Hi Greg,
Just try to copy any aromatic ring the way I described it and at the end do:
fragMol->updatePropertyCache();
MolOps::sanitizeMol(fragMol);
I believe aromaticity suppose to be set in sanitize and I do not need to
call MolOps::setAromaticity....
Regards,
Evgueni
2009/10/20 Greg Landrum <greg.land...@gmail.com>
> Dear Evgueni,
>
> On Mon, Oct 19, 2009 at 9:11 PM, Evgueni Kolossov <ekolos...@gmail.com>
> 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
>
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
