deepmodeling/deepmd-kit

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

Language: Python - Size: 63.5 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1,642 - Forks: 546

MDAnalysis/mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Language: Python - Size: 511 MB - Last synced at: 4 days ago - Pushed at: 7 days ago - Stars: 1,423 - Forks: 711

lmmentel/awesome-python-chemistry

A curated list of Python packages related to chemistry

Size: 224 KB - Last synced at: 16 days ago - Pushed at: 7 months ago - Stars: 1,220 - Forks: 220

psi4/psi4

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

Language: C++ - Size: 133 MB - Last synced at: 3 days ago - Pushed at: 9 days ago - Stars: 1,053 - Forks: 463

3dmol/3Dmol.js

WebGL accelerated JavaScript molecular graphics library

Language: Jupyter Notebook - Size: 861 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 858 - Forks: 206

mir-group/nequip

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

Language: Python - Size: 3.8 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 718 - Forks: 154

gnina/gnina

A deep learning framework for molecular docking

Language: C++ - Size: 240 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 704 - Forks: 157

Mariewelt/OpenChem

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

Language: Python - Size: 162 MB - Last synced at: 13 days ago - Pushed at: over 1 year ago - Stars: 703 - Forks: 116

grimme-lab/xtb

Semiempirical Extended Tight-Binding Program Package

Language: Fortran - Size: 5.46 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 653 - Forks: 158

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: 540 - Forks: 172

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: 69.8 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 526 - Forks: 191

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: 12 days ago - Pushed at: almost 2 years ago - Stars: 522 - Forks: 54

JuDFTteam/best-of-atomistic-machine-learning

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

Size: 5.63 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 490 - Forks: 44

JuliaMolSim/DFTK.jl

Density-functional toolkit

Language: Julia - Size: 86.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 474 - Forks: 93

MolSSI/cookiecutter-cms

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

Language: Python - Size: 340 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 424 - Forks: 92

mir-group/allegro

Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials

Language: Python - Size: 468 KB - Last synced at: about 20 hours ago - Pushed at: about 21 hours ago - Stars: 394 - Forks: 55

cclib/cclib

Parsers and algorithms for computational chemistry logfiles

Language: Python - Size: 75.8 MB - Last synced at: about 6 hours ago - Pushed at: about 7 hours ago - Stars: 362 - Forks: 170

psi4/psi4numpy

Combining Psi4 and Numpy for education and development.

Language: Jupyter Notebook - Size: 11.6 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 360 - Forks: 164

MinkaiXu/GeoDiff

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

Language: Python - Size: 2.19 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 354 - Forks: 78

glotzerlab/freud

Powerful, efficient particle trajectory analysis in scientific Python.

Language: C++ - Size: 82.4 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 292 - Forks: 51

PytLab/VASPy

Manipulating VASP files with Python.

Language: Python - Size: 21.1 MB - Last synced at: about 20 hours ago - Pushed at: almost 3 years ago - Stars: 282 - Forks: 99

lukasturcani/stk

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

Language: Python - Size: 44.8 MB - Last synced at: 11 days ago - Pushed at: 6 months ago - Stars: 261 - Forks: 51

atomicarchitects/equiformer_v2

[ICLR 2024] EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations

Language: Python - Size: 7.64 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 254 - Forks: 35

jensengroup/xyz2mol

Converts an xyz file to an RDKit mol object

Language: Python - Size: 170 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 254 - Forks: 70

choderalab/software-development

A primer on software development best practices for computational chemistry

Size: 151 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 247 - Forks: 79

atomicarchitects/equiformer

[ICLR 2023 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs

Language: Python - Size: 3.95 MB - Last synced at: 13 days ago - Pushed at: 3 months ago - Stars: 233 - Forks: 44

crest-lab/crest

CREST - A program for the automated exploration of low-energy molecular chemical space.

