On Mit, 2009-07-01 at 19:25 +0200, Egon Willighagen wrote: > On Wed, Jul 1, 2009 at 6:25 PM, sebi<sebastian.kl...@hispeed.ch> wrote: > > On Mit, 2009-07-01 at 18:20 +0200, sebi wrote: > >> On Mit, 2009-07-01 at 11:06 +0200, Egon Willighagen wrote: > > # 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 > > That should do it... OK, can you try the following... save both > molecules (read from file, and parsed from SMILES) and save that to > CML, and post that here... preferably with the same atom ordering... > > Egon >
Just for completeness the output of the CMLWriter before any manipulation. It's clear, differences are the aromaticity and the hydrogens in SMILES. Setting them for the MDL returns the same descriptor values. Sebi -----MDL----- <?xml version="1.0" encoding="ISO-8859-1"?> <molecule id="m1" xmlns="http://www.xml-cml.org/schema";> <atomArray> <atom id="a1" elementType="C" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="12"/> <atom id="a2" elementType="C" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="12"/> <atom id="a3" elementType="O" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="16"/> <atom id="a4" elementType="O" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="16"/> <atom id="a5" elementType="C" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="12"/> <atom id="a6" elementType="C" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="12"/> <atom id="a7" elementType="C" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="12"/> <atom id="a8" elementType="C" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="12"/> <atom id="a9" elementType="C" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="12"/> <atom id="a10" elementType="C" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="12"/> <atom id="a11" elementType="C" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="12"/> <atom id="a12" elementType="O" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="16"/> <atom id="a13" elementType="O" x2="0.0" y2="0.0" formalCharge="0" isotopeNumber="16"/> </atomArray> <bondArray> <bond id="b1" atomRefs2="a2 a1" order="S"/> <bond id="b2" atomRefs2="a3 a2" order="D"/> <bond id="b3" atomRefs2="a4 a2" order="S"/> <bond id="b4" atomRefs2="a5 a4" order="S"/> <bond id="b5" atomRefs2="a6 a5" order="D"/> <bond id="b6" atomRefs2="a7 a6" order="S"/> <bond id="b7" atomRefs2="a8 a7" order="D"/> <bond id="b8" atomRefs2="a9 a8" order="S"/> <bond id="b9" atomRefs2="a10 a9" order="D"/> <bond id="b10" atomRefs2="a10 a5" order="S"/> <bond id="b11" atomRefs2="a11 a10" order="S"/> <bond id="b12" atomRefs2="a12 a11" order="D"/> <bond id="b13" atomRefs2="a13 a11" order="S"/> </bondArray> </molecule> -----SMILES----- <?xml version="1.0" encoding="ISO-8859-1"?> <molecule id="m1" xmlns="http://www.xml-cml.org/schema";> <atomArray> <atom id="a1" elementType="C" formalCharge="0" hydrogenCount="3"/> <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="0"/> <atom id="a3" elementType="O" formalCharge="0" hydrogenCount="0"/> <atom id="a4" elementType="O" formalCharge="0" hydrogenCount="0"/> <atom id="a5" elementType="C" formalCharge="0" hydrogenCount="0"/> <atom id="a6" elementType="C" formalCharge="0" hydrogenCount="1"/> <atom id="a7" elementType="C" formalCharge="0" hydrogenCount="1"/> <atom id="a8" elementType="C" formalCharge="0" hydrogenCount="1"/> <atom id="a9" elementType="C" formalCharge="0" hydrogenCount="1"/> <atom id="a10" elementType="C" formalCharge="0" hydrogenCount="0"/> <atom id="a11" elementType="C" formalCharge="0" hydrogenCount="0"/> <atom id="a12" elementType="O" formalCharge="0" hydrogenCount="0"/> <atom id="a13" elementType="O" formalCharge="0" hydrogenCount="1"/> </atomArray> <bondArray> <bond id="b1" atomRefs2="a2 a1" order="S"/> <bond id="b2" atomRefs2="a3 a2" order="D"/> <bond id="b3" atomRefs2="a4 a2" order="S"/> <bond id="b4" atomRefs2="a5 a4" order="S"/> <bond id="b5" atomRefs2="a6 a5" order="D"> <bondType dictRef="cdk:aromaticBond"/> </bond> <bond id="b6" atomRefs2="a7 a6" order="S"> <bondType dictRef="cdk:aromaticBond"/> </bond> <bond id="b7" atomRefs2="a8 a7" order="D"> <bondType dictRef="cdk:aromaticBond"/> </bond> <bond id="b8" atomRefs2="a9 a8" order="S"> <bondType dictRef="cdk:aromaticBond"/> </bond> <bond id="b9" atomRefs2="a10 a9" order="D"> <bondType dictRef="cdk:aromaticBond"/> </bond> <bond id="b10" atomRefs2="a10 a5" order="S"> <bondType dictRef="cdk:aromaticBond"/> </bond> <bond id="b11" atomRefs2="a11 a10" order="S"/> <bond id="b12" atomRefs2="a12 a11" order="D"/> <bond id="b13" atomRefs2="a13 a11" order="S"/> </bondArray> </molecule> ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
