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/constants.py
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| a | b/constants.py | ||
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| 1 | import numpy as np |
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| 2 | from rdkit import Chem |
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| 3 | import torch |
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| 4 | |||
| 5 | # ------------------------------------------------------------------------------ |
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| 6 | # Computational |
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| 7 | # ------------------------------------------------------------------------------ |
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| 8 | FLOAT_TYPE = torch.float32 |
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| 9 | INT_TYPE = torch.int64 |
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| 10 | |||
| 11 | |||
| 12 | # ------------------------------------------------------------------------------ |
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| 13 | # Bond parameters |
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| 14 | # ------------------------------------------------------------------------------ |
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| 15 | |||
| 16 | # margin1, margin2, margin3 = 10, 5, 3 |
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| 17 | margin1, margin2, margin3 = 3, 2, 1 |
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| 18 | |||
| 19 | allowed_bonds = {'H': 1, 'C': 4, 'N': 3, 'O': 2, 'F': 1, 'B': 3, 'Al': 3, |
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| 20 | 'Si': 4, 'P': [3, 5], |
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| 21 | 'S': 4, 'Cl': 1, 'As': 3, 'Br': 1, 'I': 1, 'Hg': [1, 2], |
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| 22 | 'Bi': [3, 5]} |
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| 23 | |||
| 24 | # Bond lengths from: |
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| 25 | # http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html |
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| 26 | # And: |
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| 27 | # http://chemistry-reference.com/tables/Bond%20Lengths%20and%20Enthalpies.pdf |
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| 28 | bonds1 = {'H': {'H': 74, 'C': 109, 'N': 101, 'O': 96, 'F': 92, |
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| 29 | 'B': 119, 'Si': 148, 'P': 144, 'As': 152, 'S': 134, |
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| 30 | 'Cl': 127, 'Br': 141, 'I': 161}, |
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| 31 | 'C': {'H': 109, 'C': 154, 'N': 147, 'O': 143, 'F': 135, |
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| 32 | 'Si': 185, 'P': 184, 'S': 182, 'Cl': 177, 'Br': 194, |
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| 33 | 'I': 214}, |
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| 34 | 'N': {'H': 101, 'C': 147, 'N': 145, 'O': 140, 'F': 136, |
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| 35 | 'Cl': 175, 'Br': 214, 'S': 168, 'I': 222, 'P': 177}, |
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| 36 | 'O': {'H': 96, 'C': 143, 'N': 140, 'O': 148, 'F': 142, |
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| 37 | 'Br': 172, 'S': 151, 'P': 163, 'Si': 163, 'Cl': 164, |
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| 38 | 'I': 194}, |
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| 39 | 'F': {'H': 92, 'C': 135, 'N': 136, 'O': 142, 'F': 142, |
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| 40 | 'S': 158, 'Si': 160, 'Cl': 166, 'Br': 178, 'P': 156, |
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| 41 | 'I': 187}, |
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| 42 | 'B': {'H': 119, 'Cl': 175}, |
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| 43 | 'Si': {'Si': 233, 'H': 148, 'C': 185, 'O': 163, 'S': 200, |
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| 44 | 'F': 160, 'Cl': 202, 'Br': 215, 'I': 243 }, |
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| 45 | 'Cl': {'Cl': 199, 'H': 127, 'C': 177, 'N': 175, 'O': 164, |
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| 46 | 'P': 203, 'S': 207, 'B': 175, 'Si': 202, 'F': 166, |
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| 47 | 'Br': 214}, |
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| 48 | 'S': {'H': 134, 'C': 182, 'N': 168, 'O': 151, 'S': 204, |
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| 49 | 'F': 158, 'Cl': 207, 'Br': 225, 'Si': 200, 'P': 210, |
