On Mit, 2009-07-01 at 18:20 +0200, sebi wrote:
> On Mit, 2009-07-01 at 11:06 +0200, Egon Willighagen wrote:
> > Hi Seb,
> >
> > On Wed, Jul 1, 2009 at 10:43 AM, sebi<[email protected]>
> 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...
>
> Sorry for double post..
>
> This is the code I'm using now:
Sorry for triple post, my mailer is buggy :s
the code:
# these are RCDK methods to build the molecule instance
@mol = Lang.read_molfile(molfile)
# or
@mol = Lang.read_smiles(smiles)
# and im doing this CDK calls
Tools::Manipulator::AtomContainerManipulator.convertImplicitToExplicitHydrogens(@mol)
Tools::Manipulator::AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(@mol)
Aromaticity::CDKHueckelAromaticityDetector.detectAromaticity(@mol)
desc = XLogPDescriptor.new()
desc.calculate(@mol).getValue().doubleValue()
I looked at the SmilesParser source and couldn't find something else
that's different
sebi
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