README.md
pyproject.toml
grn/01_preprocess.py
grn/02_genie3.py
grn/03_therapy_decision.py
grn/select_targets.py
pipeline/02_physicochemical.py
pipeline/__init__.py
pipeline/active_sites.py
pipeline/adc_design.py
pipeline/admet.py
pipeline/allosteric.py
pipeline/allosteric_drug_design.py
pipeline/antibody_design.py
pipeline/binding_pockets.py
pipeline/cart_design.py
pipeline/category_classifier.py
pipeline/chemical_env.py
pipeline/clean_ec.py
pipeline/consensus.py
pipeline/cryptic_pockets.py
pipeline/cyp450.py
pipeline/deepfri_go.py
pipeline/denovo_design.py
pipeline/denovo_design_context.py
pipeline/ec_model_check.py
pipeline/esm2_embeddings.py
pipeline/evaluate_ec_model.py
pipeline/fetch_structure.py
pipeline/foldseek.py
pipeline/homology.py
pipeline/ml_ec_classifier.py
pipeline/ml_ec_features.py
pipeline/ml_ec_predict.py
pipeline/ml_ec_train.py
pipeline/ml_ec_train_v2.py
pipeline/molecular_dynamics.py
pipeline/mutational_impact.py
pipeline/physicochemical.py
pipeline/ppi_network.py
pipeline/protac_design.py
pipeline/ptm_analysis.py
pipeline/ptm_proteome_batch.py
pipeline/selectivity_optimizer.py
proteinfp/__init__.py
proteinfp/cli.py
proteinfp/deps.py
proteinfp/orchestrator.py
proteinfp/therapy.py
proteinfp.egg-info/PKG-INFO
proteinfp.egg-info/SOURCES.txt
proteinfp.egg-info/dependency_links.txt
proteinfp.egg-info/entry_points.txt
proteinfp.egg-info/requires.txt
proteinfp.egg-info/top_level.txt
sim/cell_environment_inference.py
sim/denovo_to_sim06.py
sim/step01_cell_environment.py
sim/step02_protein_ensemble.py
sim/step03_drug_distribution.py
sim/step04_binding_probability.py
sim/step05_network_perturbation.py
sim/step05_network_perturbation_patch.py
sim/step06_pharmacological_scoring.py
sim/step07_validate.py
tests/test_01_fetch_structure.py
tests/test_02_physicochemical.py
tests/test_03_active_sites.py
tests/test_04_binding_pockets.py
tests/test_05_allosteric.py
tests/test_06_chemical_env.py
tests/test_07_homology.py
tests/test_08_09_10_ai_prediction.py
tests/test_11_foldseek.py
tests/test_12_ppi_network.py
tests/test_13_consensus.py
tests/test_14_molecular_dynamics.py
tests/test_enzyme_accuracy.py
tests/test_enzyme_classifier_batch.py
tests/test_ml_ec_pipeline.py
utils/__init__.py
utils/config.py
utils/pdb_parser.py