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| 50 | 'I': 234}, |
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| 51 | 'Br': {'Br': 228, 'H': 141, 'C': 194, 'O': 172, 'N': 214, |
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| 52 | 'Si': 215, 'S': 225, 'F': 178, 'Cl': 214, 'P': 222}, |
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| 53 | 'P': {'P': 221, 'H': 144, 'C': 184, 'O': 163, 'Cl': 203, |
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| 54 | 'S': 210, 'F': 156, 'N': 177, 'Br': 222}, |
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| 55 | 'I': {'H': 161, 'C': 214, 'Si': 243, 'N': 222, 'O': 194, |
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| 56 | 'S': 234, 'F': 187, 'I': 266}, |
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| 57 | 'As': {'H': 152} |
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| 58 | } |
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| 59 | |||
| 60 | bonds2 = {'C': {'C': 134, 'N': 129, 'O': 120, 'S': 160}, |
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| 61 | 'N': {'C': 129, 'N': 125, 'O': 121}, |
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| 62 | 'O': {'C': 120, 'N': 121, 'O': 121, 'P': 150}, |
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| 63 | 'P': {'O': 150, 'S': 186}, |
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| 64 | 'S': {'P': 186, 'C': 160}} |
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| 65 | |||
| 66 | |||
| 67 | bonds3 = {'C': {'C': 120, 'N': 116, 'O': 113}, |
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| 68 | 'N': {'C': 116, 'N': 110}, |
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| 69 | 'O': {'C': 113}} |
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| 70 | |||
| 71 | bond_dict = [None, Chem.rdchem.BondType.SINGLE, Chem.rdchem.BondType.DOUBLE, |
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| 72 | Chem.rdchem.BondType.TRIPLE, Chem.rdchem.BondType.AROMATIC] |
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| 73 | |||
| 74 | # https://en.wikipedia.org/wiki/Covalent_radius#Radii_for_multiple_bonds |
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| 75 | # (2022/08/14) |
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| 76 | covalent_radii = {'H': 32, 'C': 60, 'N': 54, 'O': 53, 'F': 53, 'B': 73, |
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| 77 | 'Al': 111, 'Si': 102, 'P': 94, 'S': 94, 'Cl': 93, 'As': 106, |
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| 78 | 'Br': 109, 'I': 125, 'Hg': 133, 'Bi': 135} |
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| 79 | |||
| 80 | # ------------------------------------------------------------------------------ |
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| 81 | # Backbone geometry |
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| 82 | # Taken from: Bhagavan, N. V., and C. E. Ha. |
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| 83 | # "Chapter 4-Three-dimensional structure of proteins and disorders of protein misfolding." |
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| 84 | # Essentials of Medical Biochemistry (2015): 31-51. |
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| 85 | # https://www.sciencedirect.com/science/article/pii/B978012416687500004X |
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| 86 | # ------------------------------------------------------------------------------ |
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| 87 | N_CA_DIST = 1.47 |
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| 88 | CA_C_DIST = 1.53 |
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| 89 | N_CA_C_ANGLE = 110 * np.pi / 180 |
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| 90 | |||
| 91 | |||
| 92 | # ------------------------------------------------------------------------------ |
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| 93 | # Dataset-specific constants |
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| 94 | # ------------------------------------------------------------------------------ |
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| 95 | dataset_params = {} |
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| 96 | dataset_params['bindingmoad'] = { |
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| 97 | 'atom_encoder': {'C': 0, 'N': 1, 'O': 2, 'S': 3, 'B': 4, 'Br': 5, 'Cl': 6, 'P': 7, 'I': 8, 'F': 9}, |
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| 98 | 'atom_decoder': ['C', 'N', 'O', 'S', 'B', 'Br', 'Cl', 'P', 'I', 'F'], |
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| 99 | 'aa_encoder': {'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'P': 12, 'Q': 13, 'R': 14, 'S': 15, 'T': 16, 'V': 17, 'W': 18, 'Y': 19}, |
