Re: [Rdkit-discuss] fragments aromaticity

[Evgueni K. <eko...@gm...>]

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 <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
>



-- 
Dr. Evgueni Kolossov (PhD)
eko...@gm...
Tel.   +44(0)1628 627168
Mob. +44(0)7812070446