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lba_stats.json

@@ -0,0 +1,642 @@
+{
+  "n_total": 4463,
+  "sample_size": 4463,
+  "atoms_per_structure": {
+    "min": 115,
+    "max": 1085,
+    "mean": 397.0734931660318
+  },
+  "bounding_box_extent_angstrom": {
+    "side_min": 10.526999950408936,
+    "side_max": 47.270999908447266,
+    "diagonal_min": 25.27603114136397,
+    "diagonal_max": 59.69870791297603
+  },
+  "elements": {
+    "count": 23,
+    "atomic_numbers": [
+      1,
+      6,
+      7,
+      8,
+      9,
+      11,
+      12,
+      15,
+      16,
+      17,
+      19,
+      20,
+      25,
+      26,
+      27,
+      28,
+      29,
+      30,
+      35,
+      38,
+      48,
+      53,
+      55
+    ],
+    "symbols": [
+      "H",
+      "C",
+      "N",
+      "O",
+      "F",
+      "Na",
+      "Mg",
+      "P",
+      "S",
+      "Cl",
+      "K",
+      "Ca",
+      "Mn",
+      "Fe",
+      "Co",
+      "Ni",
+      "Cu",
+      "Zn",
+      "Br",
+      "Sr",
+      "Cd",
+      "I",
+      "Cs"
+    ],
+    "counts": {
+      "1": 682255,
+      "6": 702697,
+      "7": 178352,
+      "8": 197780,
+      "9": 995,
+      "11": 26,
+      "12": 177,
+      "15": 824,
+      "16": 7325,
+      "17": 659,
+      "19": 3,
+      "20": 61,
+      "25": 59,
+      "26": 27,
+      "27": 26,
+      "28": 8,
+      "29": 4,
+      "30": 686,
+      "35": 130,
+      "38": 1,
+      "48": 1,
+      "53": 42,
+      "55": 1
+    }
+  },
+  "label_y": {
+    "min": 2.0,
+    "max": 11.920000076293945,
+    "mean": 6.453963702605921
+  },
+  "exact": {
+    "num_complexes": 4463,
+    "unique_pdb_ids": 4463,
+    "components": {
+      "protein": {
+        "total_atoms": 27769649,
+        "min": 566,
+        "mean": 6222.1934,
+        "max": 74903,
+        "zero_length": 0
+      },
+      "pocket": {
+        "total_atoms": 1658646,
+        "min": 100,
+        "mean": 371.6437,
+        "max": 1021,
+        "zero_length": 0
+      },
+      "ligand": {
+        "total_atoms": 113493,
+        "min": 6,
+        "mean": 25.4298,
+        "max": 71,
+        "zero_length": 0
+      }
+    },
+    "pocket_provenance": "ATOM3D's OWN published selection (protein atoms within 6.0 A of any ligand atom); STORED because it is the source convention the seq-id benchmarks are defined on, not a crop we invented. It is a RESIDUE shell (0 of 122,736 pocket residues truncated) and it EXCLUDES water entirely.",
+    "elements_z": [
+      1,
+      3,
+      6,
+      7,
+      8,
+      9,
+      11,
+      12,
+      15,
+      16,
+      17,
+      19,
+      20,
+      25,
+      26,
+      27,
+      28,
+      29,
+      30,
+      34,
+      35,
+      38,
+      48,
+      53,
+      55,
+      80
+    ],
+    "elements_symbols": [
+      "H",
+      "Li",
+      "C",
+      "N",
+      "O",
+      "F",
+      "Na",
+      "Mg",
+      "P",
+      "S",
+      "Cl",
+      "K",
+      "Ca",
+      "Mn",
+      "Fe",
+      "Co",
+      "Ni",
+      "Cu",
+      "Zn",
+      "Se",
+      "Br",
+      "Sr",
+      "Cd",
+      "I",
+      "Cs",
+      "Hg"
+    ],
+    "n_elements": 26,
+    "elements_per_component": {
+      "protein": {
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+        "symbols": [
+          "H",
+          "Li",
+          "C",
+          "N",
+          "O",
+          "Na",
+          "Mg",
+          "P",
+          "S",
+          "K",
+          "Ca",
+          "Mn",
+          "Fe",
+          "Co",
+          "Ni",
+          "Cu",