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| 100 | 'aa_decoder': ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'], |
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| 101 | # PyMOL colors, see: https://pymolwiki.org/index.php/Color_Values#Chemical_element_colours |
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| 102 | 'colors_dic': ['#33ff33', '#3333ff', '#ff4d4d', '#e6c540', '#ffb5b5', '#A62929', '#1FF01F', '#ff8000', '#940094', '#B3FFFF', '#b3e3f5'], |
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| 103 | 'radius_dic': [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3], |
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| 104 | 'bonds1': [ |
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| 105 | [154.0, 147.0, 143.0, 182.0, 0.0, 194.0, 177.0, 184.0, 214.0, 135.0], |
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| 106 | [147.0, 145.0, 140.0, 168.0, 0.0, 214.0, 175.0, 177.0, 222.0, 136.0], |
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| 107 | [143.0, 140.0, 148.0, 151.0, 0.0, 172.0, 164.0, 163.0, 194.0, 142.0], |
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| 108 | [182.0, 168.0, 151.0, 204.0, 0.0, 225.0, 207.0, 210.0, 234.0, 158.0], |
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| 109 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 175.0, 0.0, 0.0, 0.0], |
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| 110 | [194.0, 214.0, 172.0, 225.0, 0.0, 228.0, 214.0, 222.0, 0.0, 178.0], |
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| 111 | [177.0, 175.0, 164.0, 207.0, 175.0, 214.0, 199.0, 203.0, 0.0, 166.0], |
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| 112 | [184.0, 177.0, 163.0, 210.0, 0.0, 222.0, 203.0, 221.0, 0.0, 156.0], |
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| 113 | [214.0, 222.0, 194.0, 234.0, 0.0, 0.0, 0.0, 0.0, 266.0, 187.0], |
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| 114 | [135.0, 136.0, 142.0, 158.0, 0.0, 178.0, 166.0, 156.0, 187.0, 142.0]], |
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| 115 | 'bonds2': [[134.0, 129.0, 120.0, 160.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 116 | [129.0, 125.0, 121.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 117 | [120.0, 121.0, 121.0, 0.0, 0.0, 0.0, 0.0, 150.0, 0.0, 0.0], |
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| 118 | [160.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 186.0, 0.0, 0.0], |
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| 119 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 120 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 121 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 122 | [0.0, 0.0, 150.0, 186.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 123 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 124 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], |
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| 125 | 'bonds3': [[120.0, 116.0, 113.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 126 | [116.0, 110.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 127 | [113.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 128 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 129 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 130 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 131 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 132 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 133 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], |
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| 134 | [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], |
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| 135 | 'lennard_jones_rm': [ |
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| 136 | [120.0, 116.0, 113.0, 160.0, 133.0, 194.0, 177.0, 184.0, 214.0, 135.0], |
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| 137 | [116.0, 110.0, 121.0, 168.0, 127.0, 214.0, 175.0, 177.0, 222.0, 136.0], |
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| 138 | [113.0, 121.0, 121.0, 151.0, 126.0, 172.0, 164.0, 150.0, 194.0, 142.0], |
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| 139 | [160.0, 168.0, 151.0, 204.0, 167.0, 225.0, 207.0, 186.0, 234.0, 158.0], |
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| 140 | [133.0, 127.0, 126.0, 167.0, 146.0, 182.0, 175.0, 167.0, 198.0, 126.0], |
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| 141 | [194.0, 214.0, 172.0, 225.0, 182.0, 228.0, 214.0, 222.0, 234.0, 178.0], |
