runtime/COMPLETE.json

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    "canonical_ligand_order": "canonical-heavy-graph-dfs-v1",
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  "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": {
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    "scopes": [
      "ligand--ligand",
      "ligand--pocket",
      "pocket--pocket"
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    "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"
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    "uncertain_pairs": 263
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  "all_noninteraction_arrays_exact": true,
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}