On 17/02/2012 16:37, kc wrote:
Hi
I am working with mostly biological compounds and in some cases, i would
like to treat coenzyme A as an entity/atom type by itself so that when i
write to svg format, it would show up as CoA and its derivatives would just
be R-S-CoA.
Is there a way in OB to specify and recognise special groups of atoms?
You can define an alias in this way by adding an entry (name and SMILES)
to superatom.txt. See
http://openbabel.org/docs/current/Command-line_tools/babel.html#aliases-for-chemical-groups.
Your alias can be introduced as an A line in a mol file, as the alias
tBu is in the the attached file. In svg format with the -xA option it
will display in the alias form or in an expanded form without it.
In C++ code an example of an alias being added to an OBMol is around
line 529 in mdlformat.cpp.
Chris
t-butyl chloride
OpenBabel02171221482D
2 1 0 0 0 0 0 0 0 0999 V2000
0.8660 -1.5000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.0000 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
A 2
tBu
M END
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