| # 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 |
|
|
