Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.0.1/data/OpenBabel/bondtyp.txt @ 5:e30a41af9d2b
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| author | marcel |
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| date | Tue, 15 Nov 2011 10:53:16 -0500 |
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| 4:af446ca2d5c6 | 5:e30a41af9d2b |
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| 1 ############################################################################## | |
| 2 # # | |
| 3 # Open Babel file: bondtyp.txt # | |
| 4 # # | |
| 5 # Copyright (c) 2002-2005 by Geoffrey R Hutchison # | |
| 6 # Part of the Open Babel package, under the GNU General Public License (GPL)# | |
| 7 # # | |
| 8 # Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders() # | |
| 9 # # | |
| 10 # List of functional groups with double, triple (etc.) bond orders # | |
| 11 # Pattern Atom1 Atom2 Bond Order (repeat as needed) # | |
| 12 # * = Any atom (for setting non-multiple bonds) # | |
| 13 # # | |
| 14 # NOTE: These are applied in order, first to last. # | |
| 15 # So it's generally better to have a long (specifc) SMARTS first. # | |
| 16 # (all bonds must be single bonds to match) # | |
| 17 # # | |
| 18 ############################################################################## | |
| 19 | |
| 20 # Porphyrin / phthalocyanine (3 patterns for three separate bonding motifs) | |
| 21 # this one has explicit bonds to all four nitrogens (e.g., metal bond or hydrogens) | |
| 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 | |
| 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 | |
| 24 | |
| 25 # this one has explicit bonds to two nitrogens (12 and 14) | |
| 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 | |
| 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 | |
| 28 | |
| 29 # and this one doesn't have any explicit bonds to the nitrogens | |
| 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 | |
| 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 | |
| 32 | |
| 33 # Azide | |
| 34 [#7D2][#7D2^1][#7D1] 0 1 2 1 2 2 | |
| 35 # Nitro | |
| 36 [#8D1][#7D3^2]([#8D1])* 0 1 2 1 2 2 1 3 1 | |
| 37 # Sulphone | |
| 38 [#16D4]([#8D1])([#8D1])(*)(*) 0 1 2 0 2 2 0 3 1 0 4 1 | |
| 39 # Phosphone | |
| 40 [#15D4]([#8D1])(*)(*)(*) 0 1 2 0 2 1 0 3 1 0 4 1 | |
| 41 | |
| 42 # Carboxylic Acid, ester, etc. | |
| 43 [#6D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1 | |
| 44 # Carbon dioxide | |
| 45 [#8D1][#6D2^1][#8D1] 0 1 2 1 2 2 | |
| 46 # Amide C(=O)N | |
| 47 [#6D3^2]([#8D1])([#7])* 0 1 2 0 2 1 0 3 1 | |
| 48 # Seleninic acid Se(=O)OH | |
| 49 [#34D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1 | |
| 50 # Thioacid / Thioester C(=O)S | |
| 51 [#6D3^2]([#8D1])([#16])* 0 1 2 0 2 1 0 3 1 | |
| 52 # dithioacid / dithioester C(=S)S | |
| 53 [#6D3^2]([#16D1])([#16])* 0 1 2 0 2 1 0 3 1 | |
| 54 # thioamide C(=S)N | |
| 55 [#6D3^2]([#16D1])([#7])* 0 1 2 0 2 1 0 3 1 | |
| 56 | |
| 57 # allene C=C=C | |
| 58 # (this is problematic -- need to make sure the center carbon is sp) | |
| 59 [#6^2][#6D2^1][#6^2] 0 1 2 1 2 2 | |
| 60 | |
| 61 # guanidinium and amidine -C(=NH)NH2 without hydrogens | |
| 62 [#6D3^2;!R]([#7D1H0;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1 | |
| 63 # and also with hydrogens | |
| 64 # (this can normally be figured out, but is needed to avoid matching the next SMARTS) | |
| 65 [#6D3^2;!R]([#7D2H1;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1 | |
| 66 # and also with more hydrogens than normal (protonated) | |
| 67 [#6D3^2;!R]([#7D3H2;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1 | |
| 68 | |
| 69 # Schiff base, protonated | |
| 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 | |
| 71 | |
| 72 ### other potential functional groups that may (or may not) be useful to add | |
| 73 # imidines ( N=C/N\C=N | |
| 74 # sulfoxides | |
| 75 # heme / porphyrin | |
| 76 # phthalocyanine |