Re: [Rdkit-discuss] fragments aromaticity

[Greg L. <gre...@gm...>]

Dear Evgueni,

On Mon, Oct 19, 2009 at 9:11 PM, Evgueni Kolossov <eko...@gm...> wrote:
> Yes, it is reproducible every time...
> Actually code is quite simple: iterate through the rings, bonds, atoms for
> each bond and add atoms and bonds to a new mol like:
> Atom *begAtom = mol.getAtomWithIds(begIdx)->copy();
> newBegIdx = fragMol->AddAtom(begAtom, false, true);
> the same for an endAtom
> etc...
>
> Bond *pNewBond = pBond->copy();
> pNewBond->setOwningMol(fragMol);
> pNewBond ->setBeginAtomIdx(newBegIdx);
> pNewBond ->setEndAtomIdx(newEndIdx);
> int nNewBondIdx = fragMol->addBond(pNewBond, true);

hmm, I'm afraid I don't really see anything here that would lead to a
molecule that has aromatic rings where all bonds are double. Do you
have a specific example you can show (preferably including the output
of debugMol) that demonstrate the problem?

-greg