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9
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1 #
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2 # SMARTS Patterns for Functional Group Classification
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3 #
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4 # written by Christian Laggner
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5 # Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH
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6 #
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7 # Released under the Lesser General Public License (LGPL license)
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8 # see http://www.gnu.org/copyleft/lesser.html
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9 # Modified from Version 221105
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10 #####################################################################################################
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11
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12 # General Stuff:
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13 # These patters were written in an attempt to represent the classification of organic compounds
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14 # from the viewpoint of an organic chemist.
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15 # They are often very restrictive. This may be generally a good thing, but it also takes some time
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16 # for filtering/indexing large compound sets.
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17 # For filtering undesired groups (in druglike compounds) one will want to have more general patterns
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18 # (e.g. you don't want *any* halide of *any* acid, *neither* aldehyde *nor* formyl esters and amides, ...).
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19 #
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20
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21 # Part I: Carbon
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22 # ==============
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23
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24
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25 # I.1: Carbon-Carbon Bonds
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26 # ------------------------
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27
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28 # I.1.1 Alkanes:
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29
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30 Primary_carbon: [CX4H3][#6]
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31
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32 Secondary_carbon: [CX4H2]([#6])[#6]
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33
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34 Tertiary_carbon: [CX4H1]([#6])([#6])[#6]
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35
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36 Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6]
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37
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38
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39 # I.1.2 C-C double and Triple Bonds
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40
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41 Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]
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42 # sp2 C may be substituted only by C or H -
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43 # does not hit ketenes and allenes, nor enamines, enols and the like
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44
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45 Alkyne: [CX2]#[CX2]
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46 # non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination
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47
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48 Allene: [CX3]=[CX2]=[CX3]
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49
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50
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51 # I.2: One Carbon-Hetero Bond
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52 # ---------------------------
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53
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54
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55 # I.2.1 Alkyl Halogenides
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56
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57 Alkylchloride: [ClX1][CX4]
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58 # will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats
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59 # a more restrictive version can be obtained by modifying the Alcohol string.
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60
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61 Alkylfluoride: [FX1][CX4]
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62
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63 Alkylbromide: [BrX1][CX4]
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64
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65 Alkyliodide: [IX1][CX4]
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66
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67
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68 # I.2.2 Alcohols and Ethers
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69
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70 Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]
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71 # nonspecific definition, no acetals, aminals, and the like
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72
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73 Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]
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74
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75 Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]
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76
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77 Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]
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78
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79 Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
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80 # no acetals and the like; no enolethers
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81
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82 Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
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83 # no acetals and the like; no enolethers
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84
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85 Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
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86 # no acetals and the like; no enolethers
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87
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88 Diarylether: [c][OX2][c]
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89
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90 Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
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91
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92 Diarylthioether: [c][SX2][c]
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93
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94 Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
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95 # can't be aromatic, thus O and not #8
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96
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97 # I.2.3 Amines
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98
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99 Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]
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100 # hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ...
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101
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102 # the following amines include also the protonated forms
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103
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104 Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
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105
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106 Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
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107
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108 Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
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109
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110 Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
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111
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112 Primary_arom_amine: [NX3H2+0,NX4H3+]c
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113
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114 Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
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115
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116 Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
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117
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118 Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
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119
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120 Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]
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121
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122 Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]
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123
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124 Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]
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125
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126 Ammonium: [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]
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127 # only C and H substituents allowed. Quaternary or protonated amines
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128 # NX4+ or Nv4+ is not recognized by Daylight's depictmatch if less than four C are present
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129
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130
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131 # I.2.4 Others
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132
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133 Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]
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134
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135 Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]
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136
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137 Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]
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138
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139 Disulfide: [SX2D2][SX2D2]
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140
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141 1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]
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142 # does not hit alpha-amino acids, enaminoalcohols, 1,2-aminoacetals, o-aminophenols, etc.
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143
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144 1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]
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145 # does not hit alpha-hydroxy acids, enolalcohols, 1,2-hydroxyacetals, 1,2-diphenols, etc.