Language: Fortran - Size: 2.03 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 231 - Forks: 49

SMTG-Bham/sumo

Heavyweight plotting tools for ab initio calculations

Language: Python - Size: 315 MB - Last synced at: 3 days ago - Pushed at: 9 days ago - Stars: 221 - Forks: 85

BioinfoMachineLearning/bio-diffusion

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

Language: Python - Size: 48.1 MB - Last synced at: 1 day ago - Pushed at: 8 months ago - Stars: 202 - Forks: 27

ecrl/padelpy

A Python wrapper for PaDEL-Descriptor software

Language: Python - Size: 19.5 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 200 - Forks: 37

westpa/westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

Language: Python - Size: 46.7 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 198 - Forks: 57

lumol-org/lumol

Universal extensible molecular simulation engine

Language: Rust - Size: 4.53 MB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 196 - Forks: 18

msmbuilder/vde

Variational Autoencoder for Dimensionality Reduction of Time-Series

Language: Jupyter Notebook - Size: 781 KB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 183 - Forks: 44

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: 802 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 182 - Forks: 33

dftd4/dftd4

Generally Applicable Atomic-Charge Dependent London Dispersion Correction

Language: Fortran - Size: 2 MB - Last synced at: 3 days ago - Pushed at: 12 days ago - Stars: 182 - Forks: 53

MolSSI/QCEngine

Quantum chemistry program executor and IO standardizer (QCSchema).

Language: Python - Size: 11 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 182 - Forks: 81

UCLCheminformatics/ScaffoldGraph

ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.

Language: Python - Size: 781 KB - Last synced at: 4 days ago - Pushed at: over 3 years ago - Stars: 180 - Forks: 40

duartegroup/autodE

automated reaction profile generation

Language: Python - Size: 71.1 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 179 - Forks: 59

markovmodel/deeptime

Deep learning meets molecular dynamics.

Language: Jupyter Notebook - Size: 2.57 MB - Last synced at: 4 days ago - Pushed at: about 6 years ago - Stars: 178 - Forks: 40

merzlab/QUICK

QUICK: A GPU-enabled ab intio quantum chemistry software package

Language: C - Size: 162 MB - Last synced at: about 24 hours ago - Pushed at: 1 day ago - Stars: 172 - Forks: 47

chemfiles/chemfiles

Library for reading and writing chemistry files

Language: C++ - Size: 100 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 171 - Forks: 51

OpenFreeEnergy/openfe

The Open Free Energy toolkit

Language: Python - Size: 65.6 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 162 - Forks: 25

MolSSI/QCElemental

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

Language: Python - Size: 34.4 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 161 - Forks: 72

MolSSI/QCFractal

A distributed compute and database platform for quantum chemistry.

Language: Python - Size: 74 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 153 - Forks: 51

theochem/iodata

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

Language: Python - Size: 5.07 MB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 137 - Forks: 48

Eipgen/Neural-Network-Models-for-Chemistry

A collection of Nerual Network Models for chemistry

Size: 649 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 124 - Forks: 18

GrossfieldLab/loos

LOOS: a lightweight object-oriented structure analysis library

Language: C++ - Size: 119 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 122 - Forks: 26

MolecularAI/QSARtuna

QSARtuna: QSAR model building with the optuna framework

Language: Jupyter Notebook - Size: 106 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 115 - Forks: 17

grimme-lab/xtb-python

Python API for the extended tight binding program package

Language: Python - Size: 131 KB - Last synced at: 2 days ago - Pushed at: 9 months ago - Stars: 113 - Forks: 32

diffqc/dqc

Differentiable Quantum Chemistry (only Differentiable Density Functional Theory and Hartree Fock at the moment)

Language: Python - Size: 70.9 MB - Last synced at: 8 days ago - Pushed at: about 3 years ago - Stars: 111 - Forks: 13

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: 6 days ago - Pushed at: 11 months ago - Stars: 110 - Forks: 66

WMD-group/SMACT

Python package to aid materials design and informatics

Language: Python - Size: 44.4 MB - Last synced at: 3 days ago - Pushed at: 11 days ago - Stars: 108 - Forks: 26

Dunni3/FlowMol

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

Language: Python - Size: 1.6 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 102 - Forks: 6

RMeli/spyrmsd

📐 Symmetry-corrected RMSD in Python

Language: Python - Size: 776 KB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 98 - Forks: 9

qubekit/QUBEKit

Quantum Mechanical Bespoke Force Field Derivation Toolkit

Language: Python - Size: 6.77 MB - Last synced at: 4 days ago - Pushed at: 11 months ago - Stars: 98 - Forks: 32

zadorlab/sella

A Python software package for saddle point optimization and minimization of atomic systems.

