: 175