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| 142 | [177.0, 175.0, 164.0, 207.0, 175.0, 214.0, 199.0, 203.0, 218.0, 166.0], |
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| 143 | [184.0, 177.0, 150.0, 186.0, 167.0, 222.0, 203.0, 221.0, 219.0, 156.0], |
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| 144 | [214.0, 222.0, 194.0, 234.0, 198.0, 234.0, 218.0, 219.0, 266.0, 187.0], |
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| 145 | [135.0, 136.0, 142.0, 158.0, 126.0, 178.0, 166.0, 156.0, 187.0, 142.0]], |
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| 146 | 'atom_hist': {'C': 545542, 'N': 90205, 'O': 132965, 'S': 9342, 'B': 109, |
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| 147 | 'Br': 1424, 'Cl': 5516, 'P': 5154, 'I': 445, 'F': 9742}, |
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| 148 | 'aa_hist': {'A': 109798, 'C': 31556, 'D': 83921, 'E': 79405, 'F': 97083, |
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| 149 | 'G': 139319, 'H': 62661, 'I': 99008, 'K': 62403, 'L': 155105, |
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| 150 | 'M': 59977, 'N': 70437, 'P': 58833, 'Q': 48254, 'R': 74215, |
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| 151 | 'S': 103286, 'T': 90972, 'V': 119954, 'W': 42017, 'Y': 90596}, |
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| 152 | } |
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| 153 | |||
| 154 | dataset_params['crossdock_full'] = { |
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| 155 | 'atom_encoder': {'C': 0, 'N': 1, 'O': 2, 'S': 3, 'B': 4, 'Br': 5, 'Cl': 6, 'P': 7, 'I': 8, 'F': 9, 'others': 10}, |
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| 156 | 'atom_decoder': ['C', 'N', 'O', 'S', 'B', 'Br', 'Cl', 'P', 'I', 'F', 'others'], |
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| 157 | 'aa_encoder': {'C': 0, 'N': 1, 'O': 2, 'S': 3, 'B': 4, 'Br': 5, 'Cl': 6, 'P': 7, 'I': 8, 'F': 9, 'others': 10}, |
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| 158 | 'aa_decoder': ['C', 'N', 'O', 'S', 'B', 'Br', 'Cl', 'P', 'I', 'F', 'others'], |
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| 159 | 'colors_dic': ['#33ff33', '#3333ff', '#ff4d4d', '#e6c540', '#ffb5b5', '#A62929', '#1FF01F', '#ff8000', '#940094', '#B3FFFF', '#ffb5b5'], |
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| 160 | 'radius_dic': [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3], |
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| 161 | 'bonds1': [[154.0, 147.0, 143.0, 182.0, 0.0, 194.0, 177.0, 184.0, 214.0, 135.0, 0.0], [147.0, 145.0, 140.0, 168.0, 0.0, 214.0, 175.0, 177.0, 222.0, 136.0, 0.0], [143.0, 140.0, 148.0, 151.0, 0.0, 172.0, 164.0, 163.0, 194.0, 142.0, 0.0], [182.0, 168.0, 151.0, 204.0, 0.0, 225.0, 207.0, 210.0, 234.0, 158.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 175.0, 0.0, 0.0, 0.0, 0.0], [194.0, 214.0, 172.0, 225.0, 0.0, 228.0, 214.0, 222.0, 0.0, 178.0, 0.0], [177.0, 175.0, 164.0, 207.0, 175.0, 214.0, 199.0, 203.0, 0.0, 166.0, 0.0], [184.0, 177.0, 163.0, 210.0, 0.0, 222.0, 203.0, 221.0, 0.0, 156.0, 0.0], [214.0, 222.0, 194.0, 234.0, 0.0, 0.0, 0.0, 0.0, 266.0, 187.0, 0.0], [135.0, 136.0, 142.0, 158.0, 0.0, 178.0, 166.0, 156.0, 187.0, 142.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], |
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| 162 | 'bonds2': [[134.0, 129.0, 120.0, 160.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [129.0, 125.0, 121.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [120.0, 121.0, 121.0, 0.0, 0.0, 0.0, 0.0, 150.0, 0.0, 0.0, 0.0], [160.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 186.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 150.0, 186.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], |
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| 163 | 'bonds3': [[120.0, 116.0, 113.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [116.0, 110.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [113.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], |
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| 164 | 'lennard_jones_rm': [[120.0, 116.0, 113.0, 160.0, 133.0, 194.0, 177.0, 184.0, 214.0, 135.0, 0.0], [116.0, 110.0, 121.0, 168.0, 127.0, 214.0, 175.0, 177.0, 222.0, 136.0, 0.0], [113.0, 121.0, 121.0, 151.0, 126.0, 172.0, 164.0, 150.0, 194.0, 142.0, 0.0], [160.0, 168.0, 151.0, 204.0, 167.0, 225.0, 207.0, 186.0, 234.0, 158.0, 0.0], [133.0, 127.0, 126.0, 167.0, 146.0, 182.0, 175.0, 167.0, 198.0, 126.0, 0.0], [194.0, 214.0, 172.0, 225.0, 182.0, 228.0, 214.0, 222.0, 234.0, 178.0, 0.0], [177.0, 175.0, 164.0, 207.0, 175.0, 214.0, 199.0, 203.0, 218.0, 166.0, 0.0], [184.0, 177.0, 150.0, 186.0, 167.0, 222.0, 203.0, 221.0, 219.0, 156.0, 0.0], [214.0, 222.0, 194.0, 234.0, 198.0, 234.0, 218.0, 219.0, 266.0, 187.0, 0.0], [135.0, 136.0, 142.0, 158.0, 126.0, 178.0, 166.0, 156.0, 187.0, 142.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], |
