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'. In my tests the
pattern matching does not work properly unless the molecular structure
is given in the smile format. To localize the problem I have
Dear Geoffrey,
Thank you for being willing to fix the issue. It will be really helpful
for projects like mine.
Igor
On 11/8/2013 9:54 AM, Geoffrey Hutchison wrote:
On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
However even for good geometries OB has problems with bond orders
Dear Geoffrey,
Thanks for your response.
The structure was optimized at MP2/aTZ level. I use XYZ-format because it
is the main format in MolPro QM program. The problem with C=N bond was met
in several compounds listed bellow.
Methanimine
EthanImine
VinylImine
Benzenemethanimine
and Imidazoline
Dear OB users,
I came across a problem of converting XYZ to HIN format for imine
compounds. In more detail, the double C=N bond in imine series is
determined as a single bond. (As a result, atom typification for Merck
force field is completely screwed up.)
See the output hin-file bellow, the C=N