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146
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147 1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]
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148
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149 Hydroperoxide: [OX2H][OX2]
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150 #does not neccessarily have to be connected to a carbon atom, includes also hydrotrioxides
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151
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152 Peroxo: [OX2D2][OX2D2]
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153
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154 Organolithium_compounds: [LiX1][#6,#14]
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155
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156 Organomagnesium_compounds: [MgX2][#6,#14]
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157 # not restricted to Grignard compounds, also dialkyl Mg
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158
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159 Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]
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160 # very general, includes all metals covalently bound to carbon
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161
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162
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163 # I.3: Two Carbon-Hetero Bonds (Carbonyl and Derivatives)
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164 # ----------------------------
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165
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166 # I.3.1 Double Bond to Hetero
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167
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168 Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1]
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169 # hits aldehydes including formaldehyde
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170
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171 Ketone: [#6][CX3](=[OX1])[#6]
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172 # does not include oxo-groups connected to a (hetero-) aromatic ring
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173
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174 Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1]
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175
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176 Thioketone: [#6][CX3](=[SX1])[#6]
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177 # does not include thioxo-groups connected to a (hetero-) aromatic ring
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178
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179 Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]
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180 # nitrogen is not part of an amidelike strukture, nor of an aromatic ring, but can be part of an aminal or similar
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181
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182 Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]
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183
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184 Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]
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185
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186 Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]
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187 # ether, not ester or amide; does not hit isoxazole
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188
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189
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190 # I.3.2. Two Single Bonds to Hetero
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191
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192 Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
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193 # does not hit hydroxy-methylesters, ketenacetals, hemiacetals, orthoesters, etc.
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194
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195 Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
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196
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197 Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6]
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198 # Ns are not part of an amide or similar. v3 ist to exclude nitro and similar groups
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199
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200 Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]
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201
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202 Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]
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203
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204 Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]
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205
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206 Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
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207 # hits chloromethylenethers and other reactive alkylating agents
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208
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209 Acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
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210 # includes all of the above and other combinations (S-C-N, hydrates, ...), but still no aminomethylenesters and similar
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211
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212 Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
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213 # also reactive alkylating agents. Acid does not have to be carboxylic acid, also S- and P-based acids allowed
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214
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215 NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
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216 # Same as above, but N,O or S instead of halogen. Ester/amide allowed only on one side
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217
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218 Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
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219 # Combination of the last two patterns
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220
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221 Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]
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222
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223
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224 # I.3.3 Single Bond to Hetero, C=C Double Bond (Enols and Similar)
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225
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226 Chloroalkene: [ClX1][CX3]=[CX3]
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227
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228 Fluoroalkene: [FX1][CX3]=[CX3]
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229
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230 Bromoalkene: [BrX1][CX3]=[CX3]
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231
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232 Iodoalkene: [IX1][CX3]=[CX3]
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233
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234 Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3]
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235 # no phenols
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236
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237 Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]
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238 # no 1,2-diphenols, ketenacetals, ...
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239
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240 Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]
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241 # finds also endiodiethers, but not enolesters, no aromats
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242
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243 Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]
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244
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245
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246 Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]
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247 # does not hit amines attached to aromatic rings, nor may the nitrogen be aromatic
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248
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249 Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3]
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250
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251 Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]
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252
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253
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254 # I.4: Three Carbon-Hetero Bonds (Carboxyl and Derivatives)
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255 # ------------------------------
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256
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257 Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1]
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258
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259 Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1]
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260
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261 Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1]
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262
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263 Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]
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264
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265 Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]
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266 # all of the above
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267
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268
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269 # The following contains all simple carboxylic combinations of O, N, S, & Hal -
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270 # - acids, esters, amides, ... as well as a few extra cases (anhydride, hydrazide...)
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271 # Cyclic structures (including aromats) like lactones, lactames, ... got their own
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272 # definitions. Structures where both heteroatoms are part of an aromatic ring
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273 # (oxazoles, imidazoles, ...) were excluded.