+          "Zn",
+          "Se",
+          "Sr",
+          "Cd",
+          "Cs",
+          "Hg"
+        ]
+      },
+      "pocket": {
+        "n": 18,
+        "symbols": [
+          "H",
+          "C",
+          "N",
+          "O",
+          "Na",
+          "Mg",
+          "S",
+          "K",
+          "Ca",
+          "Mn",
+          "Fe",
+          "Co",
+          "Ni",
+          "Cu",
+          "Zn",
+          "Sr",
+          "Cd",
+          "Cs"
+        ]
+      },
+      "ligand": {
+        "n": 9,
+        "symbols": [
+          "C",
+          "N",
+          "O",
+          "F",
+          "P",
+          "S",
+          "Cl",
+          "Br",
+          "I"
+        ]
+      }
+    },
+    "vocab_sizes": {
+      "res_name": 50,
+      "chain": 33,
+      "insertion_code": 21,
+      "hetero": 30
+    },
+    "residue_identity": {
+      "res_idx": "derived key, contiguous 0..R-1 over protein+ligand per complex; the pocket INHERITS the protein numbering, so pocket res_idx is a subset, neither contiguous nor disjoint",
+      "merged_residue_complexes": {
+        "protein": 0,
+        "pocket": 0
+      },
+      "total_residues": 3311198,
+      "residues_per_complex": {
+        "min": 89,
+        "mean": 741.922,
+        "max": 9102
+      },
+      "pocket_residues_total": 122736,
+      "pocket_res_idx_subset_of_protein": true,
+      "author_key_3part_collisions": {
+        "protein": {
+          "colliding_keys": 5,
+          "complexes": 5,
+          "pdb_ids": [
+            "3mi2",
+            "3upk",
+            "3v4t",
+            "4w9f",
+            "4w9h"
+          ]
+        },
+        "pocket": {
+          "colliding_keys": 0,
+          "complexes": 0,
+          "pdb_ids": []
+        }
+      },
+      "author_key_4part_collisions": {
+        "protein": {
+          "colliding_keys": 0,
+          "complexes": 0,
+          "pdb_ids": []
+        },
+        "pocket": {
+          "colliding_keys": 0,
+          "complexes": 0,
+          "pdb_ids": []
+        }
+      },
+      "res_seq": {
+        "protein": {
+          "min": -20,
+          "max": 5069,
+          "atoms_le_0": 18665,
+          "complexes_with_le_0": 313
+        },
+        "pocket": {
+          "min": -4,
+          "max": 4027,
+          "atoms_le_0": 197,
+          "complexes_with_le_0": 8
+        },
+        "ligand": {
+          "min": 0,
+          "max": 0,
+          "atoms_le_0": 113493,
+          "complexes_with_le_0": 4463
+        }
+      },
+      "insertion_code": {
+        "vocab_size": 21,
+        "vocab": [
+          " ",
+          "C",
+          "B",
+          "A",
+          "D",
+          "E",
+          "F",
+          "G",
+          "H",
+          "I",
+          "J",
+          "K",
+          "L",
+          "M",
+          "P",
+          "W",
+          "N",
+          "Q",
+          "R",
+          "S",
+          "T"
+        ],
+        "protein_complexes_using_one": 372,
+        "pocket_complexes_using_one": 212,
+        "protein_atoms_with_one": 86164,
+        "pocket_atoms_with_one": 9701,
+        "distinct_non_blank": 20,
+        "water_artefact": {
+          "atoms": 7866,
+          "complexes": 5,
+          "note": "NOT author insertion codes: in 5 complexes (2qwb..2qwf) ATOM3D spilled the water's chain id into this column; those waters read chain == '.'. Shipped verbatim. 15 letters are involved (E F G H J K L M N P Q R S T W); the genuine author insertion codes are the non-water rows."
