diff CADDSuite-1.0.1/data/OpenBabel/bondtyp.txt @ 5:e30a41af9d2b

Uploaded

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+++ b/CADDSuite-1.0.1/data/OpenBabel/bondtyp.txt	Tue Nov 15 10:53:16 2011 -0500
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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