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274
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275 Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]
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276 # includes carboxylate anions
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277
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278 Carboxylic_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
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279 # does not hit anhydrides or lactones
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280
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281 Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
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282 # may also be aromatic
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283
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284 Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])
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285 # anhydride formed by two carboxylic acids, no mixed anhydrides (e.g. between carboxylic acid and sulfuric acid); may be part of a ring, even aromatic
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286
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287 Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]
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288 # includes most of the structures of I.4 and many more, also 1,3-heteroaromatics such as isoxazole
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289
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290 Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]
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291 # hits both tautomeric forms, as well as anions
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292
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293 Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]
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294
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295 Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]
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296 # may also be aromatic
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297
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298 Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]
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299
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300 Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
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301
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302 Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]
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303
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304 Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]
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305
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306 Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]
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307
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308 Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]
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309
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310
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311 Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
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312 # does not hit lactames
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313
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314 Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]
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315
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316 Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]
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317
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318 Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]
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319
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320 Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
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321 # cyclic amides, may also be aromatic
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322
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323 Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
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324 # may be part of a ring, even aromatic. only C allowed at central N. May also be triacyl amide
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325
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326 N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
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327 # everything else than H or C at central N
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328
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329 Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])
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330 # can be deprotonated
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331
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332 Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
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333 # does not hit thiolactames
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334
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335 Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
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336 # cyclic thioamides, may also be aromatic
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337
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338
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339 Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]
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340 # may also be part of a ring / aromatic
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341
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342 Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]
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343 # only basic amidines, not as part of aromatic ring (e.g. imidazole)
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344
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345 Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]
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346
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347 Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]
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348 # does not hit anhydrides of carboxylic acids withs hydroxamic acids
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349
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350
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351 Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
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352 # not cyclic
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353
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354 Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
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355 # the enamide-form of lactames. may be aromatic like 2-hydroxypyridine
|
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356
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357 Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
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358 # esters of the above structures. no anhydrides.
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359
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360 Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
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361 # no oxazoles and similar
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362
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363 Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
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364 # not cyclic
|
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365
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366 Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
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367 # the enamide-form of thiolactames. may be aromatic like 2-thiopyridine
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368
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369 Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
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370 # thioesters of the above structures. no anhydrides.
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|
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371
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372 Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
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373 # no thioxazoles and similar
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374
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375 Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]
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376 # only basic amidines, not substituted by carbonyl or thiocarbonyl, not as part of a ring
|
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377
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378 Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]
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379 # one of the two C~N bonds is part of a ring (may be aromatic), but not both - thus no imidazole
|
|
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380
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381 Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
|
|
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382 # not cyclic
|
|
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383
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384 Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
|
|
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385 # may also be aromatic
|
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386
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|
387 # may be ring, aromatic, substituted with carbonyls, hetero, ...
|
|
|
388 # (everything else would get too complicated)
|
|
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389
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390 Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]
|
|
|
391 # hits both tautomers. as above, it may be ring, aromatic, substituted with carbonyls, hetero, ...
|
|
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392
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|
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393
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|
394 Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]
|
|
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395 # N may be alkylated, but not part of an amide (as in peptides), ionic forms are included
|
|
|
396 # includes also non-natural aminoacids with double-bonded or two aliph./arom. substituents at alpha-C
|
|
|
397 # N may not be aromatic as in 1H-pyrrole-2-carboxylic acid
|
|
|
398
|
|
|
399 Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-]
|
|
|
400
|
|
|
401 Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
|
|
|
402 # finds peptidic structures which are neither C- nor N-terminal. Both neighbours must be amino-acids/peptides
|
|
|
403
|
|
|
404 Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]
|
|
|
405 # finds C-terminal amino acids
|
|
|
406
|
|
|
407 Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
|
|
|
408 # finds N-terminal amino acids. As above, N may be substituted, but not part of an amide-bond.
