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7f316fe 12fea4a | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | # Core Edit Flow / pCoMole torch>=2.1.0 pytorch-lightning>=2.0.0 lightning>=2.0.0 transformers==4.46.0 datasets>=2.14.0 easydict pyyaml numpy>=1.24.0 pandas>=2.0.0 tqdm einops omegaconf joblib>=1.3.0 scikit-learn>=1.3.0 # Peptidomimetic chemistry rdkit>=2023.3.1 selfies SmilesPE networkx torch-geometric # Oracles used by pCoMole xgboost>=2.0.0 chemprop>=2.0.0 # Optional logging # wandb # Cas9 h5py # CICERO-format PAM datasets biopython # FASTA / sequence handling rapidfuzz # sequence similarity in Cas9 diagnostics # HMMER (`hmmscan`) must be on PATH for the Cas9 domain / PAM-interacting # detectors: conda install -c bioconda hmmer # protein2pam provides the PAM oracle's model class: # pip install protein2pam==0.2.0 |