+        },
+        "protein_atoms_non_water_with_one": 78298
+      },
+      "invariants_over_all_complexes": {
+        "protein_plus_ligand_is_0..R-1_per_complex": true,
+        "ligand_is_one_pseudo_residue_at_R-1": true,
+        "pocket_res_idx_subset_of_protein": true,
+        "pocket_residues": 122736,
+        "pocket_residues_truncated": 0
+      }
+    },
+    "hetero_counts": {
+      "protein": {
+        " ": 26375178,
+        "W": 1384783,
+        "H_MSE": 1729,
+        "H_ZN": 1360,
+        "H_PTR": 1250,
+        "H_CA": 974,
+        "H_MG": 770,
+        "H_TPO": 765,
+        "H_SEP": 644,
+        "H_CSO": 513,
+        "H_NA": 433,
+        "H_CD": 202,
+        "H_LLP": 176,
+        "H_MN": 156,
+        "H_PCA": 156,
+        "H_K": 96,
+        "H_NI": 78,
+        "H_FE": 67,
+        "H_KCX": 65,
+        "H_CAS": 61,
+        "H_HG": 48,
+        "H_CO": 48,
+        "H_ACE": 45,
+        "H_FE2": 22,
+        "H_CSD": 8,
+        "H_LI": 6,
+        "H_CU": 6,
+        "H_CS": 6,
+        "H_SR": 2,
+        "H_IAS": 2
+      },
+      "pocket": {
+        " ": 1657566,
+        "H_ZN": 686,
+        "H_MG": 177,
+        "H_CA": 61,
+        "H_MN": 59,
+        "H_NA": 26,
+        "H_CO": 26,
+        "H_FE": 21,
+        "H_NI": 8,
+        "H_FE2": 6,
+        "H_CU": 4,
+        "H_K": 3,
+        "H_CD": 1,
+        "H_SR": 1,
+        "H_CS": 1
+      },
+      "ligand": {
+        " ": 113493
+      }
+    },
+    "water": {
+      "hetero_W_atoms": 1384783,
+      "res_name_HOH_atoms": 1384783,
+      "identical": true,
+      "note": "waters live in the protein component; the pocket has none"
+    },
+    "entity_type_counts": {
+      "protein": {
+        "protein": 26375178,
+        "water": 1384783,
+        "metal_ion": 4333,
+        "other_hetero": 5355
+      },
+      "pocket": {
+        "protein": 1657566,
+        "metal_ion": 1080
+      },
+      "ligand": {
+        "ligand": 113493
+      }
+    },
+    "hydrogens": {
+      "protein": {
+        "n_hydrogen": 11328810,
+        "fraction": 0.408,
+        "complexes_with_zero_H": 0
+      },
+      "pocket": {
+        "n_hydrogen": 682255,
+        "fraction": 0.4113,
+        "complexes_with_zero_H": 0
+      },
+      "ligand": {
+        "n_hydrogen": 0,
+        "fraction": 0.0,
+        "complexes_with_zero_H": 4463
+      }
+    },
+    "bfactor": {
+      "protein": {
+        "min": -9.37,
+        "mean": 16.987,
+        "max": 500.54,
+        "n_atoms": 27769649,
+        "n_zero": 11329695,
+        "n_negative": 201,
+        "n_hydrogen": 11328810,
+        "n_hydrogen_zero": 11328810,
+        "n_heavy_zero": 885
+      },
+      "pocket": {
+        "min": -0.01,
+        "mean": 13.3213,
+        "max": 500.0,
+        "n_atoms": 1658646,
+        "n_zero": 682380,
+        "n_negative": 27,
+        "n_hydrogen": 682255,
+        "n_hydrogen_zero": 682255,
+        "n_heavy_zero": 125
+      },
+      "ligand": {
+        "min": 0.0,
+        "mean": 0.0,
+        "max": 0.0,
+        "n_atoms": 113493,
+        "n_zero": 113493,
+        "n_negative": 0,
+        "n_hydrogen": 0,
+        "n_hydrogen_zero": 0,
+        "n_heavy_zero": 113493
+      }
+    },
+    "occupancy": {
+      "protein": {
+        "min": -0.49,
+        "mean": 0.9959,
+        "max": 1.99,
+        "n_distinct": 117,
+        "n_not_one": 238151,
+        "n_zero": 9239,
+        "n_below_0": 2,
+        "n_above_1": 22
+      },
+      "pocket": {
