Hello Noel,
Thanks..But, If we join two molecules, then atom Index will be changed from
second molecule.
Regards,
-Hitesh Patel
On Thu, May 31, 2012 at 11:35 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Just save the atom data in a field of the SDF file, e.g.
> mol.data["marks"] = "atom 6, atom 9".
>
> - Noel
>
> On 31 May 2012 10:27, Hitesh Patel <hiteshpatel...@gmail.com> wrote:
> > Hello,
> > Here I explain a task I am trying to do using openbabel in python. But,
> I am
> > facing some difficulties.
> > I want to break a molecule in small molecules by breaking a bond
> > from predefined groups and want to mark those two atoms (atoms which
> were at
> > the two ends of broken bond). And that marking should be preserved after
> > breaking or joining molecules And I can save the molecule file with
> marking
> > data (sdf or other format). for example A molecule containing
> > amide(R1-C(=O)-N-R2) group. If I break the C-N bond in amide group, I
> wish
> > to mark these two atoms C and N. After braking the molecule in two
> parts, In
> > both parts these atoms should preserve the mark. And I can write the
> > molecule file including this data. And If I join these two parts again,
> > still those markings on the atoms should be preserved.
> > What I tried:
> > I tried to enter data (mark) on OBAtom object by OBPairData. But, I can't
> > save the file with OBPairData on atoms. If we have data on OBMol Object,
> > then It saves in sdf file, but not from OBAtom object. So, If I write a
> > molecule file, I lose the information.
> > Is there any solution?? Even if something different then this approach
> > (OBPairData), I would like to try.
> > One more option:
> > Does the idea of marking the positions with some unusual atoms [Replacing
> > with unusual atoms] sounds terribly wrong? At least i could save it then
> in
> > any format even in SMILES?
> >
> > I would appreciative your suggestions.
> > Thanks..
> >
> > Regards,
> > -Hitesh Patel
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and
> > threat landscape has changed and how IT managers can respond. Discussions
> > will include endpoint security, mobile security and the latest in malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
>
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