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| 165 | 'atom_hist': {'C': 1570767, 'N': 273858, 'O': 396837, 'S': 26352, 'B': 0, 'Br': 0, 'Cl': 15058, 'P': 25994, 'I': 0, 'F': 30687, 'others': 0}, |
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| 166 | 'aa_hist': {'C': 23302704, 'N': 6093090, 'O': 6701210, 'S': 276805, 'B': 0, 'Br': 0, 'Cl': 0, 'P': 0, 'I': 0, 'F': 0, 'others': 0}, |
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| 167 | } |
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| 168 | |||
| 169 | dataset_params['crossdock'] = { |
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| 170 | 'atom_encoder': {'C': 0, 'N': 1, 'O': 2, 'S': 3, 'B': 4, 'Br': 5, 'Cl': 6, 'P': 7, 'I': 8, 'F': 9}, |
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| 171 | 'atom_decoder': ['C', 'N', 'O', 'S', 'B', 'Br', 'Cl', 'P', 'I', 'F'], |
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| 172 | 'aa_encoder': {'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'P': 12, 'Q': 13, 'R': 14, 'S': 15, 'T': 16, 'V': 17, 'W': 18, 'Y': 19}, |
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| 173 | 'aa_decoder': ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'], |
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| 174 | # PyMOL colors, see: https://pymolwiki.org/index.php/Color_Values#Chemical_element_colours |
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| 175 | 'colors_dic': ['#33ff33', '#3333ff', '#ff4d4d', '#e6c540', '#ffb5b5', '#A62929', '#1FF01F', '#ff8000', '#940094', '#B3FFFF'], |
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| 176 | 'radius_dic': [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3], |
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| 177 | 'bonds1': [[154.0, 147.0, 143.0, 182.0, 0.0, 194.0, 177.0, 184.0, 214.0, 135.0], [147.0, 145.0, 140.0, 168.0, 0.0, 214.0, 175.0, 177.0, 222.0, 136.0], [143.0, 140.0, 148.0, 151.0, 0.0, 172.0, 164.0, 163.0, 194.0, 142.0], [182.0, 168.0, 151.0, 204.0, 0.0, 225.0, 207.0, 210.0, 234.0, 158.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 175.0, 0.0, 0.0, 0.0], [194.0, 214.0, 172.0, 225.0, 0.0, 228.0, 214.0, 222.0, 0.0, 178.0], [177.0, 175.0, 164.0, 207.0, 175.0, 214.0, 199.0, 203.0, 0.0, 166.0], [184.0, 177.0, 163.0, 210.0, 0.0, 222.0, 203.0, 221.0, 0.0, 156.0], [214.0, 222.0, 194.0, 234.0, 0.0, 0.0, 0.0, 0.0, 266.0, 187.0], [135.0, 136.0, 142.0, 158.0, 0.0, 178.0, 166.0, 156.0, 187.0, 142.0]], |
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| 178 | 'bonds2': [[134.0, 129.0, 120.0, 160.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [129.0, 125.0, 121.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [120.0, 121.0, 121.0, 0.0, 0.0, 0.0, 0.0, 150.0, 0.0, 0.0], [160.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 186.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 150.0, 186.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], |
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| 179 | 'bonds3': [[120.0, 116.0, 113.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [116.0, 110.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [113.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], |
||
| 180 | 'lennard_jones_rm': [[120.0, 116.0, 113.0, 160.0, 133.0, 194.0, 177.0, 184.0, 214.0, 135.0], [116.0, 110.0, 121.0, 168.0, 127.0, 214.0, 175.0, 177.0, 222.0, 136.0], [113.0, 121.0, 121.0, 151.0, 126.0, 172.0, 164.0, 150.0, 194.0, 142.0], [160.0, 168.0, 151.0, 204.0, 167.0, 225.0, 207.0, 186.0, 234.0, 158.0], [133.0, 127.0, 126.0, 167.0, 146.0, 182.0, 175.0, 167.0, 198.0, 126.0], [194.0, 214.0, 172.0, 225.0, 182.0, 228.0, 214.0, 222.0, 234.0, 178.0], [177.0, 175.0, 164.0, 207.0, 175.0, 214.0, 199.0, 203.0, 218.0, 166.0], [184.0, 177.0, 150.0, 186.0, 167.0, 222.0, 203.0, 221.0, 219.0, 156.0], [214.0, 222.0, 194.0, 234.0, 198.0, 234.0, 218.0, 219.0, 266.0, 187.0], [135.0, 136.0, 142.0, 158.0, 126.0, 178.0, 166.0, 156.0, 187.0, 142.0]], |
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| 181 | 'atom_hist': {'C': 1570032, 'N': 273792, 'O': 396623, 'S': 26339, 'B': 0, 'Br': 0, 'Cl': 15055, 'P': 25975, 'I': 0, 'F': 30673}, |
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| 182 | 'aa_hist': {'A': 277175, 'C': 92406, 'D': 254046, 'E': 201833, 'F': 234995, 'G': 376966, 'H': 147704, 'I': 290683, 'K': 173210, 'L': 421883, 'M': 157813, 'N': 174241, 'P': 148581, 'Q': 120232, 'R': 173848, 'S': 274430, 'T': 247605, 'V': 326134, 'W': 88552, 'Y': 226668}, |
||
| 183 | } |