|
|
|
409
|
|
|
410
|
|
|
411 Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6]
|
|
|
412 # hits also anhydride like struktures (e. g. HC(OMe)2-OC=O residues)
|
|
|
413
|
|
|
414 Ketene: [CX3]=[CX2]=[OX1]
|
|
|
415
|
|
|
416 Ketenacetal: [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]
|
|
|
417 # includes aminals, silylacetals, ketenesters, etc. C=C DB is not aromatic, everything else may be
|
|
|
418
|
|
|
419 Nitrile: [NX1]#[CX2]
|
|
|
420 # includes cyanhydrines
|
|
|
421
|
|
|
422 Isonitrile: [CX1-]#[NX2+]
|
|
|
423
|
|
|
424
|
|
|
425 Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]
|
|
|
426 # may be part of a ring, even aromatic
|
|
|
427
|
|
|
428 Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])]
|
|
|
429
|
|
|
430 Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])]
|
|
|
431
|
|
|
432 Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
433
|
|
|
434 Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]
|
|
|
435
|
|
|
436
|
|
|
437
|
|
|
438 # I.5: Four Carbon-Hetero Bonds (Carbonic Acid and Derivatives)
|
|
|
439 # -----------------------------
|
|
|
440
|
|
|
441 Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
|
|
|
442 # may be part of a ring, even aromatic
|
|
|
443
|
|
|
444 Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]
|
|
|
445
|
|
|
446 Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]
|
|
|
447 # unstable
|
|
|
448
|
|
|
449 Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6]
|
|
|
450
|
|
|
451
|
|
|
452 Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
|
|
|
453 # may be part of a ring, even aromatic
|
|
|
454
|
|
|
455 Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]
|
|
|
456
|
|
|
457 Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]
|
|
|
458
|
|
|
459
|
|
|
460 Urea:[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]
|
|
|
461 # no check whether part of imide, biuret, etc. Aromatic structures are only hit if
|
|
|
462 # both N share no double bonds, like in the dioxo-form of uracil
|
|
|
463
|
|
|
464 Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]
|
|
|
465
|
|
|
466 Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]
|
|
|
467 # O may be substituted. no check whether further amide-like bonds are present. Aromatic
|
|
|
468 # structures are only hit if single bonded N shares no additional double bond, like in
|
|
|
469 # the 1-hydroxy-3-oxo form of uracil
|
|
|
470
|
|
|
471 Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]
|
|
|
472
|
|
|
473 Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]
|
|
|
474 # also hits guanidinium salts. v3 and v4 to avoid nitroamidines
|
|
|
475
|
|
|
476 Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-]
|
|
|
477 # quite unstable, unlikely to be found. Also hits salts
|
|
|
478
|
|
|
479 Urethan: [#7X3][#6](=[OX1])[#8X2][#6]
|
|
|
480 # also hits when part of a ring, no check whether the last C is part of carbonyl
|
|
|
481
|
|
|
482 Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]
|
|
|
483
|
|
|
484 Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
|
|
|
485
|
|
|
486 Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]
|
|
|
487
|
|
|
488 Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
|
|
|
489
|
|
|
490 Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]
|
|
|
491
|
|
|
492 Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
|
|
|
493
|
|
|
494 Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]
|
|
|
495
|
|
|
496 Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
|
|
|
497
|
|
|
498 Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]
|
|
|
499
|
|
|
500
|
|
|
501 Isocyanate: [NX2]=[CX2]=[OX1]
|
|
|
502
|
|
|
503 Cyanate: [OX2][CX2]#[NX1]
|
|
|
504
|
|
|
505 Isothiocyanate: [NX2]=[CX2]=[SX1]
|
|
|
506
|
|
|
507 Thiocyanate: [SX2][CX2]#[NX1]
|
|
|
508
|
|
|
509 Carbodiimide: [NX2]=[CX2]=[NX2]
|
|
|
510
|
|
|
511 Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]
|
|
|
512 # halogen allowed just once, to avoid mapping to -OCF3 and similar groups (much more
|
|
|
513 # stable as for example C(OCH3)4)
|
|
|
514
|
|
|
515
|
|
|
516 # I.6 Aromatics
|
|
|
517 # -------------
|
|
|
518
|
|
|
519 # I know that this classification is not very logical, arylamines are found under I.2 ...
