On Mit, 2009-07-01 at 11:06 +0200, Egon Willighagen wrote:
> Hi Seb,
>
> On Wed, Jul 1, 2009 at 10:43 AM, sebi<sebastian.kl...@hispeed.ch> wrote:
> > when calculating xLogP and tPSA descriptors with CDK from SMILES i get
> > values similar to those from PubChem.
> > When i calculate them from molfile I get different values.
> > Any idea? Am I doing something wrong?
>
> What code are you using? Are you making sure you do the same
> preprocessing for both? E.g. the SMILES parser will do aromaticity
> detection, the MDL V2000 molfile reader would not...
Maybe this is it. How can I do that for any instance of "Molecule"?
I added the follwing lines (Ruby code)
---
iterator = finder.findAllRings(@mol).atomContainers.iterator
while iterator.hasNext
ring = iterator.next
Aromaticity::AromaticityCalculator.isAromatic(ring, @mol)
end
---
to the calculation, it just returns true for Aspirin. How can I set the
aromaticity? Am I missing some point?
> You can use the classes in the org.openscience.cdk.diff package to see
> what differences there are in the data model, which could cause the
> deviation...
Hm, can't find this class in the jchempaint-primary branch. Is it in the
1.2.x? If so, I'll wait until you merged the patches in master.
> Egon
>
Thanks again for the fast response
Sebi
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