LICENSE
README.md
pyproject.toml
pathogenicity_gates/__init__.py
pathogenicity_gates/predictor.py
pathogenicity_gates.egg-info/PKG-INFO
pathogenicity_gates.egg-info/SOURCES.txt
pathogenicity_gates.egg-info/dependency_links.txt
pathogenicity_gates.egg-info/entry_points.txt
pathogenicity_gates.egg-info/requires.txt
pathogenicity_gates.egg-info/top_level.txt
pathogenicity_gates/adapters/__init__.py
pathogenicity_gates/adapters/direct_builder.py
pathogenicity_gates/adapters/v18_adapter.py
pathogenicity_gates/annotations/__init__.py
pathogenicity_gates/annotations/loader.py
pathogenicity_gates/channels/__init__.py
pathogenicity_gates/channels/context.py
pathogenicity_gates/channels/registry.py
pathogenicity_gates/channels/experimental/__init__.py
pathogenicity_gates/channels/idr/__init__.py
pathogenicity_gates/channels/idr/ch10_slim.py
pathogenicity_gates/channels/idr/ch11_idr_pro.py
pathogenicity_gates/channels/idr/ch12_idr_gly.py
pathogenicity_gates/channels/structural/__init__.py
pathogenicity_gates/channels/structural/ch01_dna.py
pathogenicity_gates/channels/structural/ch02_zn.py
pathogenicity_gates/channels/structural/ch03_core.py
pathogenicity_gates/channels/structural/ch04_ss.py
pathogenicity_gates/channels/structural/ch05_loop.py
pathogenicity_gates/channels/structural/ch06_ppi.py
pathogenicity_gates/channels/structural/ch08_oligomer.py
pathogenicity_gates/channels/structural/ch09_salt_bridge.py
pathogenicity_gates/channels/universal/__init__.py
pathogenicity_gates/channels/universal/ch07_ptm.py
pathogenicity_gates/cli/__init__.py
pathogenicity_gates/cli/__main__.py
pathogenicity_gates/cli/main.py
pathogenicity_gates/cli/utils.py
pathogenicity_gates/cli/commands/__init__.py
pathogenicity_gates/cli/commands/explain.py
pathogenicity_gates/cli/commands/list_proteins.py
pathogenicity_gates/cli/commands/predict.py
pathogenicity_gates/cli/commands/predict_batch.py
pathogenicity_gates/cli/formatters/__init__.py
pathogenicity_gates/cli/formatters/compact_fmt.py
pathogenicity_gates/cli/formatters/json_fmt.py
pathogenicity_gates/cli/formatters/table_fmt.py
pathogenicity_gates/data/brca1/annotation.yaml
pathogenicity_gates/data/brca1/brca1_sequence.json
pathogenicity_gates/data/brca1/brca1_uniprot_features.json
pathogenicity_gates/data/brca1/pdb/1JM7.pdb
pathogenicity_gates/data/brca1/pdb/1JNX.pdb
pathogenicity_gates/data/brca1/pdb/brca1_ring_brct.pdb
pathogenicity_gates/data/kras/annotation.yaml
pathogenicity_gates/data/kras/kras_sequence.json
pathogenicity_gates/data/kras/kras_uniprot_features.json
pathogenicity_gates/data/kras/pdb/4OBE.pdb
pathogenicity_gates/data/p53/annotation.yaml
pathogenicity_gates/data/p53/p53_ppi_interface.json
pathogenicity_gates/data/p53/p53_ppi_union.json
pathogenicity_gates/data/p53/p53_sequence.json
pathogenicity_gates/data/p53/p53_uniprot_features.json
pathogenicity_gates/data/p53/partner_face.json
pathogenicity_gates/data/p53/ptm_consistency_report.md
pathogenicity_gates/data/p53/tp53_clinvar_missense.json
pathogenicity_gates/data/p53/pdb/1TSR.pdb
pathogenicity_gates/data/p53/pdb/1YCR.pdb
pathogenicity_gates/data/p53/pdb/2J0Z.pdb
pathogenicity_gates/data/p53/pdb/2K8F.pdb
pathogenicity_gates/data/p53/pdb/2L14.pdb
pathogenicity_gates/data/p53/pdb/2MZD.pdb
pathogenicity_gates/data/p53/pdb/5HOU.pdb
pathogenicity_gates/data/p53/pdb/5HPD.pdb
pathogenicity_gates/data/tdp43/annotation.yaml
pathogenicity_gates/data/tdp43/tdp43_sequence.json
pathogenicity_gates/data/tdp43/tdp43_uniprot_features.json
pathogenicity_gates/legacy/__init__.py
pathogenicity_gates/legacy/p53_gate_v17_idr.py
pathogenicity_gates/legacy/p53_gate_v18_final.py
pathogenicity_gates/legacy/ssoc_v332.py
pathogenicity_gates/physics/__init__.py
pathogenicity_gates/physics/constants.py
pathogenicity_gates/physics/corrections.py
pathogenicity_gates/physics/geometry.py
pathogenicity_gates/scripts/__init__.py
pathogenicity_gates/scripts/build_uniprot_features.py
pathogenicity_gates/scripts/extract_partner_face.py
pathogenicity_gates/scripts/verify_ptm_consistency.py
pathogenicity_gates/structure/__init__.py
pathogenicity_gates/structure/features.py
pathogenicity_gates/structure/parser.py
tests/test_no_legacy_leak.py
tests/test_phase1_v18_regression.py
tests/test_phase2_yaml_regression.py
tests/test_phase3_channel_isolation.py
tests/test_phase4_transferability.py
tests/test_phase5_cli.py