CITATION.cff
LICENSE_PENDING.md
MANIFEST.in
README.md
pyproject.toml
checkpoints/README.md
configs/etflow_protocol_audit.yaml
configs/external_validation_development_matrix_v1.yaml
configs/external_validation_v1.yaml
configs/geomanimol.yaml
configs/hif2a_manimol_case_studies_clean.yaml
configs/manimol.yaml
configs/mean_dispersion_fixed_target.yaml
configs/mean_dispersion_local.yaml
configs/mixmanifold_server.yaml
configs/mixture_form.yaml
configs/reproduce_route2_paper.yaml
docs/release.md
docs/superpowers/plans/2026-09-30-public-inference-release.md
docs/superpowers/specs/2026-09-30-public-inference-release-design.md
examples/basic_generation.py
examples/evaluate_conformers.py
src/args_parse.py
src/candidate_corrector.py
src/candidate_scorer.py
src/exputils.py
src/infer.py
src/infer1.py
src/infer_mean_dispersion_torsion.py
src/infer_torsion.py
src/infer_torsion5.py
src/manimol_stage1.py
src/mixture_torsion_flow.py
src/pgraph_controls.py
src/torsion_manifold.py
src/train.py
src/train2.py
src/train5.py
src/train7.py
src/train8.py
src/train_mean_dispersion_torsion_prior.py
src/train_torsion_manifold_prior.py
src/trainer.py
src/dataset/__init__.py
src/dataset/drugdataset.py
src/dataset/manifold.py
src/dataset/sharded_drugdataset.py
src/dataset/smiles2graph.py
src/manimol/__init__.py
src/manimol/__main__.py
src/manimol/cli.py
src/manimol/full_cli.py
src/manimol/manifest.py
src/manimol/priors.py
src/manimol/protocols.py
src/manimol/runtime.py
src/manimol/selection.py
src/manimol/torsion.py
src/manimol/train_cli.py
src/manimol.egg-info/PKG-INFO
src/manimol.egg-info/SOURCES.txt
src/manimol.egg-info/dependency_links.txt
src/manimol.egg-info/entry_points.txt
src/manimol.egg-info/requires.txt
src/manimol.egg-info/top_level.txt
src/mixture_flow/src/__init__.py
src/mixture_flow/src/_path.py
src/mixture_flow/src/infer28_mixture_torsion_flow.py
src/mixture_flow/src/mixture_torsion_flow.py
src/mixture_flow/src/summarize_mixture_debug.py
src/mixture_flow/src/train28_mixture_torsion_flow.py
src/models/ manifold_learning.py
src/models/__init__.py
src/models/dist.py
src/models/dist2coords.py
src/models/egnn.py
src/models/experimental_backbones.py
src/models/gnnconv.py
src/models/kernel_inversion.py
src/models/kernels.py
src/models/losses.py
src/models/mean_dispersion_bridge.py
src/models/mean_dispersion_torsion_context.py
src/models/model.py
src/models/model0.py
src/models/vis.py
src/scripts/__init__.py
src/scripts/analyze_basin_alignment.py
src/scripts/analyze_hif2a_conformer_aggregation.py
src/scripts/analyze_hif2a_contact_pharmacophore.py
src/scripts/analyze_hif2a_fixed_budget.py
src/scripts/analyze_hif2a_pharmacophore.py
src/scripts/analyze_hif2a_pharmacophore_match_metric.py
src/scripts/analyze_p_control_candidate_flow.py
src/scripts/analyze_scaffold_basin.py
src/scripts/audit_dispersion_proposals.py
src/scripts/audit_etflow_protocol.py
src/scripts/audit_external_overlap.py
src/scripts/audit_oldbest_fulltrainval_split.py
src/scripts/audit_pdbbind_contact_pharmacophores.py
src/scripts/audit_qm9_geomol_test_split.py
src/scripts/audit_stage1_stage2_cross.py
src/scripts/build_geom_drugs_lowref_diagnostic.py
src/scripts/build_qm9_backfill_manifest.py
src/scripts/check_etflow_runtime.py
src/scripts/compare_prior_sources.py
src/scripts/compose_binding_mode_figure.py
src/scripts/compose_hif2a_contact_pharmacophore_suppfig.py
src/scripts/compose_hif2a_functional_geometry_pipeline.py
src/scripts/compose_manimol_internal_architecture.py
src/scripts/diagnose_flow_basin_intervention.py
src/scripts/diagnose_hif2a_pharmacophore_budget.py
src/scripts/diagnose_route2_p_ranking.py
src/scripts/discover_binding_mode_inputs.py
src/scripts/evaluate_functional_prior_stage1.py
src/scripts/evaluate_geomanimol.py
src/scripts/evaluate_geomanimol_flow.py
src/scripts/evaluate_geomanimol_multiscaffold.py