|
|
|
520
|
|
|
521 Phenol: [OX2H][c]
|
|
|
522
|
|
|
523 1,2-Diphenol: [OX2H][c][c][OX2H]
|
|
|
524
|
|
|
525 Arylchloride: [Cl][c]
|
|
|
526
|
|
|
527 Arylfluoride: [F][c]
|
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528
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529 Arylbromide: [Br][c]
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530
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531 Aryliodide: [I][c]
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532
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533 Arylthiol: [SX2H][c]
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534
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535 Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]
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536 # N may be substituted with H or C, but not carbonyl or similar
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537 # aromatic atom is always C, not S or P (these are not planar when substituted)
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538
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539 Oxoarene: [c]=[OX1]
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540
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541 Thioarene: [c]=[SX1]
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542
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543 Hetero_N_basic_H: [nX3H1+0]
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544 # as in pyrole. uncharged to exclude pyridinium ions
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545
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546 Hetero_N_basic_no_H: [nX3H0+0]
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547 # as in N-methylpyrole. uncharged to exclude pyridinium ions
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548
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549 Hetero_N_nonbasic: [nX2,nX3+]
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550 # as in pyridine, pyridinium
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551
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552 Hetero_O: [o]
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553
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554 Hetero_S: [sX2]
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555 # X2 because Daylight's depictmatch falsely describes C1=CS(=O)C=C1 as aromatic
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556 # (is not planar because of lonepair at S)
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557
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558 Heteroaromatic: [a;!c]
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559
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560
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561 # Part II: N, S, P, Si, B
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562 # =======================
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563
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564
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565 # II.1 Nitrogen
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566 # -------------
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567
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568 Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])]
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569 # hits nitrous acid, its anion, esters, and other O-substituted derivatives
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570
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571 Thionitrite: [SX2][NX2]=[OX1]
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572
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573 Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])]
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574 # hits nitric acid, its anion, esters, and other O-substituted derivatives
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575
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576 Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]
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577 # hits nitro groups attached to C,N, ... but not nitrates
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578
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579 Nitroso: [NX2](=[OX1])[!#7;!#8]
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580 # no nitrites, no nitrosamines
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581
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582 Azide: [NX1]~[NX2]~[NX2,NX1]
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583 # hits both mesomeric forms, also anion
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584
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585 Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1]
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586
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587 Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])]
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588
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589 Diazonium: [#6][NX2+]#[NX1]
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590
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591 Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1]
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592
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593 Nitrosamide: [NX2](=[OX1])N-*=O
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594 # includes nitrososulfonamides
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|
595
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596 N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]
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597 # Hits both forms. Won't hit azoxy, nitro, nitroso, or nitrate.
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598
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599
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600 Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]
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601 # no hydrazides
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|
|
602
|
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|
603 Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]
|
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|
604
|
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605 Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]
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606 # no discrimination between O-, N-, and O,N-substitution
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607
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608
|
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|
609 # II.2 Sulfur
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|
610 # -----------
|
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611
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|
612 Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])]
|
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|
613 # can't be aromatic, thus S and not #16
|
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614
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615 Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])]
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616
|
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|
