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1 #!/usr/bin/env python
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2 __all__ = ['weights_max', 'weights_mean', 'weights_none', 'default']
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3
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4 # Silicos-it
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5 from errors import WrongArgument
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6
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7 # RDKit
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8 from rdkit.Chem import Descriptors
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9 from rdkit import Chem
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10
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11 # General
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12 from copy import deepcopy
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13 from math import exp, log
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14 import sys, os, re
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15 import argparse
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16
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17 def check_filetype(filepath):
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18 mol = False
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19 possible_inchi = True
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20 for line_counter, line in enumerate(open(filepath)):
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21 if line_counter > 10000:
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22 break
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23 if line.find('$$$$') != -1:
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24 return 'sdf'
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25 elif line.find('@<TRIPOS>MOLECULE') != -1:
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26 return 'mol2'
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27 elif line.find('ligand id') != -1:
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28 return 'drf'
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29 elif possible_inchi and re.findall('^InChI=', line):
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30 return 'inchi'
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31 elif re.findall('^M\s+END', line):
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32 mol = True
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33 # first line is not an InChI, so it can't be an InChI file
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34 possible_inchi = False
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35
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36 if mol:
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37 # END can occures before $$$$, so and SDF file will
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38 # be recognised as mol, if you not using this hack'
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39 return 'mol'
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40 return 'smi'
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41
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42 AliphaticRings = Chem.MolFromSmarts('[$([A;R][!a])]')
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43
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44 AcceptorSmarts = [
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45 '[oH0;X2]',
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46 '[OH1;X2;v2]',
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47 '[OH0;X2;v2]',
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48 '[OH0;X1;v2]',
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49 '[O-;X1]',
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50 '[SH0;X2;v2]',
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51 '[SH0;X1;v2]',
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52 '[S-;X1]',
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53 '[nH0;X2]',
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54 '[NH0;X1;v3]',
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55 '[$([N;+0;X3;v3]);!$(N[C,S]=O)]'
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56 ]
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57 Acceptors = []
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58 for hba in AcceptorSmarts:
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59 Acceptors.append(Chem.MolFromSmarts(hba))
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60
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61 StructuralAlertSmarts = [
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62 '*1[O,S,N]*1',
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63 '[S,C](=[O,S])[F,Br,Cl,I]',
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64 '[CX4][Cl,Br,I]',
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65 '[C,c]S(=O)(=O)O[C,c]',
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66 '[$([CH]),$(CC)]#CC(=O)[C,c]',
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67 '[$([CH]),$(CC)]#CC(=O)O[C,c]',
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68 'n[OH]',
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69 '[$([CH]),$(CC)]#CS(=O)(=O)[C,c]',
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70 'C=C(C=O)C=O',
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71 'n1c([F,Cl,Br,I])cccc1',
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72 '[CH1](=O)',
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73 '[O,o][O,o]',
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74 '[C;!R]=[N;!R]',
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75 '[N!R]=[N!R]',
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76 '[#6](=O)[#6](=O)',
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77 '[S,s][S,s]',
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78 '[N,n][NH2]',
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79 'C(=O)N[NH2]',
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80 '[C,c]=S',
