Dear OpenBabel community:
I'm faced with a problem of selecting atoms by SMARTS patterns that
include charge descriptor "+/-" such as '[O-][N+](=O)C'. The pattern
matching does not work properly unless the molecular structure is given
in the smile format. To localize the problem I have tested different
smarts with "obgrep" application by searching in Nitromethane.mol2
structure. The mol2-format is used because it provides atomic charge
information. (Mol and hin-formats were also tested and resulted in the
same problem.) All patterns with charge descriptor result in no matches
in Nitromethane (canonical smile C[N+](=O)[O-]):
'C[N+](=O)[O-]'
'C-[N+]([O-])=O'
'C-[N]([O-])=O'
'[O-][N+](=O)C'
'O[N+](=O)C'
are failed. The only successful patterns are that which have no charge
descriptors. For example, the command:
obgrep -imol2 'C-[N]([O])=O' Nitromethane.mol2
has a match and outputs the structure:
@<TRIPOS>MOLECULE
Nitromethane.hin
7 6 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O 1.4119 0.9932 -0.0000 O.2 1 LIG11 -0.5820
2 O 1.3830 -1.0017 -0.0000 O.2 1 LIG11 0.0340
3 N 0.7869 0.0029 -0.0000 N.pl3 1 LIG11 0.0348
4 C -0.6030 0.0054 0.0000 C.3 1 LIG11 0.1981
5 H -0.9794 -0.5079 0.8877 H 1 LIG11 0.1050
6 H -0.9794 -0.5079 -0.8877 H 1 LIG11 0.1050
7 H -1.0199 1.0160 0.0000 H 1 LIG11 0.1050
@<TRIPOS>BOND
1 1 3 1
2 2 3 2
3 3 4 1
4 4 5 1
5 4 6 1
6 4 7 1
Does OBabel support smarts charge-descriptors for matching 3D
structures? Or what I am I doing wrong? (In my tests matching works only
for smi-files).
Thank you,
Igor
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