computational-chemistry

There are 120 repositories under computational-chemistry topic.

deepmd-kit
deepmodeling / deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
deep-learning molecular-dynamics deepmd lammps potential-energy python tensorflow cpp cuda rocm ipi ase computational-chemistry materials-science c nodejs pytorch jax
Language:C++ 1506
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 1321
lmmentel / awesome-python-chemistry
A curated list of Python packages related to chemistry
chemistry quantum-chemistry python-chemistry molecular-dynamics simulation computational-chemistry atomistic-simulations
1140
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++ 982
3dmol / 3Dmol.js
WebGL accelerated JavaScript molecular graphics library
computational-biology computational-chemistry molecular-graphics molecular-modeling
Language:Jupyter Notebook 814
Mariewelt / OpenChem
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
computational-biology computational-chemistry deep-learning deep-neural-networks drug-design drug-discovery graph-convolutional-networks machine-learning predictive-modeling pytorch qsar
Language:Python 681
nequip
mir-group / nequip
NequIP is a code for building E(3)-equivariant interatomic potentials
machine-learning atomistic-simulations molecular-dynamics computational-chemistry deep-learning interatomic-potentials force-fields pytorch drug-discovery materials-science
Language:Python 637
gnina / gnina
A deep learning framework for molecular docking
cheminformatics computational-chemistry convolutional-neural-networks drug-discovery molecular-modeling
Language:C++ 632
xtb
grimme-lab / xtb
Semiempirical Extended Tight-Binding Program Package
atomistic-simulations computational-chemistry force-field quantum-chemistry tight-binding
Language:Fortran 590
nwchemgit / nwchem
NWChem: Open Source High-Performance Computational Chemistry
chemistry computational-chemistry density-functional-theory electronic-structure-calculations hartree-fock molecular-simulation nwchem parallel-computing quantum-chemistry
Language:Fortran 513
junxia97 / awesome-pretrain-on-molecules
[IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models
awesome chemical-language-models computational-chemistry drug-discovery drug-discovery-and-development finetuning gnns graph-representation-learning molecular-representation-learning molecule self-supervised-learning survey transfer-learning
496
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.
avogadro chemistry compchem computational-chemistry cross-platform desktop hacktoberfest open-science open-source openchemistry opengl qt5 scientific-computing visualization
Language:C++ 461
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 445
JuDFTteam / best-of-atomistic-machine-learning
🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.
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 scientific-computing surrogate-models scientific-machine-learning quantum-chemistry ai4science
399
MolSSI / cookiecutter-cms
Python-centric Cookiecutter for Molecular Computational Chemistry Packages
computational-chemistry conda-environment conda-forge cookiecutter github-actions molecular-sciences pytest python-packages
Language:Python 399
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 347
psi4 / psi4numpy
Combining Psi4 and Numpy for education and development.
computational-chemistry numpy psi python scipy tutorial
Language:Jupyter Notebook 347
cclib / cclib
Parsers and algorithms for computational chemistry logfiles
computational-chemistry hacktoberfest python quantum-chemistry
Language:Python 336
MinkaiXu / GeoDiff
Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
computational-biology computational-chemistry conformation diffusion-models generative-models graph-neural-networks iclr iclr2022 molecule score-matching
Language:Python 332
freud
glotzerlab / freud
Powerful, efficient particle trajectory analysis in scientific Python.
analysis computational-chemistry computational-physics data-analysis hacktoberfest molecular-dynamics monte-carlo-simulation particle-system python science scientific-computing spatial-analysis
Language:C++ 280
PytLab / VASPy
Manipulating VASP files with Python.
catalysis-informatics chemistry computational-chemistry data-processing data-visualization vasp
Language:Python 271
choderalab / software-development
A primer on software development best practices for computational chemistry
computational-chemistry development-practices python
262
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 252
jensengroup / xyz2mol
Converts an xyz file to an RDKit mol object
computational-chemistry
Language:Python 250
atomicarchitects / equiformer_v2
[ICLR 2024] 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 216
atomicarchitects / equiformer
[ICLR 2023 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 211
crest-lab / crest
CREST - A program for the automated exploration of low-energy molecular chemical space.
atomistic-simulations computational-chemistry conformational-analysis metadynamics tight-binding
Language:Fortran 203
SMTG-Bham / sumo
Heavyweight plotting tools for ab initio calculations
computational-chemistry materials-science plotting python
Language:Python 202
westpa / westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
computational-chemistry molecular-simulation
Language:Python 194
lumol-org / lumol
Universal extensible molecular simulation engine
atomistic-simulations computational-chemistry molecular-dynamics molecular-simulation monte-carlo
Language:Rust 190
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 186
ecrl / padelpy
A Python wrapper for PaDEL-Descriptor software
computational-chemistry command-line-wrapper molecular-descriptors molecular-fingerprints padel python
Language:Python 184
markovmodel / deeptime
Deep learning meets molecular dynamics.
pytorch tensorflow dimension-reduction markov-model data-analysis machine-learning autoencoder time-series computational-biology computational-chemistry python deep-learning
Language:Jupyter Notebook 175
duartegroup / autodE
automated reaction profile generation
computational-chemistry open-science
Language:Python 172
MolSSI / QCEngine
Quantum chemistry program executor and IO standardizer (QCSchema).
chemistry computational-chemistry python3 quantum-chemistry standards
Language:Python 169
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 167