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81 '[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]=[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]',
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82 'C1(=[O,N])C=CC(=[O,N])C=C1',
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83 'C1(=[O,N])C(=[O,N])C=CC=C1',
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84 'a21aa3a(aa1aaaa2)aaaa3',
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85 'a31a(a2a(aa1)aaaa2)aaaa3',
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86 'a1aa2a3a(a1)A=AA=A3=AA=A2',
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87 'c1cc([NH2])ccc1',
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88 '[Hg,Fe,As,Sb,Zn,Se,se,Te,B,Si,Na,Ca,Ge,Ag,Mg,K,Ba,Sr,Be,Ti,Mo,Mn,Ru,Pd,Ni,Cu,Au,Cd,Al,Ga,Sn,Rh,Tl,Bi,Nb,Li,Pb,Hf,Ho]',
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89 'I',
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90 'OS(=O)(=O)[O-]',
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91 '[N+](=O)[O-]',
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92 'C(=O)N[OH]',
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93 'C1NC(=O)NC(=O)1',
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94 '[SH]',
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95 '[S-]',
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96 'c1ccc([Cl,Br,I,F])c([Cl,Br,I,F])c1[Cl,Br,I,F]',
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97 'c1cc([Cl,Br,I,F])cc([Cl,Br,I,F])c1[Cl,Br,I,F]',
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98 '[CR1]1[CR1][CR1][CR1][CR1][CR1][CR1]1',
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99 '[CR1]1[CR1][CR1]cc[CR1][CR1]1',
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100 '[CR2]1[CR2][CR2][CR2][CR2][CR2][CR2][CR2]1',
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101 '[CR2]1[CR2][CR2]cc[CR2][CR2][CR2]1',
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102 '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1',
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103 '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1',
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104 'C#C',
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105 '[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]',
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106 '[$([N+R]),$([n+R]),$([N+]=C)][O-]',
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107 '[C,c]=N[OH]',
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108 '[C,c]=NOC=O',
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109 '[C,c](=O)[CX4,CR0X3,O][C,c](=O)',
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110 'c1ccc2c(c1)ccc(=O)o2',
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111 '[O+,o+,S+,s+]',
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112 'N=C=O',
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113 '[NX3,NX4][F,Cl,Br,I]',
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114 'c1ccccc1OC(=O)[#6]',
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115 '[CR0]=[CR0][CR0]=[CR0]',
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116 '[C+,c+,C-,c-]',
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117 'N=[N+]=[N-]',
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118 'C12C(NC(N1)=O)CSC2',
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119 'c1c([OH])c([OH,NH2,NH])ccc1',
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120 'P',
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121 '[N,O,S]C#N',
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122 'C=C=O',
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123 '[Si][F,Cl,Br,I]',
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124 '[SX2]O',
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125 '[SiR0,CR0](c1ccccc1)(c2ccccc2)(c3ccccc3)',
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126 'O1CCCCC1OC2CCC3CCCCC3C2',
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127 'N=[CR0][N,n,O,S]',
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128 '[cR2]1[cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2][cR2]1[cR2]2[cR2][cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2]2',
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129 'C=[C!r]C#N',
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130 '[cR2]1[cR2]c([N+0X3R0,nX3R0])c([N+0X3R0,nX3R0])[cR2][cR2]1',
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131 '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2]c([N+0X3R0,nX3R0])[cR2]1',
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132 '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2][cR2]c1([N+0X3R0,nX3R0])',
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133 '[OH]c1ccc([OH,NH2,NH])cc1',
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134 'c1ccccc1OC(=O)O',
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135 '[SX2H0][N]',
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136 'c12ccccc1(SC(S)=N2)',
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137 'c12ccccc1(SC(=S)N2)',
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138 'c1nnnn1C=O',
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139 's1c(S)nnc1NC=O',
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140 'S1C=CSC1=S',
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141 'C(=O)Onnn',
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142 'OS(=O)(=O)C(F)(F)F',
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143 'N#CC[OH]',
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144 'N#CC(=O)',
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145 'S(=O)(=O)C#N',
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146 'N[CH2]C#N',
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147 'C1(=O)NCC1',
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148 'S(=O)(=O)[O-,OH]',
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149 'NC[F,Cl,Br,I]',
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150 'C=[C!r]O',
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151 '[NX2+0]=[O+0]',
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152 '[OR0,NR0][OR0,NR0]',
