Please take a look at the attached file.
##############################################################################
# #
# 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
# Sulfones
[#16D4]([#8D1])([#8D1])([*!#8])([*!#8]) 0 1 2 0 2 2 0 3 1 0 4 1
# Sulfates
[#16D4]([#8D1])([#8D1])([#8-,#8])([#8-,#8]) 0 1 2 0 2 2 0 3 1 0 4 1
# Thiosulfates
[#16D4]([#16D1])([#8D1])([#8-,#8])([#8-,#8]) 0 1 2 0 2 2 0 3 1 0 4 1
# Sulfoxides
[#16D3]([#8D1])([*!#8])([*!#8]) 0 1 2 0 2 1 0 3 1
# Sulfite
[#16D3]([#8D1])([#8D1-])([#8D1-]) 0 1 2 0 2 1 0 3 1
# Sulfur trioxide
[#16D3]([#8D1])([#8D1])([#8D1]) 0 1 2 0 2 2 0 3 2
# Sulfites
[#16D3]([#8D1])([#8])([#8]) 0 1 2 0 2 1 0 3 1
# Disulfur monoxide
[#16D2]([#8D1])([#16D1]) 0 1 2 0 2 2
# Sulfmonoxides
[#16D2]([#8D1])([*!#8]) 0 1 2 0 2 1
# Sulfur dioxide
[#16D2]([#8D1])([#8D1]) 0 1 2 0 2 2
#Phosphite
[#15D3]([#8D1])([#8D1])([#8D2]) 0 1 2 0 2 2 0 3 1
#oxophosphane
#[#15D2]([#8D1])([#1]) 0 1 2 0 2 1
#Nitrosyl Hydride
[#7D2]([#8D1])([#1]) 0 1 2 0 2 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
# ene-one C=C=O
[#6^2][#6D2^1][#8D1] 0 1 2 1 2 2
# C=C=C=C
[#6D3][#6D2][#6D2][#6D3] 0 1 2 1 2 2 2 3 2 3 4 2
# isonitrile / isocyano
[#6D1][#7D2^1]* 0 1 3 1 2 1
# NR2 in ring with hybridized carbon neighbors
[#7D2R][#6D3^2][#8D2] 0 1 2 1 2 1
[#7D2R][#6D3^2][#7D2] 0 1 2 1 2 1
# if three N are present in R-N-guanidine-ish, prefer double bond to the
# non-terminal N (i.e. D2 if present)
[#6D3^2;!R]([#7D2;!R])([#7D1;!R])~[#7D1;!R] 0 1 2 0 2 1 0 3 1
# 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
Thanks,
Mohammad
> On Feb 5, 2016, at 8:09 PM, Geoffrey Hutchison <geoff.hutchi...@gmail.com>
> wrote:
>
> Strange. Can you send the bondtyp.txt or post it on GitHub?
>
> Thanks,
> -Geoff
>
>> On Feb 5, 2016, at 9:54 AM, Mohammad Mehdi Ghahremanpour
>> <ghahramanpou...@gmail.com> wrote:
>>
>> Hello,
>>
>> I defined some new bond types in bondtyp.txt file and the compilation was
>> done successfully and obenergy also worked well.
>> For instance, it recognizes the atom type for hypervalent phosphorous in
>> different molecules more accurate.
>> However, the test number 38 related to test_gzip_1 failed afterward.
>>
>>
>> Start 38: test_gzip_1
>> 38/145 Test #38: test_gzip_1 ......................***Failed 0.27 sec
>>
>> Any comments?
>>
>> Cheers,
>> Mohammad
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