+        "min": 0.0,
+        "mean": 0.9954,
+        "max": 1.21,
+        "n_distinct": 98,
+        "n_not_one": 16451,
+        "n_zero": 298,
+        "n_below_0": 0,
+        "n_above_1": 1
+      },
+      "ligand": {
+        "min": 1.0,
+        "mean": 1.0,
+        "max": 1.0,
+        "n_distinct": 1,
+        "n_not_one": 0,
+        "n_zero": 0,
+        "n_below_0": 0,
+        "n_above_1": 0
+      }
+    },
+    "is_alpha_carbon": {
+      "protein": {
+        "n_true": 1917382,
+        "z_values": [
+          6
+        ]
+      },
+      "pocket": {
+        "n_true": 121656,
+        "z_values": [
+          6
+        ]
+      },
+      "ligand": {
+        "n_true": 0,
+        "z_values": []
+      }
+    },
+    "label_neglog_aff": {
+      "min": 2.0,
+      "mean": 6.454,
+      "max": 11.92
+    },
+    "splits": {
+      "seq-id-30": {
+        "train": 3507,
+        "val": 466,
+        "test": 490,
+        "total": 4463
+      },
+      "seq-id-60": {
+        "train": 3563,
+        "val": 448,
+        "test": 452,
+        "total": 4463
+      }
+    },
+    "ligand_bonds": {
+      "total": 121187,
+      "dtype": "torch.float32",
+      "order_counts": {
+        "1.0": 89491,
+        "2.0": 31543,
+        "3.0": 153
+      },
+      "convention": "one entry per bond (not both directions), as in HiQBind"
+    },
+    "file_sizes_gib": {
+      "complexes.pt": 0.079,
+      "protein.pt": 1.19
+    },
+    "units": {
+      "pos": "angstrom",
+      "bfactor": "angstrom^2 (B-factor)",
+      "occupancy": "fraction, nominally [0,1] but NOT clamped -- the source states -0.49 .. 1.99 and it is shipped verbatim",
+      "neglog_aff": "unitless (-log10 of the dissociation constant in M; pKd-like)"
+    },
+    "sampled_fields": "none in this block -- everything here is exact over all 4,463 complexes. The TOP-LEVEL atoms_per_structure / bounding_box_extent_angstrom / elements keys describe the pocket+ligand view only (all 4,463 complexes, so exhaustive for that view but NOT for the dataset: the protein component adds 3 elements).",
+    "v1_regression": {
+      "bitwise_identical": [
+        "ligand_edge_index",
+        "ligand_edge_ptr",
+        "ligand_pos",
+        "ligand_ptr",
+        "ligand_z",
+        "neglog_aff",
+        "pocket_pos",
+        "pocket_ptr",
+        "pocket_z",
+        "protein_pos",
+        "protein_ptr",
+        "protein_z",
+        "seqid30_split",
+        "seqid60_split"
+      ],
+      "differs": [],
+      "ligand_edge_attr": {
+        "v1_dtype": "torch.int64",
+        "v2_dtype": "torch.float32",
+        "values_equal": true
+      },
+      "v1_merged_residue_complexes": {
+        "protein": 376,
+        "pocket": 208
+      },
+      "v2_merged_residue_complexes": {
+        "protein": 0,
+        "pocket": 0
+      },
+      "is_alpha_carbon": {
+        "protein": {
+          "v1_true": 1918415,
+          "v2_true": 1917382,
+          "lost": 1033,
+          "gained": 0,
+          "z_of_lost": [
+            20
+          ],
+          "lost_residues": 1033
+        },
+        "pocket": {
+          "v1_true": 121717,
+          "v2_true": 121656,
+          "lost": 61,
+          "gained": 0,
+          "z_of_lost": [
+            20
+          ],
+          "lost_residues": 61
+        }
+      },
+      "v1_missing_fields": [
+        "hetero",
+        "insertion_code",
+        "n_residues",
+        "occupancy",
+        "res_seq"
+      ]
+    }
+  }
+}