[Rdkit-discuss] fragments aromaticity
Hi Greg, 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? Regards, Evgueni -- 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
Re: [Rdkit-discuss] fragments aromaticity
On Mon, Oct 19, 2009 at 12:06 PM, Evgueni Kolossov 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 -- 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
Re: [Rdkit-discuss] fragments aromaticity
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 > On Mon, Oct 19, 2009 at 12:06 PM, Evgueni Kolossov > 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) 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