Language: Python - Size: 451 KB - Last synced at: 20 days ago - Pushed at: 7 months ago - Stars: 96 - Forks: 24

SUNCAT-Center/CatKit

General purpose tools for high-throughput catalysis

Language: Python - Size: 24.9 MB - Last synced at: about 6 hours ago - Pushed at: about 6 hours ago - Stars: 94 - Forks: 54

SMTG-Bham/ShakeNBreak

Defect structure-searching employing chemically-guided bond distortions

Language: Python - Size: 98.9 MB - Last synced at: 3 days ago - Pushed at: 9 days ago - Stars: 92 - Forks: 20

swsoyee/r3dmol

🧬 An R package for visualizing molecular data in 3D

Language: JavaScript - Size: 31.4 MB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 90 - Forks: 5

cxhernandez/molencoder

Molecular AutoEncoder in PyTorch

Language: Python - Size: 49.8 MB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 90 - Forks: 17

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: 146 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 87 - Forks: 31

grimme-lab/dxtb

Efficient And Fully Differentiable Extended Tight-Binding

Language: Python - Size: 3.52 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 87 - Forks: 15

Nix-QChem/NixOS-QChem

Nix expressions for HPC/Quantum chemistry software packages

Language: Nix - Size: 6.86 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 87 - Forks: 17

zotko/xyz2graph

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

Language: Python - Size: 7.61 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 86 - Forks: 23

qcscine/sparrow

Language: C++ - Size: 58.2 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 84 - Forks: 15

michellab/BioSimSpace

Code and resources for the EPSRC BioSimSpace project.

Language: Python - Size: 36.1 MB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 79 - Forks: 19

bio-phys/MDBenchmark

Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

Language: Python - Size: 1.29 MB - Last synced at: 29 days ago - Pushed at: 8 months ago - Stars: 78 - Forks: 17

OpenBioSim/biosimspace

An interoperable Python framework for biomolecular simulation.

Language: Python - Size: 38.7 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 75 - Forks: 11

QuantumPackage/qp2

Quantum Package : a programming environment for wave function methods

Language: Fortran - Size: 45.3 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 74 - Forks: 36

hande-qmc/hande

Open source stochastic quantum chemistry

Language: Fortran - Size: 129 MB - Last synced at: 1 day ago - Pushed at: 25 days ago - Stars: 74 - Forks: 18

wonmor/ElectronVisualized

Public Archive: Beautiful and Elegant Quantum Mechanics Visualization.

Language: JavaScript - Size: 102 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 71 - Forks: 2

dralgroup/mlatom

AI-enhanced computational chemistry

Language: Python - Size: 194 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 70 - Forks: 11

theochem/grid

Python library for numerical integration, interpolation, and differentiation on (molecular) grids.

Language: Python - Size: 84.8 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 67 - Forks: 27

tjz21/DFT_PIB_Code

Interactive Jupyter Notebooks for learning the fundamentals of Density-Functional Theory (DFT)

Language: Jupyter Notebook - Size: 45.2 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 66 - Forks: 11

cyllab/CalcUS

Quantum Chemistry Web Platform

Language: JavaScript - Size: 312 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 65 - Forks: 19

dftd3/simple-dftd3

Library first implementation of the D3 dispersion correction

Language: Fortran - Size: 1.72 MB - Last synced at: 3 days ago - Pushed at: 11 days ago - Stars: 64 - Forks: 31

tencent-quantum-lab/TenCirChem

Quantum computational chemistry based on TensorCircuit

Language: Python - Size: 2.51 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 64 - Forks: 13

AstraZeneca/kallisto

Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.

