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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 27 11:51:18 2024
@author: benjaminlear
Adapted by M.Buchhorn, thank you Ben!
"""
atom_colors = [
"#000000", # 0 Unknown
"#dddddd", # 1 H
"cyan", # 2 He
"violet", # 3 Li
"#B22222", # 4 Be
"beige", # 5 B
"#444444", # 6 C
"blue", # 7 N
"red", # 8 O
"green", # 9 F
"cyan", # 10 Ne
"#FF1493", # 11 Na
"#A52A2A", # 12 Mg
"#800080", # 13 Al
"#D2691E", # 14 Si
"#228B22", # 15 P
"yellow", # 16 S
"green", # 17 Cl
"cyan", # 18 Ar
"#0000CD", # 19 K
"#8B4513", # 20 Ca
"#8FBC8F", # 21 Sc
"#B8860B", # 22 Ti
"#4682B4", # 23 V
"#B22222", # 24 Cr
"#2E8B57", # 25 Mn
"#FFD700", # 26 Fe
"#DAA520", # 27 Co
"#A52A2A", # 28 Ni
"#4169E1", # 29 Cu
"#708090", # 30 Zn
"#C0C0C0", # 31 Ga
"#808000", # 32 Ge
"#00FF00", # 33 As
"#00CED1", # 34 Se
"#0000FF", # 35 Br
"cyan", # 36 Kr
"#8A2BE2", # 37 Rb
"#8B4513", # 38 Sr
"#9400D3", # 39 Y
"#FF4500", # 40 Zr
"#4682B4", # 41 Nb
"#B22222", # 42 Mo
"#FFD700", # 43 Tc
"#A52A2A", # 44 Ru
"#228B22", # 45 Rh
"#8B4513", # 46 Pd
"#00CED1", # 47 Ag
"#696969", # 48 Cd
"#C0C0C0", # 49 In
"#808000", # 50 Sn
"#228B22", # 51 Sb
"#D2691E", # 52 Te
"#00FF00", # 53 I
"cyan", # 54 Xe
"#8A2BE2", # 55 Cs
"#8B4513", # 56 Ba
"#FF4500", # 57 La
"#FF1493", # 58 Ce
"#9400D3", # 59 Pr
"#4682B4", # 60 Nd
"#DAA520", # 61 Pm
"#B22222", # 62 Sm
"#228B22", # 63 Eu
"#A52A2A", # 64 Gd
"#B8860B", # 65 Tb
"#8FBC8F", # 66 Dy
"#4682B4", # 67 Ho
"#DAA520", # 68 Er
"#B22222", # 69 Tm
"#228B22", # 70 Yb
"#FF4500", # 71 Lu
"#A52A2A", # 72 Hf
"#4682B4", # 73 Ta
"#DAA520", # 74 W
]
atom_symbols = [
"unk", # 0
"H", # 1
"He", # 2
"Li", # 3
"Be", # 4
"B", # 5
"C", # 6
"N", # 7
"O", # 8
"F", # 9
"Ne", # 10
"Na", # 11
"Mg", # 12
"Al", # 13
"Si", # 14
"P", # 15
"S", # 16
"Cl", # 17
"Ar", # 18
"K", # 19
"Ca", # 20
"Sc", # 21
"Ti", # 22
"V", # 23
"Cr", # 24
"Mn", # 25
"Fe", # 26
"Co", # 27
"Ni", # 28
"Cu", # 29
"Zn", # 30
"Ga", # 31
"Ge", # 32
"As", # 33
"Se", # 34
"Br", # 35
"Kr", # 36
"Rb", # 37
"Sr", # 38
"Y", # 39
"Zr", # 40
"Nb", # 41
"Mo", # 42
"Tc", # 43
"Ru", # 44
"Rh", # 45
"Pd", # 46
"Ag", # 47
"Cd", # 48
"In", # 49
"Sn", # 50
"Sb", # 51
"Te", # 52
"I", # 53
"Xe", # 54
"Cs", # 55
"Ba", # 56
"La", # 57
"Ce", # 58
"Pr", # 59
"Nd", # 60
"Pm", # 61
"Sm", # 62
"Eu", # 63
"Gd", # 64
"Tb", # 65
"Dy", # 66
"Ho", # 67
"Er", # 68
"Tm", # 69
"Yb", # 70
"Lu", # 71
"Hf", # 72
"Ta", # 73
"W", # 74
"Re", # 75
"Os", # 76
"Ir", # 77
"Pt", # 78
"Au", # 79
"Hg", # 80
"Tl", # 81
"Pb", # 82
"Bi", # 83
"Po", # 84
"At", # 85
"Rn", # 86
"Fr", # 87
"Ra", # 88
"Ac", # 89
"Th", # 90
"Pa", # 91
"U", # 92
"Np", # 93
"Pu", # 94
"Am", # 95
"Cm", # 96
"Bk", # 97
"Cf", # 98
"Es", # 99
"Fm", # 100
"Md", # 101
"No", # 102
"Lr", # 103
"Rf", # 104
"Db", # 105
"Sg", # 106
"Bh", # 107
"Hs", # 108
"Mt", # 109
"Ds", # 110
"Rg", # 111
"Cn", # 112
"Nh", # 113
"Fl", # 114
"Mc", # 115
"Lv", # 116
"Ts", # 117
"Og", # 118
]
vdw_radii = [
1.70, # 0 Unknown, same as Carbon
1.20, # 1 H
1.40, # 2 He
1.82, # 3 Li
1.53, # 4 Be
1.92, # 5 B
1.70, # 6 C
1.55, # 7 N
1.52, # 8 O
1.47, # 9 F
1.54, # 10 Ne
2.27, # 11 Na
1.73, # 12 Mg
1.84, # 13 Al
2.10, # 14 Si
1.80, # 15 P
1.80, # 16 S
1.75, # 17 Cl
1.88, # 18 Ar
2.75, # 19 K
2.31, # 20 Ca
2.11, # 21 Sc
2.00, # 22 Ti
2.00, # 23 V
2.00, # 24 Cr
2.00, # 25 Mn
2.00, # 26 Fe
2.00, # 27 Co
1.63, # 28 Ni
1.40, # 29 Cu
1.39, # 30 Zn
1.87, # 31 Ga
2.11, # 32 Ge
1.85, # 33 As
1.90, # 34 Se
1.85, # 35 Br
2.02, # 36 Kr
3.03, # 37 Rb
2.49, # 38 Sr
2.19, # 39 Y
2.06, # 40 Zr
2.00, # 41 Nb
2.00, # 42 Mo
2.00, # 43 Tc
2.00, # 44 Ru
2.00, # 45 Rh
2.00, # 46 Pd
1.72, # 47 Ag
1.58, # 48 Cd
1.93, # 49 In
2.17, # 50 Sn
2.00, # 51 Sb
2.06, # 52 Te
1.98, # 53 I
2.16, # 54 Xe
3.43, # 55 Cs
2.68, # 56 Ba
2.50, # 57 La
2.48, # 58 Ce
2.47, # 59 Pr
2.45, # 60 Nd
2.43, # 61 Pm
2.42, # 62 Sm
2.40, # 63 Eu
2.38, # 64 Gd
2.37, # 65 Tb
2.35, # 66 Dy
2.33, # 67 Ho
2.32, # 68 Er
2.30, # 69 Tm
2.28, # 70 Yb
2.27, # 71 Lu
2.16, # 72 Hf
2.09, # 73 Ta
2.02, # 74 W
]
vdw_radii_dict = dict(zip(atom_symbols, vdw_radii))
atom_colors_dict = dict(zip(atom_symbols, atom_colors))