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view CADDSuite/data/OpenBabel/bondtyp.txt @ 8:9ab6da6cd36c
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| author | marcel |
|---|---|
| date | Fri, 02 Sep 2011 08:48:21 -0400 |
| parents | bac3c274238f |
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############################################################################## # # # Open Babel file: bondtyp.txt # # # # Copyright (c) 2002-2005 by Geoffrey R Hutchison # # Part of the Open Babel package, under the GNU General Public License (GPL)# # # # Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders() # # # # List of functional groups with double, triple (etc.) bond orders # # Pattern Atom1 Atom2 Bond Order (repeat as needed) # # * = Any atom (for setting non-multiple bonds) # # # # NOTE: These are applied in order, first to last. # # So it's generally better to have a long (specifc) SMARTS first. # # (all bonds must be single bonds to match) # # # ############################################################################## # Porphyrin / phthalocyanine (3 patterns for three separate bonding motifs) # this one has explicit bonds to all four nitrogens (e.g., metal bond or hydrogens) #0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 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 # this one has explicit bonds to two nitrogens (12 and 14) #0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 *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 # and this one doesn't have any explicit bonds to the nitrogens #0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 *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 # Azide [#7D2][#7D2^1][#7D1] 0 1 2 1 2 2 # Nitro [#8D1][#7D3^2]([#8D1])* 0 1 2 1 2 2 1 3 1 # Sulphone [#16D4]([#8D1])([#8D1])(*)(*) 0 1 2 0 2 2 0 3 1 0 4 1 # Phosphone [#15D4]([#8D1])(*)(*)(*) 0 1 2 0 2 1 0 3 1 0 4 1 # Carboxylic Acid, ester, etc. [#6D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1 # Carbon dioxide [#8D1][#6D2^1][#8D1] 0 1 2 1 2 2 # Amide C(=O)N [#6D3^2]([#8D1])([#7])* 0 1 2 0 2 1 0 3 1 # Seleninic acid Se(=O)OH [#34D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1 # Thioacid / Thioester C(=O)S [#6D3^2]([#8D1])([#16])* 0 1 2 0 2 1 0 3 1 # dithioacid / dithioester C(=S)S [#6D3^2]([#16D1])([#16])* 0 1 2 0 2 1 0 3 1 # thioamide C(=S)N [#6D3^2]([#16D1])([#7])* 0 1 2 0 2 1 0 3 1 # allene C=C=C # (this is problematic -- need to make sure the center carbon is sp) [#6^2][#6D2^1][#6^2] 0 1 2 1 2 2 # guanidinium and amidine -C(=NH)NH2 without hydrogens [#6D3^2;!R]([#7D1H0;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1 # and also with hydrogens # (this can normally be figured out, but is needed to avoid matching the next SMARTS) [#6D3^2;!R]([#7D2H1;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1 # and also with more hydrogens than normal (protonated) [#6D3^2;!R]([#7D3H2;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1 # Schiff base, protonated [#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 ### other potential functional groups that may (or may not) be useful to add # imidines ( N=C/N\C=N # sulfoxides # heme / porphyrin # phthalocyanine