cownowan/dlmatreview

https://www.nature.com/articles/s41524-022-00734-6

dlmatreview

This repository contains links to software packages and databases used in deep-learning applications for materials science and engineering. If you would like to contribute similar repositories/packages, please fork this repository, add the information in the current format and make a pull request to this repository. We welcome your contributions!

Citation

https://www.nature.com/articles/s41524-022-00734-6

Atomistic databases and software packages

Database name	Datasize	Web
QM9	134k	http://quantum-machine.org/datasets/
ANI	20 mil	https://github.com/isayev/ANI1 dataset
MD17	1mil	http://quantum-machine.org/datasets/#md-datasets
Tox21	760k	https://tox21.gov/resources/
CCCBDB	2069	https://cccbdb.nist.gov/
HOPV15	350	https://doi.org/10.6084/m9.figshare.1610063
C2DB	4000	https://cmr.fysik.dtu.dk/c2db/c2db.html
FreeSolv	504	https://github.com/MobleyLab/FreeSolv
MP	144k	https://materialsproject.org/
OQMD	816k	http://oqmd.org/
AFLOW	3.5 mil	http://www.aflowlib.org/
JARVIS-DFT	56k	https://jarvis.nist.gov/jarvisdft/
JARVIS-FF	2.5k	https://jarvis.nist.gov/jarvisff/
NOMAD	11 mil	https://nomad-lab.eu/prod/rae/gui/search
MCloud	22mil	https://www.materialscloud.org/home#statistics
CoreMOF	163k	https://mof.tech.northwestern.edu/
QMOF	22k	https://github.com/arosen93/QMOF
PDB	183k	https://www.rcsb.org/
PDBBind	23k	http://www.pdbbind.org.cn/
MOAD	39k	http://www.bindingmoad.org/

Software packages

Modelname	Applications	Web
ALIGNN	Mol,Sol	https://github.com/usnistgov/alignn
SchNetPack	Mol,Sol	https://github.com/atomistic-machine-learning/schnetpack
CGCNN	Sol	https://github.com/txie-93/cgcnn
MEGNet	Mol,Sol	https://github.com/materialsvirtuallab/megnet
DimeNet	Mol	https://github.com/klicperajo/dimenet
MPNN	Mol	https://github.com/priba/nmpqc
ANI	Mol	https://github.com/isayev/ASEANI
Amp	Sol	https://bitbucket.org/andrewpeterson/amp
TensorMol	Mol	https://github.com/jparkhill/TensorMol
PROPhet	Sol	https://github.com/biklooost/PROPhet
DeepMD	Mol	https://github.com/deepmodeling/deepmd-kit
ænet	Sol	https://github.com/atomisticnet/aenet
E3NN	Mol	https://github.com/e3nn/e3nn
neural-fingerprint	Mol	https://github.com/HIPS/neural-fingerprint
DeepChemStable	Mol	https://github.com/MingCPU/DeepChemStable
MoleculeNet	Mol,Sol	https://github.com/deepchem/deepchem
dgl-lifesci	Prot	https://github.com/awslabs/dgl-lifesci
gnina	Prot	https://github.com/gnina/gnina

---

Chemicalformula

Modelname	Web
MatMiner	https://github.com/hackingmaterials/matminer
MagPie	https://bitbucket.org/wolverton/magpie
DScribe	https://github.com/SINGROUP/dscribe
ElemNet	https://github.com/NU-CUCIS/ElemNet
IRNet	https://github.com/NU-CUCIS/IRNet
Roost	https://github.com/CompRhys/roost
CrabNet	https://github.com/anthony-wang/CrabNet
CFID-Chem	https://github.com/usnistgov/jarvis/
Atom2vec	https://github.com/idocx/Atom2Vec

SMILES and fragments

Software name	Web
DeepSMILES	https://github.com/baoilleach/deepsmiles
ChemicalVAE	https://github.com/aspuru-guzik-group/chemicalvae
CVAE	https://github.com/jaechanglim/CVAE
DeepChem	https://github.com/deepchem/deepchem
DeepFRAG	https://git.durrantlab.pitt.edu/jdurrant/deepfrag/
DeepFRAG-k	https://github.com/yaohangli/DeepFragK/