src/scripts/evaluate_geomanimol_residual.py
src/scripts/evaluate_geomanimol_torsion.py
src/scripts/evaluate_hif2a_bioactive_enrichment.py
src/scripts/evaluate_hif2a_pms_suite.py
src/scripts/evaluate_pdbbind_contact_pms.py
src/scripts/evaluate_platinum_external.py
src/scripts/evaluate_platinum_pool.py
src/scripts/evaluate_route2_calibrated_p.py
src/scripts/evaluate_route2_library_components.py
src/scripts/evaluate_route2_p_basin_budget.py
src/scripts/evaluate_stage1_checkpoint_only.py
src/scripts/export_dispersion_bond_audit.py
src/scripts/export_top20_shards.py
src/scripts/external_validation_metrics.py
src/scripts/fit_topology_prior.py
src/scripts/frozen_dispersion_audit.py
src/scripts/geomanimol_debug.py
src/scripts/geomanimol_smoke.py
src/scripts/infer_etflow_matched.py
src/scripts/inspect_checkpoint.py
src/scripts/inspect_conformer_capacity.py
src/scripts/inspect_pool.py
src/scripts/make_figure3_selection_loss.py
src/scripts/make_figure3_selection_summary.py
src/scripts/make_geom_debug_subset.py
src/scripts/make_low_reference_test_subset.py
src/scripts/merge_stage1_into_stage2.py
src/scripts/place_hif2a_candidates_for_evaluation.py
src/scripts/plot_hif2a_low_budget_efficiency.py
src/scripts/plot_prior_validation.py
src/scripts/precompute_stage2_assignments.py
src/scripts/prepare_bace_activity.py
src/scripts/prepare_bace_etkdg_benchmark.py
src/scripts/prepare_figure5_4x4_cases.py
src/scripts/prepare_geom_drugs_geomol_top20.py
src/scripts/prepare_pdbbind_core_raw.py
src/scripts/prepare_platinum_raw.py
src/scripts/prepare_pubchem_etkdg.py
src/scripts/rebuild_hif2a_final_sdf_and_metrics.py
src/scripts/rebuild_hif2a_fixed_pool_sweep.py
src/scripts/rebuild_hif2a_strict.py
src/scripts/recompute_hif2a_bootstrap.py
src/scripts/reference_free_geometry.py
src/scripts/render_binding_modes.py
src/scripts/render_figure5_4x4.py
src/scripts/render_figure6_pharmacophore_pymol.py
src/scripts/render_hif2a_contact_pharmacophore_pymol.py
src/scripts/render_hif2a_figure11.py
src/scripts/run_bace_2d_baseline.py
src/scripts/run_drugs_validation_matrix.py
src/scripts/run_external_reference_free.py
src/scripts/run_manimol_finalk_sensitivity.py
src/scripts/run_manimol_oversampling_sensitivity.py
src/scripts/run_pdisp_matched_intervention.py
src/scripts/run_stage1_stage2_cross20.py
src/scripts/score_hif2a_candidates_with_pgraph.py
src/scripts/summarize_dispersion_intervention.py
src/scripts/test_mean_dispersion_bridge.py
src/scripts/train_dispersion_head_diagnostic.py
src/scripts/train_dispersion_head_streaming.py
src/scripts/train_geomanimol.py
src/scripts/train_geomanimol_flow.py
src/scripts/train_geomanimol_residual.py
src/scripts/train_geomanimol_torsion.py
src/scripts/train_quantile_representation_diagnostic.py
src/scripts/validate_mean_dispersion_prior.py
src/scripts/validate_packed_shard.py
src/scripts/validate_stage1_prior.py
src/scripts/validate_top20_shards.py
src/scripts/verify_binding_mode_figure.py
src/scripts/validation/__init__.py
src/scripts/validation/hif2a_downstream_baselines.py
src/scripts/validation/hif2a_pairwise_ranker.py
src/utils/__init__.py
src/utils/checkpoint.py
src/utils/device.py
src/utils/helpers.py
src/utils/kabsch.py
src/utils/lookup_table.py
src/utils/metrics.py
src/utils/optuna.py
src/utils/save_mol.py
src/utils/util.py
tests/conftest.py
tests/test_dispersion_head_diagnostic.py
tests/test_dispersion_head_streaming.py
tests/test_dispersion_intervention.py
tests/test_dispersion_torsion_context.py
tests/test_drugs_validation_matrix.py
tests/test_external_validation.py
tests/test_frozen_dispersion_audit.py
tests/test_infer_torsion_checkpoint_context.py
tests/test_manifest.py
tests/test_mean_dispersion_freezing.py
tests/test_oldbest_dispersion_context.py
tests/test_public_core.py
tests/test_public_protocol.py
tests/test_public_runtime.py
tests/test_stage2_context.py
tests/test_trainer_progress.py