617 Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
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|
618 # can't be aromatic, thus S and not #16
|
|
|
619
|
|
|
620 Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
|
|
|
621 # includes anions
|
|
|
622
|
|
|
623 Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
624
|
|
|
625 Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
626
|
|
|
627 Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
|
|
|
628
|
|
|
629 Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
630
|
|
|
631 Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
632
|
|
|
633 Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6]
|
|
|
634 # everything else (would not be a "true" derivative of sulfuric acid, if one of the substituents were less electronegative
|
|
|
635 # than sulfur, but this should be very very rare, anyway)
|
|
|
636
|
|
|
637
|
|
|
638
|
|
|
639 #### sulfurous acid and derivatives missing!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
|
640
|
|
|
641
|
|
|
642
|
|
|
643
|
|
|
644 Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]
|
|
|
645
|
|
|
646 Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
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647
|
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648 Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]
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649
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|
650 Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]
|
|
|
651
|
|
|
652 Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]
|
|
|
653 # includes all of the above and many more
|
|
|
654 # for comparison: this is what "all sulfonic derivatives but not the ones above" would look like:
|
|
|
655 # [$([SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6;!O])[!#6]),$([SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[!$([FX1,ClX1,BrX1,IX1]);!$([#6]);!$([OX2H]);!$([OX1-]);!$([OX2][#6;!$(C=[O,N,S])]);!$([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])])]
|
|
|
656
|
|
|
657
|
|
|
658 Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]
|
|
|
659
|
|
|
660 Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
661
|
|
|
662 Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
|
|
|
663
|
|
|
664 Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]
|
|
|
665
|
|
|
666 Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6]
|
|
|
667
|
|
|
668 Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]
|
|
|
669
|
|
|
670 Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
671
|
|
|
672 Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]
|
|
|
673
|
|
|
674 Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]
|
|
|
675
|
|
|
676 Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6]
|
|
|
677
|
|
|
678
|
|
|
679 # II.3 Phosphorous
|
|
|
680 # ----------------
|
|
|
681
|
|
|
682 Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])]
|
|
|
683 # similar to amine, but less restrictive: includes also amide- and aminal-analogues
|
|
|
684
|
|
|
685 Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])]
|
|
|
686
|
|
|
687 Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])]
|
|
|
688 # similar to Ammonium
|
|
|
689
|
|
|
690 Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])]
|
|
|
691
|
|
|
692
|
|
|
693 # conventions for the following acids and derivatives:
|
|
|
694 # acids find protonated and deprotonated acids
|
|
|
695 # esters do not find mixed anhydrides ( ...P-O-C(=O))
|
|
|
696 # derivatives: subtituents which go in place of the OH and =O are not H or C (may also be O,
|
|
|
697 # thus including acids and esters)
|
|
|
698
|
|
|
699 Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
|
|
|
700 # includes anions
|
|
|
701
|
|
|
702 Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
703
|
|
|
704 Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
705
|
|
|
706 Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
707
|
|
|
708 Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
709
|
|
|
710 Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
711
|
|
|
712 Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6]
|
|
|
713 # all of the above and much more
|
|
|
714
|
|
|
715
|
|
|
716 Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
|
|
|
717 # includes anions
|
|
|
718
|
|
|
719 Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
720
|
|
|
721 Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
722
|
|
|
723 Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
724
|
|
|
725 Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
726
|
|
|
727 Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
728
|
|
|
729 Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
730
|
|
|
731 Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
732
|
|
|
733 Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
734
|
|
|
735 Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
736
|
|
|
737 Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6]
|
|
|
738
|
|
|
739
|
|
|
740 Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]
|
|
|
741
|
|
|
742 Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
|
|
|
743
|
|
|
744 Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
745
|
|
|
746 Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]
|
|
|
747
|
|
|
748
|
|
|
749 Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
|
|
|
750
|
|
|
751 Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
752
|
|
|
753 Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
|
|
|
754
|
|
|
755 Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
756
|
|
|
757 Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
758
|
|
|
759 Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
760
|
|
|
761 Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6]
|
|
|
762
|
|
|
763
|
|
|
764 Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]
|
|
|
765
|
|
|
766 Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]
|
|
|
767
|
|
|
768 Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
|
|
|
769
|
|
|
770 Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]
|
|
|
771
|
|
|
772
|
|
|
773 # II.4 Silicon
|
|
|
774 # ------------
|
|
|
775
|
|
|
776 Quart_silane: [SiX4]([#6])([#6])([#6])[#6]
|
|
|
777 # four C-substituents. non-reactive, non-toxic, in experimental phase for drug development
|
|
|
778
|
|
|
779 Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]
|
|
|
780 # has 1-4 hydride(s), reactive. Daylight's depictmatch does not add hydrogens automatically to
|
|
|
781 # the free positions at Si, thus Hs had to be added implicitly
|
|
|
782
|
|
|
783 Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]
|
|
|
784 # reagents for inserting protection groups
|
|
|
785
|
|
|
786 Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6]
|
|
|
787 # mostly acid-labile protection groups such as trimethylsilyl-ethers
|
|
|
788
|
|
|
789 Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6]
|
|
|
790
|
|
|
791 Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6]
|
|
|
792
|
|
|
793 Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6]
|
|
|
794 # four substituent which are neither C nor H
|
|
|
795
|
|
|
796
|
|
|
797 # II.5 Boron
|
|
|
798 # ----------
|
|
|
799
|
|
|
800 Trialkylborane: [BX3]([#6])([#6])[#6]
|
|
|
801 # also carbonyls allowed
|
|
|
802
|
|
|
803 Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6]
|
|
|
804 # includes acids, esters, amides, ... H-substituent at B is very rare.