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153 'C(=O)O[C,H1].C(=O)O[C,H1].C(=O)O[C,H1]',
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154 '[CX2R0][NX3R0]',
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155 'c1ccccc1[C;!R]=[C;!R]c2ccccc2',
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156 '[NX3R0,NX4R0,OR0,SX2R0][CX4][NX3R0,NX4R0,OR0,SX2R0]',
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157 '[s,S,c,C,n,N,o,O]~[n+,N+](~[s,S,c,C,n,N,o,O])(~[s,S,c,C,n,N,o,O])~[s,S,c,C,n,N,o,O]',
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158 '[s,S,c,C,n,N,o,O]~[nX3+,NX3+](~[s,S,c,C,n,N])~[s,S,c,C,n,N]',
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159 '[*]=[N+]=[*]',
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160 '[SX3](=O)[O-,OH]',
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161 'N#N',
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162 'F.F.F.F',
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163 '[R0;D2][R0;D2][R0;D2][R0;D2]',
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164 '[cR,CR]~C(=O)NC(=O)~[cR,CR]',
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165 'C=!@CC=[O,S]',
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166 '[#6,#8,#16][C,c](=O)O[C,c]',
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167 'c[C;R0](=[O,S])[C,c]',
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168 'c[SX2][C;!R]',
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169 'C=C=C',
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170 'c1nc([F,Cl,Br,I,S])ncc1',
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171 'c1ncnc([F,Cl,Br,I,S])c1',
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172 'c1nc(c2c(n1)nc(n2)[F,Cl,Br,I])',
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173 '[C,c]S(=O)(=O)c1ccc(cc1)F',
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174 '[15N]',
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175 '[13C]',
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176 '[18O]',
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177 '[34S]'
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178 ]
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179
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180 StructuralAlerts = []
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181 for smarts in StructuralAlertSmarts:
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182 StructuralAlerts.append(Chem.MolFromSmarts(smarts))
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183
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184
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185 # ADS parameters for the 8 molecular properties: [row][column]
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186 # rows[8]: MW, ALOGP, HBA, HBD, PSA, ROTB, AROM, ALERTS
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187 # columns[7]: A, B, C, D, E, F, DMAX
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188 # ALOGP parameters from Gregory Gerebtzoff (2012, Roche)
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189 pads1 = [ [2.817065973, 392.5754953, 290.7489764, 2.419764353, 49.22325677, 65.37051707, 104.9805561],
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190 [0.486849448, 186.2293718, 2.066177165, 3.902720615, 1.027025453, 0.913012565, 145.4314800],
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191 [2.948620388, 160.4605972, 3.615294657, 4.435986202, 0.290141953, 1.300669958, 148.7763046],
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192 [1.618662227, 1010.051101, 0.985094388, 0.000000001, 0.713820843, 0.920922555, 258.1632616],
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193 [1.876861559, 125.2232657, 62.90773554, 87.83366614, 12.01999824, 28.51324732, 104.5686167],
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194 [0.010000000, 272.4121427, 2.558379970, 1.565547684, 1.271567166, 2.758063707, 105.4420403],
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195 [3.217788970, 957.7374108, 2.274627939, 0.000000001, 1.317690384, 0.375760881, 312.3372610],
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196 [0.010000000, 1199.094025, -0.09002883, 0.000000001, 0.185904477, 0.875193782, 417.7253140] ]
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197 # ALOGP parameters from the original publication
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198 pads2 = [ [2.817065973, 392.5754953, 290.7489764, 2.419764353, 49.22325677, 65.37051707, 104.9805561],
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199 [3.172690585, 137.8624751, 2.534937431, 4.581497897, 0.822739154, 0.576295591, 131.3186604],
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200 [2.948620388, 160.4605972, 3.615294657, 4.435986202, 0.290141953, 1.300669958, 148.7763046],
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201 [1.618662227, 1010.051101, 0.985094388, 0.000000001, 0.713820843, 0.920922555, 258.1632616],
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202 [1.876861559, 125.2232657, 62.90773554, 87.83366614, 12.01999824, 28.51324732, 104.5686167],
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203 [0.010000000, 272.4121427, 2.558379970, 1.565547684, 1.271567166, 2.758063707, 105.4420403],
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204 [3.217788970, 957.7374108, 2.274627939, 0.000000001, 1.317690384, 0.375760881, 312.3372610],
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205 [0.010000000, 1199.094025, -0.09002883, 0.000000001, 0.185904477, 0.875193782, 417.7253140] ]
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206
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207 def ads(x, a, b, c, d, e, f, dmax):
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208 return ((a+(b/(1+exp(-1*(x-c+d/2)/e))*(1-1/(1+exp(-1*(x-c-d/2)/f))))) / dmax)
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209
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210 def properties(mol):
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211 """
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212 Calculates the properties that are required to calculate the QED descriptor.
