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constants.py
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constants.py
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import numpy as np
from rdkit import Chem
import torch
# ------------------------------------------------------------------------------
# Computational
# ------------------------------------------------------------------------------
FLOAT_TYPE = torch.float32
INT_TYPE = torch.int64
# ------------------------------------------------------------------------------
# Bond parameters
# ------------------------------------------------------------------------------
# margin1, margin2, margin3 = 10, 5, 3
margin1, margin2, margin3 = 3, 2, 1
allowed_bonds = {'H': 1, 'C': 4, 'N': 3, 'O': 2, 'F': 1, 'B': 3, 'Al': 3,
'Si': 4, 'P': [3, 5],
'S': 4, 'Cl': 1, 'As': 3, 'Br': 1, 'I': 1, 'Hg': [1, 2],
'Bi': [3, 5]}
# Bond lengths from:
# http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html
# And:
# http://chemistry-reference.com/tables/Bond%20Lengths%20and%20Enthalpies.pdf
bonds1 = {'H': {'H': 74, 'C': 109, 'N': 101, 'O': 96, 'F': 92,
'B': 119, 'Si': 148, 'P': 144, 'As': 152, 'S': 134,
'Cl': 127, 'Br': 141, 'I': 161},
'C': {'H': 109, 'C': 154, 'N': 147, 'O': 143, 'F': 135,
'Si': 185, 'P': 184, 'S': 182, 'Cl': 177, 'Br': 194,
'I': 214},
'N': {'H': 101, 'C': 147, 'N': 145, 'O': 140, 'F': 136,
'Cl': 175, 'Br': 214, 'S': 168, 'I': 222, 'P': 177},
'O': {'H': 96, 'C': 143, 'N': 140, 'O': 148, 'F': 142,
'Br': 172, 'S': 151, 'P': 163, 'Si': 163, 'Cl': 164,
'I': 194},
'F': {'H': 92, 'C': 135, 'N': 136, 'O': 142, 'F': 142,
'S': 158, 'Si': 160, 'Cl': 166, 'Br': 178, 'P': 156,
'I': 187},
'B': {'H': 119, 'Cl': 175},
'Si': {'Si': 233, 'H': 148, 'C': 185, 'O': 163, 'S': 200,
'F': 160, 'Cl': 202, 'Br': 215, 'I': 243 },
'Cl': {'Cl': 199, 'H': 127, 'C': 177, 'N': 175, 'O': 164,
'P': 203, 'S': 207, 'B': 175, 'Si': 202, 'F': 166,
'Br': 214},
'S': {'H': 134, 'C': 182, 'N': 168, 'O': 151, 'S': 204,
'F': 158, 'Cl': 207, 'Br': 225, 'Si': 200, 'P': 210,
'I': 234},
'Br': {'Br': 228, 'H': 141, 'C': 194, 'O': 172, 'N': 214,
'Si': 215, 'S': 225, 'F': 178, 'Cl': 214, 'P': 222},
'P': {'P': 221, 'H': 144, 'C': 184, 'O': 163, 'Cl': 203,
'S': 210, 'F': 156, 'N': 177, 'Br': 222},
'I': {'H': 161, 'C': 214, 'Si': 243, 'N': 222, 'O': 194,
'S': 234, 'F': 187, 'I': 266},
'As': {'H': 152}
}
bonds2 = {'C': {'C': 134, 'N': 129, 'O': 120, 'S': 160},
'N': {'C': 129, 'N': 125, 'O': 121},
'O': {'C': 120, 'N': 121, 'O': 121, 'P': 150},
'P': {'O': 150, 'S': 186},
'S': {'P': 186, 'C': 160}}
bonds3 = {'C': {'C': 120, 'N': 116, 'O': 113},
'N': {'C': 116, 'N': 110},
'O': {'C': 113}}
bond_dict = [None, Chem.rdchem.BondType.SINGLE, Chem.rdchem.BondType.DOUBLE,
Chem.rdchem.BondType.TRIPLE, Chem.rdchem.BondType.AROMATIC]
