Dear John,
Thanks for the explanation and inputs. I require these modifications in order
to depict a the molecule without much complexity. I will remember the warnings
and do accordingly.
Thanks a lot once again for your help.
Have a nice evening.
Kind regards,
Kohulan.R
--
Kohulan Rajan
PhD Student
Faculty of Chemistry and Geosciences
Institute of Inorganic and Analytical Chemistry - Cheminformatics and
Chemometrics
Friedrich-Schiller-University
Lessingstraße 8
07743 Jena , Germany
Phone : +49 3641 948783
“It is our choices that show what we truly are, far more than our abilities.” -
Albus Dumbledore Monday, 29 October 2018, 06:17PM +01:00 from John Mayfield
john.wilkinson...@gmail.com :
>I am still curious why, this kind of dubious manipulation is how errors start
>propagating. Anyways I can only ask twice :-). These are not depiction options
>but you can achieve it by modifying the molecule.
>
>1) I think what you're asking is to get the "parent" molecule. You should
>define a list of the salts (counter ions) you want to remove and just remove
>them from the IAtomContainer. A common hack is to remove everything but the
>largest component (OEChem has the amusingly name:
>OETheFunctionFormerlyKnownAsStripSalts ). In CDK you would use the
>ConnectivityChecker sort by size and take the largest one. Note you may end
>up with a non-neutral form if care is not taken and if there are two
>components of the same size you should decide what to do.
>
>2) Remove the stereochemistry,
>container.setStereoElements(Collections.emptyList()) ; prior to generating
>coordinates. Or if you already have coordinates, iterate over the bonds and
>setStereo(IBond.Stereo.NONE) . Depending on what you're asking you may want to
>set the bond order to single ( setOrder(IBond.Order.SINGLE) ) too, note this
>will then mess up valence and so you'd have radicals, so you'd have to sort
>that out etc. Again removing information from the molecule is not a good.
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