Upload verified data

runtime/COMPLETE.json

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+{
+  "ready": true,
+  "version": "fsbfpocket-all-scope-interactions-20260928",
+  "diagnostic_only": false,
+  "examples": 1240225,
+  "shards": 4845,
+  "source": "/extra/murrellb/BranchingLDDM/exports/protein_ligand_collection_v6_canonical_20260922",
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+    "sha256sums_sha256": "bcf3d36b2107bc594f8fb4201aa0d864be6c06dfa07424e0fdc18666d24c6a5c",
+    "verification_sha256": "dca4017911744a4eacb4d92fd75cac1c5c9743e0f75a4311391e1ee403a1fb4f",
+    "parent_manifest_sha256": "39163ac9d72ecabe9be1a48529a62aa2e880217417a6fba6b82b82e501e28678",
+    "canonical_ligand_order": "canonical-heavy-graph-dfs-v1",
+    "training_unchanged": true
+  },
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+  "splits_unchanged": true,
+  "all_values_readback_checked": true,
+  "all_input_hashes_checked": true,
+  "aromatic_changed_rows": 20020392,
+  "seconds": 3689.078926584916,
+  "packed": true,
+  "all_packed_values_readback_exact": true,
+  "interaction_schema": "pli-interaction-evidence-v2-all-scopes",
+  "annotation_source": "/extra/murrellb/BranchingLDDM/cache/interaction_evidence_v7_all_scopes_20260928",
+  "annotation_complete_sha256": "d059ae28b25a7c4b27189f6f32a43cb6383b17172572ff95b7133a14ee340cca",
+  "annotation_policy": {
+    "schema": "pli-interaction-evidence-v2-all-scopes",
+    "scopes": [
+      "ligand--ligand",
+      "ligand--pocket",
+      "pocket--pocket"
+    ],
+    "scope_by": "stored role, never peptide/protein chemical class",
+    "peptide_intraligand_included": true,
+    "pocket_pocket_interactions": true,
+    "pair_radius_A": 8.0,
+    "ring_candidate_centroid_radius_A": 8.0,
+    "default_nonbonded_minimum_graph_separation": 3,
+    "protein_chemistry": "ProLIF named-AA templates; HIS -> neutral HIE convention; ARG/LYS +1, ASP/GLU -1; no pH prediction",
+    "protein_uncertainty": "All inferred; unsupported/incomplete residues remain geometry-only. Crop-boundary N is not assumed a terminal amine.",
+    "hydrogens": "No added H coordinates; preserved ligand attached-H counts; implicit H-bond geometry; uncertain protein H states flagged",
+    "non_tetrahedral_stereo": "Recover private permutation from source SMILES via chirality-constrained graph isomorphism in original heavy-atom order; no 3D reassignment",
+    "unsupported_hbond_geometry": "Keep candidate, angles, atom identities and explicit unknown mask; never label unsupported geometry a confident negative",
+    "hbond_candidates": "All donor/acceptor matches within 5 A, including failed geometry and topological exclusions",
+    "ring_candidates": "All disjoint aromatic ring pairs in scope within 8 A, including failed/default-unsupported ring geometries",
+    "outside_envelope": "Unchanged complete stored coordinates/graphs retained for recomputation; no claim that 8 A is universal",
+    "interaction_counts_are_not_independent_physical_bonds": true,
+    "water_bridges": "Not annotated: original prepared crops exclude waters",
+    "source": "https://prolif.readthedocs.io/en/v2.2.1/source/modules/interaction-fingerprint.html",
+    "topology": "Full retained ligand AND protein covalent graph; exclude graph distance1/2 in every scope",
+    "ring_geometry": "All-atom least-squares plane; sign-free acute angles; unordered ring pairs",
+    "pi_parallel": "centroids<=5.5A; plane angle<=35deg; either normal-centroid angle<=33deg",
+    "pi_t_shaped": "centroids<=6.5A; plane angle>=50deg; either normal-centroid angle<=30deg; either centroid within1.5A of intersection line",
+    "implicit_hbond_plane": "Plane through site fitted to ALL direct heavy-neighbor vectors, or all direct plus second neighbors if fewer than2; same pinned angle thresholds",
+    "geometry_degeneracy": "Undefined/ambiguous plane or missing local geometry is explicit uncertainty, never confident negative",
+    "ring_candidate_sizes": "All aromatic SSSR rings retained; stacking defaults on5/6member rings, as pinned ProLIF patterns",
+    "directional_evidence": "Both H-bond donor orientations; complementary halogen/metal detectors; directions retained before symmetric projection"
+  },
+  "parent_runtime": "/extra/murrellb/BranchingLDDM/fsbfpocket/v2/cache_packed",
+  "parent_runtime_complete_sha256": "b8ff562077fd72f303b2e1d1f1276833e172e0df5a19c88d7bb9e54f33293230",
+  "pair_replacement_counts": {
+    "examples": 1240225,
+    "positive_ll": 40089761,
+    "positive_lp": 16756716,
+    "positive_pp": 165406867,
+    "uncertain_pairs": 263
+  },
+  "all_noninteraction_arrays_exact": true,
+  "parent_cache": "/extra/murrellb/BranchingLDDM/fsbfpocket/v5_all_scopes/cache",
+  "parent_complete_sha256": "f300779a44cf3d370fa205657de971441c00b6db5fe6f6d7053628e8f9733184",
+  "packed_numeric_arrays": 24804500,
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+  "packed_arrays_sha256": "004ed1d10497d43c72b366dfa454c7ee1f0656ba8d21fa6f7b9abe557b302ddc",
+  "index_sha256": "1b2d0673a879cfb19c30d8db22f70186e204498bb694356f043351bdeeb63849"
+}