|
|
|
805
|
|
|
806 Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6]
|
|
|
807 # # includes acids, esters, amides, ...
|
|
|
808
|
|
|
809 Borohydride: [BH1,BH2,BH3,BH4]
|
|
|
810 # at least one H attached to B
|
|
|
811
|
|
|
812 Quaternary_boron: [BX4]
|
|
|
813 # mostly borates (negative charge), in complex with Lewis-base
|
|
|
814
|
|
|
815
|
|
|
816
|
|
|
817 # Part III: Some Special Patterns
|
|
|
818 # ===============================
|
|
|
819
|
|
|
820
|
|
|
821 # III.1 Chains
|
|
|
822 # ------------
|
|
|
823
|
|
|
824 # some simple chains
|
|
|
825
|
|
|
826
|
|
|
827
|
|
|
828 # III.2 Rings
|
|
|
829 # -----------
|
|
|
830
|
|
|
831 Aromatic: a
|
|
|
832
|
|
|
833 Heterocyclic: [!#6;!R0]
|
|
|
834 # may be aromatic or not
|
|
|
835
|
|
|
836 Epoxide: [OX2r3]1[#6r3][#6r3]1
|
|
|
837 # toxic/reactive. may be annelated to aromat, but must not be aromatic itself (oxirane-2,3-dione)
|
|
|
838
|
|
|
839 NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1
|
|
|
840 # toxic/reactive according to Maybridge's garbage filter
|
|
|
841
|
|
|
842 Spiro: [D4R;$(*(@*)(@*)(@*)@*)]
|
|
|
843 # at least two different rings can be found which are sharing just one atom.
|
|
|
844 # these two rings can be connected by a third ring, so it matches also some
|
|
|
845 # bridged systems, like morphine
|
|
|
846
|
|
|
847 Annelated_rings: [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]
|
|
|
848 # two different rings sharing exactly two atoms
|
|
|
849
|
|
|
850 Bridged_rings: [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])]
|
|
|
851 # part of two or more rings, not spiro, not annelated -> finds bridgehead atoms,
|
|
|
852 # but only if they are not annelated at the same time - otherwise impossible (?)
|
|
|
853 # to distinguish from non-bridgehead annelated atoms
|
|
|
854
|
|
|
855 # some basic ring-patterns (just size, no other information):
|
|
|
856
|
|
|
857
|
|
|
858
|
|
|
859
|
|
|
860
|
|
|
861 # III.3 Sugars and Nucleosides/Nucleotides, Steroids
|
|
|
862 # --------------------------------------------------
|
|
|
863
|
|
|
864 # because of the large variety of sugar derivatives, different patterns can be applied.
|
|
|
865 # The choice of patterns and their combinations will depend on the contents of the database
|
|
|
866 # e.g. natural products, nucleoside analoges with modified sugars, ... as well as on the
|
|
|
867 # desired restriction
|
|
|
868
|
|
|
869
|
|
|
870 Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]
|
|
|
871 # 5 or 6-membered ring containing one O and at least one (r5) or two (r6) oxygen-substituents.
|
|
|
872
|
|
|
873 Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
|
|
|
874 # 5 or 6-membered ring containing one O and an acetal-like bond at postion 2.
|
|
|
875
|
|
|
876 Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]
|
|
|
877 # combination of the two above
|
|
|
878
|
|
|
879 Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]
|
|
|
880 # 5 or 6-membered cyclic hemi-acetal
|
|
|
881
|
|
|
882 Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
|
|
|
883 # 5 or 6-membered cyclic hemi-acetal
|
|
|
884
|
|
|
885 Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
|
|
|
886 # 5 or 6-membered cyclic hemi-acetal
|
|
|
887
|
|
|
888 ##Poly_sugar_1: ([OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)].[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)])
|
|
|
889 # pattern1 occours more than once (in same molecule, but moieties don't have to be adjacent!)
|
|
|
890
|
|
|
891 ##Poly_sugar_2: ([OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)].[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)])
|
|
|
892 # pattern2 occours more than once (in same molecule, but moieties don't have to be adjacent!)
