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1 #Comments after SMARTS
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2 ##############################################################################
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3 # #
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4 # Open Babel file: patterns.txt #
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5 # #
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6 # Copyright (c) 2005 Chris Morley #
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7 # Part of the Open Babel package, under the GNU General Public License (GPL)#
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8 # #
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9 # Functional groups for molecular fingerprinting based on Checkmol: #
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10 # http://merian.pch.univie.ac.at/~nhaider/cheminf/fgtable.pdf #
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11 # (Numbers 200+ are from Chris Swain) #
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12 # SMARTS Patterns are used by finger3.cpp:PatternFP #
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13 # Format of each line is a SMARTS pattern, then optionally #
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14 # followed by a tab character and a pattern number and/or description #
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15 # (everything after the tab will be ignored by the code) #
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16 # A file of this format needs the same first line as this one. #
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17 # An alternative format, as in SMARTS_InteLigand.txt, can also be used #
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18 # #
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19 # INCOMPLETE!! Really only useful to test the fingerprint FP3 #
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20 ##############################################################################
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21 [+] 1 cation
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22 [-] 2 anion
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23 [#6][CX3](=O) 3 aldehyde or ketone
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24 [CX3H1](=O)[#6] 4 aldehyde
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25 [#6][CX3](=O)[#6] 5 ketone
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26 [#6][CX3](=S) 6 thioaldehyde or thioketone
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27 [CX3H1](=S) 7 thioaldehyde
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28 [#6]C(=[S])[#6] 8 thioketone
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29 [CX3]=N([#6,#1])[#6,#1] 9 imine
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30 [#6,#1]C([#6,#1])=[N][N]([#6,#1])[#6,#1] 10 hydrazone
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31 [#6,#1]C([#6,#1])=[N][N]([#6,#1])C(=[O])[N]([#6,#1])[#6,#1] 11 semicarbazone
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32 [#6,#1]C([#6,#1])=[N][N]([#6,#1])C(=[S])[N]([#6,#1])[#6,#1] 12 thiosemicarbazone
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33 [#6,#1]C([#6,#1])=[N][OH] 13 oxime
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34 [#6,#1]C([#6,#1])=[N][O][#6] 14 oxime ether
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35 [CX3]=C=O 15 ketene
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36 [CX3]=C=O 16 keten acetyl derivative***
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37 [#6,#1]C([#6,#1])([OH])([OH]) 17 carbonyl hydrate
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38 [#6,#1]C([#6,#1])([OH])(O[#6]) 18 hemiacetal
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39 [#6,#1]C([#6,#1])(O[#6])(O[#6]) 19 acetal
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40 [#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])(O[#6]) 20 hemiaminal
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41 [#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])(N([#6,#1])[#6,#1]) 21 aminal
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42 [#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])([S][#6]) 22 thiohemiaminal
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43 [#6,#1]C([#6,#1])([S][#6])([S][#6]) 23 thioacetal
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44 [#6,#1]C([#6,#1])=C([#6,#1])N([#6,#1])[#6,#1] 24 enamine
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45 [#6,#1]C([#6,#1])=C([#6,#1])[OH] 25 enol
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46 [#6,#1]C([#6,#1])=C([#6,#1])O[#6] 26 enol ether
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47 [#6][OH] 27 hydroxy compound
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48 C[OH] 28 alcohol
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49 [#6][CH2][OH] 29 primary alcohol
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50 [#6][CH]([#6])[OH] 30 secondary alcohol
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51 [#6][C]([#6])([#6])[OH] 31 tertiary alcohol
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52 [#6,#1]C([#6,#1])([OH])C([#6,#1])([#6,#1])[OH] 32 1,2-diol
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53 [#6,#1]C([#6,#1])([OH])C([#6,#1])([#6,#1])[NH2] 33 1,2-aminoalcohol
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54 c[OH] 34 phenol
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55 [OH]cc[OH] 35 1,2-diphenol
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56 [OH]C=C[OH] 36 enediol
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57 [#6]O[#6] 37 ether
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58 COC 38 dialkyl ether
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59 cOC 39 alkylaryl ether
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60 cOc 40 diaryl ether
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61 [#6]S[#6] 41 thioether
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62 [#6]SS[#6] 42 disulfide
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63 [#6]OO[#6] 43 peroxide
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64 [#6]O[OH] 44 hydroperoxide
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65 [a] 200 aryl
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66 [!#6;$([N,O,S,F,Cl,Br,I,P])] 201 heteroatom
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67 [!#6;!$([+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])] 202 HBA
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68 [$([N,O;!H0]),$(N(C)(C)C)] 203 HBD
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69 [R] 204 Ring
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70 [$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C[$([O;$([H1&-0,H0&-1])])]);$(C[#6,#1])])] 205 carboxylic acid
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71 [$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C(=O)O[#6]);$(C[#6,#1])])] 206 ester
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72 [$([N;+0,+1;$(N(=O)~[O;H0;-0,-1])])] 207 nitro
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73 [$([C;$(C#[N;D1])])] 208 nitrile
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74 [$([N;!$(N*=[!#6])]);$(N[$([a])]);!$(N~[!#6])] 209 aniline
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75 [$([N;$(N[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C(=O)(N)N)])])])] 210 urea
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