computational-chemistry

There are 117 repositories under computational-chemistry topic.

deepmd-kit
deepmodeling / deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
ase c computational-chemistry cpp cuda deep-learning deepmd ipi lammps materials-science molecular-dynamics nodejs potential-energy python pytorch rocm tensorflow
Language:C++ 1408
MDAnalysis / mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
molecular-dynamics python science trajectory-analysis molecular-simulation molecular-dynamics-simulation mdanalysis computational-chemistry
Language:Python 1256
lmmentel / awesome-python-chemistry
A curated list of Python packages related to chemistry
atomistic-simulations chemistry computational-chemistry molecular-dynamics python-chemistry quantum-chemistry simulation
1054
psi4 / psi4
Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python
c-plus-plus chemistry computational-chemistry physics python quantum-chemistry
Language:C++ 938
3dmol / 3Dmol.js
WebGL accelerated JavaScript molecular graphics library
computational-biology computational-chemistry molecular-graphics molecular-modeling
Language:Jupyter Notebook 770
Mariewelt / OpenChem
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
computational-chemistry computational-biology deep-learning deep-neural-networks graph-convolutional-networks drug-discovery drug-design qsar predictive-modeling machine-learning pytorch
Language:Python 667
gnina / gnina
A deep learning framework for molecular docking
convolutional-neural-networks cheminformatics computational-chemistry molecular-modeling drug-discovery
Language:C++ 573
nequip
mir-group / nequip
NequIP is a code for building E(3)-equivariant interatomic potentials
atomistic-simulations computational-chemistry deep-learning drug-discovery force-fields interatomic-potentials machine-learning materials-science molecular-dynamics pytorch
Language:Python 559
xtb
grimme-lab / xtb
Semiempirical Extended Tight-Binding Program Package
quantum-chemistry tight-binding computational-chemistry atomistic-simulations force-field
Language:Fortran 552
nwchemgit / nwchem
NWChem: Open Source High-Performance Computational Chemistry
computational-chemistry parallel-computing electronic-structure-calculations molecular-simulation density-functional-theory nwchem chemistry hartree-fock quantum-chemistry
Language:Fortran 481
junxia97 / awesome-pretrain-on-molecules
[IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models
gnns transfer-learning drug-discovery molecule self-supervised-learning survey awesome graph-representation-learning finetuning molecular-representation-learning computational-chemistry drug-discovery-and-development chemical-language-models
464
avogadrolibs
OpenChemistry / avogadrolibs
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
chemistry scientific-computing open-source open-science opengl visualization desktop compchem avogadro computational-chemistry openchemistry hacktoberfest cross-platform qt5
Language:C++ 417
DFTK.jl
JuliaMolSim / DFTK.jl
Density-functional toolkit
electronic-structure density-functional-theory kohn-sham toolkit mathematical-analysis julia plane-wave ab-initio numerical-analysis computational-chemistry materials-science
Language:Julia 412
MolSSI / cookiecutter-cms
Python-centric Cookiecutter for Molecular Computational Chemistry Packages
cookiecutter python-packages molecular-sciences conda-environment pytest conda-forge computational-chemistry github-actions
Language:Python 370
psi4 / psi4numpy
Combining Psi4 and Numpy for education and development.
computational-chemistry numpy psi python scipy tutorial
Language:Jupyter Notebook 329
cclib / cclib
Parsers and algorithms for computational chemistry logfiles
computational-chemistry hacktoberfest python quantum-chemistry
Language:Python 319
MinkaiXu / GeoDiff
Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
molecule graph-neural-networks generative-models conformation iclr iclr2022 diffusion-models score-matching computational-biology computational-chemistry
Language:Python 314
mir-group / allegro
Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials
atomistic-simulations computational-chemistry deep-learning drug-discovery force-fields interatomic-potentials machine-learning materials-science molecular-dynamics pytorch
Language:Python 297
JuDFTteam / best-of-atomistic-machine-learning
🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.
ai4science atomistic-machine-learning awesome-list best-of-list computational-chemistry computational-materials-science condensed-matter density-functional-theory drug-discovery electronic-structure interatomic-potentials materials-discovery materials-informatics molecular-dynamics quantum-chemistry scientific-computing scientific-machine-learning surrogate-models
268
PytLab / VASPy
Manipulating VASP files with Python.
vasp data-processing data-visualization chemistry catalysis-informatics computational-chemistry
Language:Python 263
freud
glotzerlab / freud
Powerful, efficient particle trajectory analysis in scientific Python.
molecular-dynamics analysis scientific-computing python monte-carlo-simulation data-analysis spatial-analysis particle-system computational-chemistry computational-physics science hacktoberfest
Language:C++ 262
choderalab / software-development
A primer on software development best practices for computational chemistry
computational-chemistry development-practices python
254
stk
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.
chemistry cheminformatics reactions computational-science computational-chemistry materials-science materials-design materials-discoveries materials-screening molecular-structures molecular-modeling molecular-evolution
Language:Python 242
jensengroup / xyz2mol
Converts an xyz file to an RDKit mol object
computational-chemistry
Language:Python 241
lumol-org / lumol
Universal extensible molecular simulation engine
molecular-dynamics monte-carlo molecular-simulation computational-chemistry atomistic-simulations
Language:Rust 184
msmbuilder / vde
Variational Autoencoder for Dimensionality Reduction of Time-Series
variational-autoencoder molecular-dynamics computational-chemistry computational-biology time-series deep-learning pytorch python
Language:Jupyter Notebook 184
westpa / westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
computational-chemistry molecular-simulation
Language:Python 184
crest-lab / crest
CREST - A program for the automated exploration of low-energy molecular chemical space.
computational-chemistry tight-binding conformational-analysis atomistic-simulations metadynamics
Language:Fortran 182
SMTG-Bham / sumo
Heavyweight plotting tools for ab initio calculations
computational-chemistry materials-science plotting python
Language:Python 181
atomicarchitects / equiformer
[ICLR'23 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs
catalyst-design computational-chemistry deep-learning drug-discovery equivariant-graph-neural-network force-fields interatomic-potentials machine-learning molecular-dynamics pytorch ai-for-science equivariant-neural-networks graph-neural-networks e3nn geometric-deep-learning materials-science
Language:Python 180
markovmodel / deeptime
Deep learning meets molecular dynamics.
autoencoder computational-biology computational-chemistry data-analysis deep-learning dimension-reduction machine-learning markov-model python pytorch tensorflow time-series
Language:Jupyter Notebook 172
ecrl / padelpy
A Python wrapper for PaDEL-Descriptor software
computational-chemistry command-line-wrapper molecular-descriptors molecular-fingerprints padel python
Language:Python 170
atomicarchitects / equiformer_v2
[ICLR'24] EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations
catalyst-design computational-chemistry computational-physics deep-learning drug-discovery equivariant-graph-neural-network equivariant-neural-networks force-fields interatomic-potentials machine-learning molecular-dynamics pytorch ai-for-science graph-neural-networks e3nn geometric-deep-learning materials-science
Language:Python 164
duartegroup / autodE
automated reaction profile generation
computational-chemistry open-science
Language:Python 161
MolSSI / QCEngine
Quantum chemistry program executor and IO standardizer (QCSchema).
chemistry computational-chemistry python3 quantum-chemistry standards
Language:Python 161
ScaffoldGraph
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.
rdkit networkx scaffold-networks scaffold-trees cheminformatics murcko fragments molecules scaffolds hiers chemistry computational-chemistry
Language:Python 161