|
|
|
893
|
|
|
894
|
|
|
895 # III.4 Everything else...
|
|
|
896 # ------------------------
|
|
|
897
|
|
|
898 Conjugated_double_bond: *=*[*]=,#,:[*]
|
|
|
899
|
|
|
900 Conjugated_tripple_bond: *#*[*]=,#,:[*]
|
|
|
901
|
|
|
902 Cis_double_bond: */[D2]=[D2]\*
|
|
|
903 # only one single-bonded substituent on each DB-atom. no aromats.
|
|
|
904 # only found when character of DB is explicitely stated.
|
|
|
905
|
|
|
906 Trans_double_bond: */[D2]=[D2]/*
|
|
|
907 # analog
|
|
|
908
|
|
|
909 Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]
|
|
|
910 # should hits all combinations of two acids
|
|
|
911
|
|
|
912 Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6]
|
|
|
913
|
|
|
914 Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])]
|
|
|
915 # Halogen which is not mono-substituted nor an anion, e.g. chlorate.
|
|
|
916 # Most of these cases should be also filtered by Halogen_on_hetero.
|
|
|
917
|
|
|
918 Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])
|
|
|
919 # C with three F attached, connected to anything which is not another halogen
|
|
|
920
|
|
|
921 C_ONS_bond: [#6]~[#7,#8,#16]
|
|
|
922 # probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter
|
|
|
923
|
|
|
924 ## Mixture: (*).(*)
|
|
|
925 # two or more seperate parts, may also be salt
|
|
|
926 # component-level grouping is not yet supported in Open Babel Version 2.0
|
|
|
927
|
|
|
928
|
|
|
929 Charged: [!+0]
|
|
|
930
|
|
|
931 Anion: [-1,-2,-3,-4,-5,-6,-7]
|
|
|
932
|
|
|
933 Kation: [+1,+2,+3,+4,+5,+6,+7]
|
|
|
934
|
|
|
935 Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7])
|
|
|
936 # two or more seperate components with opposite charges
|
|
|
937
|
|
|
938 ##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7])
|
|
|
939 # both negative and positive charges somewhere within the same molecule.
|
|
|
940
|
|
|
941 1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)]
|
|
|
942 # 1,3 migration of H allowed. Includes keto/enol and amide/enamide.
|
|
|
943 # Aromatic rings must stay aromatic - no keto form of phenol
|
|
|
944
|
|
|
945 1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)]
|
|
|
946
|
|
|
947 Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
|
|
|
948 # taken from http://www.daylight.com/support/contrib/smarts/content.html
|
|
|
949
|
|
|
950 Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]
|
|
|
951 # the classical case: C=C near carbonyl, nitrile, nitro, or similar
|
|
|
952 # Oxo-heteroaromats and similar are not included.
|
|
|
953
|
|
|
954 Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])
|
|
|
955 # Michael-like acceptor, see Mitsunobu reaction
|
|
|
956
|
|
|
957 # H-Bond_donor:
|
|
|
958
|
|
|
959 # H-Bond_acceptor:
|
|
|
960
|
|
|
961 # Pos_ionizable:
|
|
|
962
|
|
|
963 # Neg_ionizable:
|
|
|
964
|
|
|
965 # Unlikely_ions:
|
|
|
966 # O+,N-,C+,C-, ...
|
|
|
967
|
|
|
968 CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]
|
|
|
969 # C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed.
|
|
|
970 # pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded.
|
|
|
971 # hits also CH-acidic_strong
|
|
|
972
|
|
|
973 CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]
|
|
|
974 # same as above (without pentadiene), but carbonyl or similar on two or three sides
|
|
|
975
|
|
|
976 Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]
|
|
|
977 # Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string
|
|
|
978 # depictmach does not find oxonium, sulfonium, or sulfoxides!
|
|
|
979
|
|
|
980 # Chiral_center_unspecified: [$([*@?](~*)(~*)(*)*),$([*@?H](*)(*)*),$([*@?](~*)(*)*),$([*@?H](~*)~*)]
|
|
|
981 # Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string
|
|
|
982 # "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0
|
|
|
983 |
