Fwd: adding fragments to your molecule in avogadro

Begin forwarded message:

From: “Tim Vandermeersch” tim.vandermeersch@gmail.com
Date: November 9, 2007 4:01:27 PM EST
Subject: [OpenBabel-Devel] adding fragments to your molecule in
avogadro

Hi,

sorry to spam the list with all my messages…

But I wanted to add a feature to avogadro where you could add
fragments to a molecule.
When using the tool, first you would have to select the ring fragment
you want to add. Then I was thinking of showing a new 3D window with
the fragment rendered, in that window you could then select which atom
(=atom index ib for the smarts pattern) to connect the fragment with.
Next you would also have to select the atom (=atol inex ia for mol)
from the molecule to which to fragment will be added.

The function to call from avogadro would look like
OBBuilder::Attatchfragment(OBMol &mol, const char *smarts, int ia,
int ib)

example to add phenyl to atom 3 of mol: builder.AttatchFragment(mol,
“a1aaaa1”, 3, 1)

This would add the fragment with all carbons, the types can then be
changed with the drawing tool.

But I have no idea how to do the “new 3D window” in avogadro. So if
anyone likes this idea and wants too help, please let me know. Or if
you know a better way to do this let me know…

Thanks in advance,
Tim


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