On Jan 23, 2008, at 8:34 PM, Manoj Rajagopalan wrote:
> I am new to OpenBabel. I am writing an app in which I would like to
> store "chunks" of a molecule - groups of atoms and bonds such that
> of the atoms may have unsatisfied valences that reach out across the
> "chunk" boundary to bond to other atoms or chunks.
You may want to take a look at OBMol::Separate() and obfragment in the
SVN trunk. These do some similar things. Basically, what I wrote into
obfragment was to delete non-ring bonds and then use OBMol::Separate
to break out those "chunks."
We've talked about an OBFragment class, which would generalized
OBResidue (i.e., an OBFragment would represent a chunk of a molecule:
a set of atoms and bonds). No one has stepped up to write that code. I
can certainly give suggestions on what needs to happen if you (or
someone else) would like pointers.