Language: Python - Size: 445 KB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 64 - Forks: 21

SMTG-Bham/surfaxe

Dealing with slabs for first principles calculations of surfaces

Language: Jupyter Notebook - Size: 36.5 MB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 63 - Forks: 14

jag1g13/pycgtool

Generate coarse-grained molecular dynamics models from atomistic trajectories.

Language: Python - Size: 6.39 MB - Last synced at: 19 days ago - Pushed at: over 2 years ago - Stars: 63 - Forks: 12

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: over 1 year ago - Pushed at: almost 4 years ago - Stars: 63 - Forks: 21

servierhub/top-pharma50

Top open source software from the top 50 pharmaceutical companies

Language: Makefile - Size: 540 KB - Last synced at: 8 days ago - Pushed at: 11 months ago - Stars: 62 - Forks: 3

pnnl/isicle

In silico chemical library engine for high-accuracy chemical property prediction

Language: Python - Size: 19.9 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 60 - Forks: 20

aromanro/PythonCompphys

Some python workbooks with various topics from Computational Physics

Language: Jupyter Notebook - Size: 62.4 MB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 59 - Forks: 12

aromanro/HartreeFock

A program implementing the Hartree–Fock (also post-HF: MP2, CCSD(T), CIS and TDHF/RPA)/self-consistent field method (also DIIS) with Gaussian orbitals

Language: C++ - Size: 718 KB - Last synced at: 25 days ago - Pushed at: 10 months ago - Stars: 57 - Forks: 17

ncfrey/litmatter

Rapid experimentation and scaling of deep learning models on molecular and crystal graphs.

Language: Jupyter Notebook - Size: 511 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 55 - Forks: 13

Qiskit/qiskit-addon-sqd

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

Language: Python - Size: 2.74 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 54 - Forks: 16

XieResearchGroup/Physics-aware-Multiplex-GNN

Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"

Language: Python - Size: 1.43 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 54 - Forks: 10

SMTG-Bham/easyunfold

Band structure unfolding made easy!

Language: Python - Size: 231 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 53 - Forks: 11

lipelopesoliveira/pyCOFBuilder

A package for Covalent Organic Frameworks structure assembly based on specific building block, topology and functional groups based on the reticular approach

Language: Python - Size: 31.4 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 53 - Forks: 4

chopralab/lemon

A framework for rapidly mining structural information from the Protein Data Bank

Language: C++ - Size: 7.62 MB - Last synced at: 4 days ago - Pushed at: almost 5 years ago - Stars: 53 - Forks: 12

SMTG-Bham/ThermoParser

A tool for streamlining data analysis and visualisation for thermoelectrics and charge carrier transport in computational materials science.

Language: Python - Size: 198 MB - Last synced at: 3 days ago - Pushed at: 8 days ago - Stars: 52 - Forks: 16

akensert/molgraph

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

Language: Python - Size: 1.71 MB - Last synced at: about 7 hours ago - Pushed at: 2 months ago - Stars: 52 - Forks: 5

MinkaiXu/ConfVAE-ICML21

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming (ICML'21)

Language: Python - Size: 381 KB - Last synced at: about 1 month ago - Pushed at: almost 4 years ago - Stars: 51 - Forks: 15

QChASM/AaronTools.py

Python tools for automating routine tasks encountered when running quantum chemistry computations.

Language: Python - Size: 8.17 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 49 - Forks: 8

geem-lab/overreact

⚛️📈 Create and analyze chemical microkinetic models built from computational chemistry data. Crafted at the @geem-lab.

Language: Python - Size: 96.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 48 - Forks: 7

Koushikphy/Interactive_Data_Editor

A Software to interactively edit data in a graphical manner

Language: JavaScript - Size: 41.6 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 46 - Forks: 10

qcscine/chemoton

Language: Python - Size: 1.19 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 46 - Forks: 6

lanl/Architector

The architector python package - for 3D metal complex design. C22085

Language: Python - Size: 14.1 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 45 - Forks: 8

LCPQ/quantum_package 📦

Set of quantum chemistry programs and libraries

Language: Fortran - Size: 38.7 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 45 - Forks: 39