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213 """
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214 matches = []
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215 if (mol is None):
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216 raise WrongArgument("properties(mol)", "mol argument is \'None\'")
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217 x = [0] * 9
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218 x[0] = Descriptors.MolWt(mol) # MW
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219 x[1] = Descriptors.MolLogP(mol) # ALOGP
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220 for hba in Acceptors: # HBA
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221 if (mol.HasSubstructMatch(hba)):
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222 matches = mol.GetSubstructMatches(hba)
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223 x[2] += len(matches)
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224 x[3] = Descriptors.NumHDonors(mol) # HBD
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225 x[4] = Descriptors.TPSA(mol) # PSA
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226 x[5] = Descriptors.NumRotatableBonds(mol) # ROTB
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227 x[6] = Chem.GetSSSR(Chem.DeleteSubstructs(deepcopy(mol), AliphaticRings)) # AROM
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228 for alert in StructuralAlerts: # ALERTS
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229 if (mol.HasSubstructMatch(alert)): x[7] += 1
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230 ro5_failed = 0
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231 if x[3] > 5:
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232 ro5_failed += 1 #HBD
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233 if x[2] > 10:
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234 ro5_failed += 1 #HBA
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235 if x[0] >= 500:
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236 ro5_failed += 1
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237 if x[1] > 5:
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238 ro5_failed += 1
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239 x[8] = ro5_failed
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240 return x
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241
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242
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243 def qed(w, p, gerebtzoff):
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244 d = [0.00] * 8
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245 if gerebtzoff:
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246 for i in range(0, 8):
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247 d[i] = ads(p[i], pads1[i][0], pads1[i][1], pads1[i][2], pads1[i][3], pads1[i][4], pads1[i][5], pads1[i][6])
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248 else:
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249 for i in range(0, 8):
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250 d[i] = ads(p[i], pads2[i][0], pads2[i][1], pads2[i][2], pads2[i][3], pads2[i][4], pads2[i][5], pads2[i][6])
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251 t = 0.0
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252 for i in range(0, 8):
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253 t += w[i] * log(d[i])
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254 return (exp(t / sum(w)))
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255
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256
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257 def weights_max(mol, gerebtzoff = True, props = False):
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258 """
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259 Calculates the QED descriptor using maximal descriptor weights.
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260 If props is specified we skip the calculation step and use the props-list of properties.
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261 """
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262 if not props:
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263 props = properties(mol)
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264 return qed([0.50, 0.25, 0.00, 0.50, 0.00, 0.50, 0.25, 1.00], props, gerebtzoff)
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265
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266
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267 def weights_mean(mol, gerebtzoff = True, props = False):
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268 """
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269 Calculates the QED descriptor using average descriptor weights.
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270 If props is specified we skip the calculation step and use the props-list of properties.
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271 """
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272 if not props:
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273 props = properties(mol)
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274 return qed([0.66, 0.46, 0.05, 0.61, 0.06, 0.65, 0.48, 0.95], props, gerebtzoff)
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275
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276
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277 def weights_none(mol, gerebtzoff = True, props = False):
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278 """
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279 Calculates the QED descriptor using unit weights.
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280 If props is specified we skip the calculation step and use the props-list of properties.
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281 """
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282 if not props:
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283 props = properties(mol)
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284 return qed([1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00], props, gerebtzoff)
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285
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286
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287 def default(mol, gerebtzoff = True):
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288 """
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289 Calculates the QED descriptor using average descriptor weights and Gregory Gerebtzoff parameters.
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290 """
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291 return weights_mean(mol, gerebtzoff)
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292
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293
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294 if __name__ == "__main__":
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295 parser = argparse.ArgumentParser()
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296 parser.add_argument('-i', '--input',
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297 required=True,
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298 help='path to the input file name')
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299 parser.add_argument("-m", "--method",
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300 dest="method",
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301 choices=['max', 'mean', 'unweighted'],
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302 default="mean",
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303 help="Specify the method you want to use.")