Spectra based

DBname	Datasize	Web
MPXAS-DB	490k	https://materialsproject.org/
JVDielec.func.	16k	http://jarvis.nist.gov/jarvisdft
JVInfrared	5k	http://jarvis.nist.gov/jarvisdft
RRUFF	3527	https://rruff.info
ICDDXRD	1076439	https://www.icdd.com/pdf-product-summary/
ICSDXRD	150000	https://icsd.nist.gov/
MPXRD	140000	https://materialsproject.org/
JVXRD	60000	https://jarvis.nist.gov/jarvisdft/
Ramanopendb	1133	https://solsa.crystallography.net/rod/index.php
Chem.WebBook	1133	https://webbook.nist.gov/chemistry/
SDBS	34600	http://sdbs.riodb.aist.go.jp/sdbs/cgi-bin/creindex.cgi
NMRShiftDB	44371	https://nmrshiftdb.nmr.uni-koeln.de/
SpectraBase	?	https://spectrabase.com/
SOPspectrallib.	325	https://soprano.kikirpa.be/index.php?lib=sop
HTEM	140000	https://htem.nrel.gov/

Softwarename	Applications	Webpage
DOSNet	Sol	https://github.com/vxfung/DOSnet
PCA-CGCNN	Sol	https://github.com/kihoon-bang/PCA-CGCNN
autoXRD	Sol	https://github.com/PV-Lab/autoXRD

Image based

DB Name	Link
JARVIS-STM	https://jarvis.nist.gov/jarvisstm
atomagined	https://github.com/MaterialEyes/atomagined
deep damage	https://git.rwth-aachen.de/Sandra.Korte.Kerzel/DeepDamage/
NanoSEM	https://doi.org/10.1038/sdata.2018.172
UHCSDB	http://hdl.handle.net/11256/940
UHCS microconst. DB	http://hdl.handle.net/11256/964
SmBFO	https://drive.google.com/
Diranet	https://github.com/arturluis/diranet
Peregrine v2021-03	https://doi.org/10.13139/ORNLNCCS/1779073
Microscopy Datasets	https://github.com/Je�rey-Ede/datasets/wiki
Software packages

Package Name	Link
PyCroscopy	https://github.com/pycroscopy/pycroscopy
Prismatic	https://github.com/prism-em/prismatic
py4DSTEM	https://github.com/py4dstem/py4DSTEM
abTEM	https://github.com/jacobjma/abTEM
QSTEM	https://github.com/QSTEM/QSTEM
MuSTEM	https://github.com/HamishGBrown/MuSTEM
AICrystallographer	https://github.com/pycroscopy/AICrystallographer
AtomAI	https://github.com/pycroscopy/atomai
NionSwift	https://github.com/nion-software/nionswift
EENCM	https://github.com/ceright1/Prediction-material-property
DefectSegNet	https://github.com/rajatsainju/DefectSegNet
AMPIS	https://github.com/rccohn/AMPIS
partial-STEM	https://github.com/Jefrey-Ede/partial-STEM/tree/1.0.0
ZeroCostDL4Mic	https://github.com/HenriquesLab/ZeroCostDL4Mic

NLP

Softwarename	Link
Borges	https://github.com/CederGroupHub/Borges
ChemDataExtractor	http://chemdataextractor.org
ChemicalTagger	https://github.com/BlueObelisk/chemicaltagger
ChemListem	https://bitbucket.org/rscapplications/chemlistem/
ChemSpot	https://github.com/rockt/ChemSpot
LBNLP	https://github.com/lbnlp/lbnlp
mat2vec	https://github.com/materialsintelligence/mat2vec
MaterialsParser	https://github.com/CederGroupHub/MaterialParser
OSCAR4	https://github.com/BlueObelisk/oscar4
SynthesisProject	https://www.synthesisproject.org
tmChem	https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/tmchem/