DeepSEQreen_fast_build / requirements.txt
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# deep learning
# Install with conda
torch >= 2.1
torch_geometric
lightning >= 2.1
torchmetrics
transformers
scikit-learn
dgl
dglgo
dgllife
# configuration and utilities
hydra-core
pandas
swifter
tensorboard
biopython
# model-specific requirements
subword-nmt # MolTrans
tape_proteins # TransformerCPI2
gensim
fair-esm # CoaDTI-pro
# apex # recommended by TAPE-BERT
# feature extraction
rdkit
mordred
networkx >= 3.2
mhfp
panel
plotly
seaborn
# tmap