Re: [Rdkit-discuss] fragments aromaticity

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

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);
................

Regards,
Evgueni



2009/10/19 Greg Landrum <gre...@gm...>

> On Mon, Oct 19, 2009 at 12:06 PM, Evgueni Kolossov <eko...@gm...>
> wrote:
> >
> > I got a small problem with the fragments - aromatic cycles coming with
> all
> > bonds as double. If I save it into SDF and open SDF than it all Ok.
> > I believe I saw somewhere fix for this. Can you please point me to the
> right
> > place?
>
> hmm, that's weird; it's not really sounding familiar. Do you have a
> reproducible example of it happening?
>
> -greg
>



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