prfrl
/
Rxitect
connected to https://github.com/prfrl/Rxitect.git


  
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            stages:
  pretrain_selfies_lstm:
    cmd: python src/rxitect/training/pretrain_selfies_rnn.py
    deps:
    - data/processed/selfies_chembl_corpus.csv
    - data/processed/selfies_ligand_corpus.csv
    - data/processed/selfies_voc.txt
    outs:
    - models/pretrained_selfies_rnn.ckpt
  featurization:
    cmd: python src/rxitect/features/featurize_selfies.py
    deps:
    - data/processed/smiles_chembl_corpus.txt
    - data/processed/smiles_ligand_corpus.txt
    outs:
    - data/processed/selfies_chembl_corpus.csv
    - data/processed/selfies_ligand_corpus.csv
    - data/processed/selfies_voc.txt
  generate_smiles_corpora:
    cmd: python src/rxitect/features/generate_smiles_corpora.py
    deps:
    - data/raw/chembl_26.sdf.gz
    - data/raw/ligand_raw.tsv
    outs:
    - data/processed/smiles_chembl_corpus.txt
    - data/processed/smiles_ligand_corpus.txt
    - data/processed/smiles_voc.txt
  fine_tune_selfies_lstm:
    cmd: python src/rxitect/training/fine_tune_selfies_rnn.py
    deps:
    - data/processed/selfies_voc.txt
    - models/pretrained_selfies_rnn.ckpt
    outs:
    - models/fine_tuned_selfies_rnn.ckpt
  train_predictors:
    cmd: python src/rxitect/training/train_predictors.py
    deps:
    - data/raw/ligand_raw.tsv
    outs:
    - models/RF_REG_CHEMBL226.pkg
    - models/RF_REG_CHEMBL240.pkg
    - models/RF_REG_CHEMBL251.pkg