> I can find documentation and examples on reading reactions in one format and
> saving them to a different one using obabel or language bindings, but I can't
> find anything for applying a reaction SMARTS to a molecule and obtaining the
> result.
You want the OBChemTsfm class:
http://openbabel.org/api/2.3/classOpenBabel_1_1OBChemTsfm.shtml
> For example, If I want to convert all carboxyl groups in an input file to
> chlorides (throwing away the COOH), is that easy to do in obabel or in
> python? Is there some examples or documentation on this that I am missing?
I know that OBChemTsfm is available in the Python bindings. You'd take an
expression like this:
[nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1
I haven't tried this in Python, but you'd do something like this (written in
C++)
OBChemTsfm rxn;
rxn.Init("[nD2:1]1c[nH]cc1", "[n+:1]1c[nH]cc1");
rxn.Apply(mol);
The bigger problem is building up an open database, but if there are interested
parties I think a pool of reactions would be very interesting for many uses.
Hope that helps,
-Geoff------------------------------------------------------------------------------
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