Adds the Cas9 vertical alongside gfp and peptidomimetics: the pCoMole
editor, its three objectives (Cas9-likeness, deletion count, PAM
matching), constraints, data-prep scripts, run scripts, and config.
- cas9/model/ and cas9/logic/ are vendored because the Cas9 Edit Flow
keeps the reparameterized models inside base_models.py, whereas the
repo root splits them into reparam_models.py. The two are not
interchangeable, so Cas9 imports its own copies.
- objectives.py is trimmed to the three Cas9 classes; the ADMET oracles
already ship in peptidomimetics/objectives.py.
- Oracle and checkpoint locations resolve through paths.py
(PROTEIN2PAM_ROOT, CAS_PREDICTOR_ROOT, CAS9_CLASSIFIER_CKPT,
CAS9_CLASSIFIER_CONFIG, CAS9_HMM_DIR) instead of absolute paths.
- Ten Cas9 ortholog seeds ship as cas9/data/orthologs.fasta.
Checkpoints and oracle packages are not included in this commit;
cas9/ckpt/, cas9/classifier_ckpt/ and cas9/hmm/ are placeholders.
Co-Authored-By: Claude Opus 5 <norepl…