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304 parser.add_argument("--iformat",
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305 help="Input format. It must be supported by openbabel.")
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306 parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'),
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307 default=sys.stdout,
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308 help="path to the result file, default it sdtout")
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309 parser.add_argument("--header", dest="header", action="store_true",
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310 default=False,
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311 help="Write header line.")
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312
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313
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314 args = parser.parse_args()
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315
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316 # Elucidate filetype and open supplier
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317 ifile = os.path.abspath(args.input)
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318 if not os.path.isfile(ifile):
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319 print "Error: ", ifile, " is not a file or cannot be found."
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320 sys.exit(1)
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321 if not os.path.exists(ifile):
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322 print "Error: ", ifile, " does not exist or cannot be found."
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323 sys.exit(1)
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324 if not os.access(ifile, os.R_OK):
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325 print "Error: ", ifile, " is not readable."
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326 sys.exit(1)
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327
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328 if not args.iformat:
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329 # try to guess the filetype
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330 filetype = check_filetype( ifile )
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331 else:
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332 filetype = args.iformat # sdf or smi
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333
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334
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335 """
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336 We want to store the original SMILES in the output. So in case of a SMILES file iterate over the file and convert each line separate.
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337 """
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338 if filetype == 'sdf':
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339 supplier = Chem.SDMolSupplier( ifile )
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340 # Process file
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341 if args.header:
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342 args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n")
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343 count = 0
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344 for mol in supplier:
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345 count += 1
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346 if mol is None:
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347 print "Warning: skipping molecule ", count, " and continuing with next."
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348 continue
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349 props = properties(mol)
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350
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351 if args.method == 'max':
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352 calc_qed = weights_max(mol, True, props)
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353 elif args.method == 'unweighted':
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354 calc_qed = weights_none(mol, True, props)
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355 else:
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356 calc_qed = weights_mean(mol, True, props)
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357
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358 args.outfile.write( "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\n" % (
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359 props[0],
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360 props[1],
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361 props[2],
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362 props[3],
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363 props[4],
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364 props[5],
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365 props[6],
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366 props[7],
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367 props[8],
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368 calc_qed,
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369 mol.GetProp("_Name"),
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370 ))
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|
371 elif filetype == 'smi':
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372 supplier = Chem.SmilesMolSupplier( ifile, " \t", 0, 1, False, True )
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373
|
|
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374 # Process file
|
|
|
375 if args.header:
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376 args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\tSMILES\n")
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377 count = 0
|
|
|
378 for line in open(ifile):
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|
379 tokens = line.strip().split('\t')
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|
|
380 if len(tokens) > 1:
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|
|
381 smiles, title = tokens
|
|
|
382 else:
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|
|
383 smiles = tokens[0]
|
|
|
384 title = ''
|
|
|
385 mol = Chem.MolFromSmiles(smiles)
|
|
|
386 count += 1
|
|
|
387 if mol is None:
|
|
|
388 print "Warning: skipping molecule ", count, " and continuing with next."
|
|
|
389 continue
|
|
|
390 props = properties(mol)
|
|
|
391
|
|
|
392 if args.method == 'max':
|
|
|
393 calc_qed = weights_max(mol, True, props)
|
|
|
394 elif args.method == 'unweighted':
|
|
|
395 calc_qed = weights_none(mol, True, props)
|
|
|
396 else:
|
|
|
397 calc_qed = weights_mean(mol, True, props)
|
|
|
398
|
|
|
399 args.outfile.write( "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\t%s\n" % (
|
|
|
400 props[0],
|
|
|
401 props[1],
|
|
|
402 props[2],
|
|
|
403 props[3],
|
|
|
404 props[4],
|
|
|
405 props[5],
|
|
|
406 props[6],
|
|
|
407 props[7],
|
|
|
408 props[8],
|
|
|
409 calc_qed,
|
|
|
410 title,
|
|
|
411 smiles
|
|
|
412 ))
|
|
|
413 else:
|
|
|
414 sys.exit("Error: unknown file-type: ", filetype)
|
