computational-chemistry

There are 113 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
Language:C++ 1358
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 1220
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
1023
psi4 / psi4
Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python
quantum-chemistry c-plus-plus python computational-chemistry chemistry physics
Language:C++ 921
3dmol / 3Dmol.js
WebGL accelerated JavaScript molecular graphics library
molecular-graphics molecular-modeling computational-biology computational-chemistry
Language:Jupyter Notebook 754
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 657
gnina / gnina
A deep learning framework for molecular docking
cheminformatics computational-chemistry convolutional-neural-networks drug-discovery molecular-modeling
Language:C++ 550
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 528
xtb
grimme-lab / xtb
Semiempirical Extended Tight-Binding Program Package
quantum-chemistry tight-binding computational-chemistry atomistic-simulations force-field
Language:Fortran 525
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 456
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
449
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++ 406
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 398
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 356
psi4 / psi4numpy
Combining Psi4 and Numpy for education and development.
python psi numpy tutorial scipy computational-chemistry
Language:Jupyter Notebook 323
cclib / cclib
Parsers and algorithms for computational chemistry logfiles
python computational-chemistry quantum-chemistry hacktoberfest
Language:Python 309
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 295
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 284
PytLab / VASPy
Manipulating VASP files with Python.
vasp data-processing data-visualization chemistry catalysis-informatics computational-chemistry
Language:Python 261
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++ 257
choderalab / software-development
A primer on software development best practices for computational chemistry
computational-chemistry development-practices python
250
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
240
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 236
jensengroup / xyz2mol
Converts an xyz file to an RDKit mol object
computational-chemistry
Language:Python 235
msmbuilder / vde
Variational Autoencoder for Dimensionality Reduction of Time-Series
computational-biology computational-chemistry deep-learning molecular-dynamics python pytorch time-series variational-autoencoder
Language:Jupyter Notebook 183
lumol-org / lumol
Universal extensible molecular simulation engine
molecular-dynamics monte-carlo molecular-simulation computational-chemistry atomistic-simulations
Language:Rust 182
westpa / westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
computational-chemistry molecular-simulation
Language:Python 181
SMTG-Bham / sumo
Heavyweight plotting tools for ab initio calculations
computational-chemistry materials-science plotting python
Language:Python 177
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 169
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 164
ecrl / padelpy
A Python wrapper for PaDEL-Descriptor software
command-line-wrapper computational-chemistry molecular-descriptors molecular-fingerprints padel python
Language:Python 164
chemfiles / chemfiles
Library for reading and writing chemistry files
computational-chemistry library files compchem cheminformatics chemistry hacktoberfest
Language:C++ 160
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 159
duartegroup / autodE
automated reaction profile generation
computational-chemistry open-science
Language:Python 158
MolSSI / QCEngine
Quantum chemistry program executor and IO standardizer (QCSchema).
chemistry computational-chemistry python3 quantum-chemistry standards
Language:Python 152
dftd4
dftd4 / dftd4
Generally Applicable Atomic-Charge Dependent London Dispersion Correction
quantum-chemistry dispersion-correction ase computational-chemistry pyscf qcschema fortran-package-manager
Language:Fortran 144