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hiqbind_stats.json

@@ -2,20 +2,21 @@
   "n_total": 31572,
   "sample_size": 8000,
   "atoms_per_structure": {
-    "min": 78,
-    "max": 1140,
-    "mean": 487.016125
+    "min": 709,
+    "max": 50092,
+    "mean": 6829.78375
   },
   "bounding_box_extent_angstrom": {
-    "side_min": 9.102400183677673,
-    "side_max": 45.03310012817383,
-    "diagonal_min": 19.85606805466951,
-    "diagonal_max": 62.20783647464335
+    "side_min": 21.65899658203125,
+    "side_max": 221.00599670410156,
+    "diagonal_min": 45.237691696034425,
+    "diagonal_max": 274.62297143473495
   },
   "elements": {
-    "count": 12,
+    "count": 14,
     "atomic_numbers": [
       1,
+      4,
       6,
       7,
       8,
@@ -26,10 +27,12 @@
       33,
       34,
       35,
-      53
+      53,
+      80
     ],
     "symbols": [
       "H",
+      "Be",
       "C",
       "N",
       "O",
@@ -40,21 +43,24 @@
       "As",
       "Se",
       "Br",
-      "I"
+      "I",
+      "Hg"
     ],
     "counts": {
-      "1": 1895748,
-      "6": 1308600,
-      "7": 323339,
-      "8": 347266,
-      "9": 2686,
-      "15": 1540,
-      "16": 15059,
+      "1": 27169131,
+      "4": 1,
+      "6": 17498478,
+      "7": 4701257,
+      "8": 5119687,
+      "9": 2694,
+      "15": 2375,
+      "16": 142235,
       "17": 1496,
-      "33": 1,
-      "34": 34,
+      "33": 121,
+      "34": 431,
       "35": 276,
-      "53": 84
+      "53": 84,
+      "80": 4
     }
   },
   "label_y": {
@@ -75,13 +81,6 @@
         "max": 50050,
         "zero_length": 0
       },
-      "pocket": {
-        "total_atoms": 14289607,
-        "min": 38,
-        "mean": 442.7,
-        "max": 1315,
-        "zero_length": 0
-      },
       "ligand": {
         "total_atoms": 1528172,
         "min": 4,
@@ -89,15 +88,22 @@
         "max": 233,
         "zero_length": 0
       },
+      "water": {
+        "total_atoms": 7276591,
+        "min": 0,
+        "mean": 225.5,
+        "max": 2232,
+        "zero_length": 1392
+      },
       "additives": {
-        "total_atoms": 8301449,
+        "total_atoms": 1024858,
         "min": 0,
-        "mean": 257.2,
-        "max": 2469,
-        "zero_length": 593
+        "mean": 31.8,
+        "max": 912,
+        "zero_length": 9256
       }
     },
-    "pocket_cutoff_angstrom": 6.0,
+    "pocket": "NOT shipped \u2014 HiQBind provides none; use HiQBind(pocket_cutoff=<A>) at load",
     "elements_z": [
       1,
       3,
@@ -219,11 +225,12 @@
     "n_elements": 57,
     "res_name_vocab_size": 1043,
     "chain_vocab_size": 56,
-    "n_pocket_residues": {
-      "min": 2,
-      "mean": 27.7,
-      "max": 81
+    "residues_per_complex": {
+      "min": 61,
+      "mean": 655.8,
+      "max": 4735
     },
+    "insertion_code_vocab_size": 25,
     "ligand_bond_orders": [
       1.0,
       2.0,
@@ -313,6 +320,59 @@
       "mean": 0.502505,
       "n_nan": 0
     },
+    "additives_composition": {
+      "total_atoms": 1024858,
+      "distinct_residue_names": 966,
+      "note": "classes are indicative, from a curated residue list used ONLY for this summary \u2014 the shipped data classifies nothing beyond entity_type (water / metal_ion / other_hetero). Cofactors are the largest class but a minority, which is why the component is called \"additives\" and not \"cofactors\".",
+      "by_class": {
+        "cofactor_nucleotide": {
+          "atoms": 375002,
+          "percent": 36.6
+        },
+        "cryoprotectant_buffer_detergent": {
+          "atoms": 220225,
+          "percent": 21.5
+        },
+        "other_incl_lipid": {
+          "atoms": 147312,
+          "percent": 14.4
+        },
+        "ion_salt_small_anion": {
+          "atoms": 145998,
+          "percent": 14.2
+        },
+        "sugar": {
+          "atoms": 136321,
+          "percent": 13.3
+        }
+      },
+      "top20_residues": {
+        "NAG": 104832,
+        "HEM": 103103,
+        "NAP": 76604,
+        "SO4": 69000,
+        "GOL": 60238,
+        "EDO": 56687,
+        "FAD": 38961,
+        "NAD": 36195,
+        "H4B": 29818,
+        "NDP": 27909,
+        "DMS": 26721,
+        "ACT": 14920,
+        "PO4": 12905,
+        "1PE": 10885,
+        "BTB": 10808,
+        "PEG": 9888,
+        "ZN": 9331,
+        "CLR": 9156,
+        "ADP": 7886,
+        "GTP": 6408
+      }
+    },
+    "water": {
+      "total_atoms": 7276591,
+      "note": "HOH only, split into its own file so it can be excluded from the download"
+    },
     "units": {
       "pos": "angstrom",
       "neglog_aff": "unitless (-log10 of affinity in M; pKd-like)",