# https://en.wikipedia.org/wiki/Covalent_radius#Radii_for_multiple_bonds
# (2022/08/14)
covalent_radii = {'H': 32, 'C': 60, 'N': 54, 'O': 53, 'F': 53, 'B': 73,
'Al': 111, 'Si': 102, 'P': 94, 'S': 94, 'Cl': 93, 'As': 106,
'Br': 109, 'I': 125, 'Hg': 133, 'Bi': 135}
# ------------------------------------------------------------------------------
# Backbone geometry
# Taken from: Bhagavan, N. V., and C. E. Ha.
# "Chapter 4-Three-dimensional structure of proteins and disorders of protein misfolding."
# Essentials of Medical Biochemistry (2015): 31-51.
# https://www.sciencedirect.com/science/article/pii/B978012416687500004X
# ------------------------------------------------------------------------------
N_CA_DIST = 1.47
CA_C_DIST = 1.53
N_CA_C_ANGLE = 110 * np.pi / 180
# ------------------------------------------------------------------------------
# Dataset-specific constants
# ------------------------------------------------------------------------------
dataset_params = {}
dataset_params['bindingmoad'] = {
'atom_encoder': {'C': 0, 'N': 1, 'O': 2, 'S': 3, 'B': 4, 'Br': 5, 'Cl': 6, 'P': 7, 'I': 8, 'F': 9},
'atom_decoder': ['C', 'N', 'O', 'S', 'B', 'Br', 'Cl', 'P', 'I', 'F'],
'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},
'aa_decoder': ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'],
# PyMOL colors, see: https://pymolwiki.org/index.php/Color_Values#Chemical_element_colours
'colors_dic': ['#33ff33', '#3333ff', '#ff4d4d', '#e6c540', '#ffb5b5', '#A62929', '#1FF01F', '#ff8000', '#940094', '#B3FFFF', '#b3e3f5'],
'radius_dic': [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3],
'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]],
'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]],
'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]],
'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]],
'atom_hist': {'C': 545542, 'N': 90205, 'O': 132965, 'S': 9342, 'B': 109,
'Br': 1424, 'Cl': 5516, 'P': 5154, 'I': 445, 'F': 9742},
'aa_hist': {'A': 109798, 'C': 31556, 'D': 83921, 'E': 79405, 'F': 97083,
'G': 139319, 'H': 62661, 'I': 99008, 'K': 62403, 'L': 155105,
'M': 59977, 'N': 70437, 'P': 58833, 'Q': 48254, 'R': 74215,
'S': 103286, 'T': 90972, 'V': 119954, 'W': 42017, 'Y': 90596},
}
dataset_params['crossdock_full'] = {
'atom_encoder': {'C': 0, 'N': 1, 'O': 2, 'S': 3, 'B': 4, 'Br': 5, 'Cl': 6, 'P': 7, 'I': 8, 'F': 9, 'others': 10},
'atom_decoder': ['C', 'N', 'O', 'S', 'B', 'Br', 'Cl', 'P', 'I', 'F', 'others'],
'aa_encoder': {'C': 0, 'N': 1, 'O': 2, 'S': 3, 'B': 4, 'Br': 5, 'Cl': 6, 'P': 7, 'I': 8, 'F': 9, 'others': 10},
'aa_decoder': ['C', 'N', 'O', 'S', 'B', 'Br', 'Cl', 'P', 'I', 'F', 'others'],
'colors_dic': ['#33ff33', '#3333ff', '#ff4d4d', '#e6c540', '#ffb5b5', '#A62929', '#1FF01F', '#ff8000', '#940094', '#B3FFFF', '#ffb5b5'],
'radius_dic': [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3],
'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]],
'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]],
'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]],
'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]],
'atom_hist': {'C': 1570767, 'N': 273858, 'O': 396837, 'S': 26352, 'B': 0, 'Br': 0, 'Cl': 15058, 'P': 25994, 'I': 0, 'F': 30687, 'others': 0},
'aa_hist': {'C': 23302704, 'N': 6093090, 'O': 6701210, 'S': 276805, 'B': 0, 'Br': 0, 'Cl': 0, 'P': 0, 'I': 0, 'F': 0, 'others': 0},
}
dataset_params['crossdock'] = {
'atom_encoder': {'C': 0, 'N': 1, 'O': 2, 'S': 3, 'B': 4, 'Br': 5, 'Cl': 6, 'P': 7, 'I': 8, 'F': 9},
'atom_decoder': ['C', 'N', 'O', 'S', 'B', 'Br', 'Cl', 'P', 'I', 'F'],
'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},
'aa_decoder': ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'],
# PyMOL colors, see: https://pymolwiki.org/index.php/Color_Values#Chemical_element_colours
'colors_dic': ['#33ff33', '#3333ff', '#ff4d4d', '#e6c540', '#ffb5b5', '#A62929', '#1FF01F', '#ff8000', '#940094', '#B3FFFF'],
'radius_dic': [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3],
'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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'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},
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