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annotate CADDSuite/data/OpenBabel/bondtyp.txt @ 0:bac3c274238f

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Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author marcel
date Tue, 07 Jun 2011 16:43:30 -0400
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bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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1 ##############################################################################
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2 # #
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3 # Open Babel file: bondtyp.txt #
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4 # #
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5 # Copyright (c) 2002-2005 by Geoffrey R Hutchison #
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6 # Part of the Open Babel package, under the GNU General Public License (GPL)#
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7 # #
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8 # Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders() #
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9 # #
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10 # List of functional groups with double, triple (etc.) bond orders #
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11 # Pattern Atom1 Atom2 Bond Order (repeat as needed) #
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12 # * = Any atom (for setting non-multiple bonds) #
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13 # #
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14 # NOTE: These are applied in order, first to last. #
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15 # So it's generally better to have a long (specifc) SMARTS first. #
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16 # (all bonds must be single bonds to match) #
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17 # #
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18 ##############################################################################
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19
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20 # Porphyrin / phthalocyanine (3 patterns for three separate bonding motifs)
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21 # this one has explicit bonds to all four nitrogens (e.g., metal bond or hydrogens)
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22 #0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
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23 *1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7D3]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#6]([#7D3]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
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25 # this one has explicit bonds to two nitrogens (12 and 14)
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26 #0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
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27 *1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#6]([#7]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
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29 # and this one doesn't have any explicit bonds to the nitrogens
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30 #0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
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31 *1[#6]([#7]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7]4)[#6][#6][#6]4*[#6]([#7]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
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33 # Azide
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34 [#7D2][#7D2^1][#7D1] 0 1 2 1 2 2
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35 # Nitro
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36 [#8D1][#7D3^2]([#8D1])* 0 1 2 1 2 2 1 3 1
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37 # Sulphone
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38 [#16D4]([#8D1])([#8D1])(*)(*) 0 1 2 0 2 2 0 3 1 0 4 1
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39 # Phosphone
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40 [#15D4]([#8D1])(*)(*)(*) 0 1 2 0 2 1 0 3 1 0 4 1
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41
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42 # Carboxylic Acid, ester, etc.
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43 [#6D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1
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44 # Carbon dioxide
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45 [#8D1][#6D2^1][#8D1] 0 1 2 1 2 2
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46 # Amide C(=O)N
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47 [#6D3^2]([#8D1])([#7])* 0 1 2 0 2 1 0 3 1
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48 # Seleninic acid Se(=O)OH
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49 [#34D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1
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50 # Thioacid / Thioester C(=O)S
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51 [#6D3^2]([#8D1])([#16])* 0 1 2 0 2 1 0 3 1
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52 # dithioacid / dithioester C(=S)S
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53 [#6D3^2]([#16D1])([#16])* 0 1 2 0 2 1 0 3 1
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54 # thioamide C(=S)N
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55 [#6D3^2]([#16D1])([#7])* 0 1 2 0 2 1 0 3 1
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56
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57 # allene C=C=C
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58 # (this is problematic -- need to make sure the center carbon is sp)
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59 [#6^2][#6D2^1][#6^2] 0 1 2 1 2 2
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60
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61 # guanidinium and amidine -C(=NH)NH2 without hydrogens
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62 [#6D3^2;!R]([#7D1H0;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
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63 # and also with hydrogens
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64 # (this can normally be figured out, but is needed to avoid matching the next SMARTS)
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65 [#6D3^2;!R]([#7D2H1;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
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66 # and also with more hydrogens than normal (protonated)
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67 [#6D3^2;!R]([#7D3H2;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
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68
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69 # Schiff base, protonated
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70 [#6D3^2;!R]([#1,#6])([#1,#6])[#7D3^2;!R]([#1])[#6] 0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
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71
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72 ### other potential functional groups that may (or may not) be useful to add
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73 # imidines ( N=C/N\C=N
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74 # sulfoxides
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75 # heme / porphyrin
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76 # phthalocyanine