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RNA3DB
File size: 4,115 Bytes
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{
  "atoms_per_structure": {
    "max": 119751,
    "mean": 16434.26075,
    "min": 37
  },
  "bounding_box_extent_angstrom": {
    "diagonal_max": 466.4383822702431,
    "diagonal_min": 20.26119095771105,
    "side_max": 372.98799896240234,
    "side_min": 8.0780029296875
  },
  "elements": {
    "atomic_numbers": [
      1,
      5,
      6,
      7,
      8,
      9,
      15,
      16,
      53
    ],
    "count": 9,
    "counts": {
      "1": 3229977,
      "15": 5999855,
      "16": 638,
      "5": 24,
      "53": 1,
      "6": 57200358,
      "7": 23423310,
      "8": 41619899,
      "9": 24
    },
    "symbols": [
      "H",
      "B",
      "C",
      "N",
      "O",
      "F",
      "P",
      "S",
      "I"
    ]
  },
  "exact": {
    "_overall_resolved_ratio": 0.9062371890833042,
    "chain_fraction_with_hydrogens": 0.06430930639207305,
    "cluster_size_max": 693,
    "cluster_size_min": 1,
    "element_counts": {
      "B": 60,
      "C": 110468344,
      "F": 66,
      "H": 6526316,
      "I": 4,
      "N": 45255247,
      "O": 80363160,
      "P": 11582022,
      "S": 1250
    },
    "element_set": [
      "H",
      "B",
      "C",
      "N",
      "O",
      "F",
      "P",
      "S",
      "I"
    ],
    "hydrogen_fraction_of_atoms": 0.025674298410494442,
    "n_atoms_total": 254196469,
    "n_chains_in_clusters_gt1": 14489,
    "n_chains_with_hydrogens": 993,
    "n_clusters": 2199,
    "n_component_0_chains": 1378,
    "n_components": 142,
    "n_hydrogen_atoms": 6526316,
    "n_singleton_clusters": 952,
    "n_structures": 15441,
    "note": "every figure under \"exact\" is computed from the FULL collated tensors (ptr.diff(), bincount(z)), not from the sample. The sampled quantities elsewhere in this file carry their own n_samples. label_key is \"resolution\" (angstrom) because RNA3DB has no y.",
    "splits": {
      "test": {
        "atoms_max": 16160,
        "atoms_mean": 1567.3758793969848,
        "atoms_median": 1052.0,
        "atoms_min": 32,
        "element_counts": {
          "B": 12,
          "C": 1348177,
          "F": 61,
          "H": 102647,
          "I": 4,
          "N": 541051,
          "O": 985114,
          "P": 142003,
          "S": 9
        },
        "n_atoms_total": 3119078,
        "n_chains_with_hydrogens": 203,
        "n_chains_with_unresolved_residues": 1227,
        "n_clusters": 660,
        "n_components": 51,
        "n_hydrogen_atoms": 102647,
        "n_no_rfam_hit": 1365,
        "n_structures": 1990,
        "resolution_max": 9.0,
        "resolution_min": 1.0499999523162842,
        "resolved_ratio": 0.7287988037199393,
        "resolved_residues_total": 142314,
        "seq_length_max": 1824,
        "seq_length_mean": 98.12663316582915,
        "seq_length_min": 32,
        "seq_residues_total": 195272
      },
      "train": {
        "atoms_max": 119751,
        "atoms_mean": 18666.076202512824,
        "atoms_median": 2579.0,
        "atoms_min": 29,
        "element_counts": {
          "B": 48,
          "C": 109120167,
          "F": 5,
          "H": 6423669,
          "N": 44714196,
          "O": 79378046,
          "P": 11440019,
          "S": 1241
        },
        "n_atoms_total": 251077391,
        "n_chains_with_hydrogens": 790,
        "n_chains_with_unresolved_residues": 7592,
        "n_clusters": 1539,
        "n_components": 91,
        "n_hydrogen_atoms": 6423669,
        "n_no_rfam_hit": 58,
        "n_structures": 13451,
        "resolution_max": 9.0,
        "resolution_min": 1.309999942779541,
        "resolved_ratio": 0.9089889080673468,
        "resolved_residues_total": 11445692,
        "seq_length_max": 19000,
        "seq_length_mean": 936.114340941194,
        "seq_length_min": 32,
        "seq_residues_total": 12591674
      }
    },
    "structure_method_counts": {
      "electron microscopy": 9625,
      "electron microscopy,solution nmr": 2,
      "x-ray diffraction": 5814
    }
  },
  "label_resolution": {
    "max": 9.0,
    "mean": 3.3148551670610904,
    "min": 1.0499999523162842
  },
  "n_total": 15441,
  "sample_size": 8000
}