| { |
| "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": { |
| "n": 22, |
| "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" |
| ] |
| } |
| } |
| } |
