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
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