Hmm, out of interest why do you want to do this? For Sp3 chiral atoms you do want this but *only* when all connecting bonds are ring bonds (e.g. steroids).
Anyways, Stephen Beisken added removeNonChiralHydrogens to handle this... ideally I'd like this to be an option on the main method: AtomContainerManipulator.suppressHydrogens(mol, HTYPE_NONSTEREO AtomContainerManipulator.suppressHydrogens(mol, HTYPE_SAFE); AtomContainerManipulator.suppressHydrogens(mol, HTYPE_ALL); ... one day maybe John On 22 November 2016 at 17:58, Dr. Martin Gütlein <[email protected]> wrote: > Hi John, > > sorry, its quite late already. It is working fine, as my example shows > (with the absolute smiles generator). > > Regards, > Martin > > > Am 22.11.2016 um 18:51 schrieb Martin Gütlein: > > Hi John, > > thanks for your response, here is my example code with your smiles: > > IAtomContainer mol = new SmilesParser( > SilentChemObjectBuilder.getInstance()).parseSmiles("[ > H]/C(C)=C(\\[H])C"); > mol = AtomContainerManipulator.suppressHydrogens(mol); > System.out.println(SmilesGenerator.generic().create(mol)); > System.out.println(SmilesGenerator.absolute().create(mol)); > > Output is: > C(C)=CC > C/C=C\C > > I can add an issue, but I am still not sure if you understood me > correctly, i.e., if suppressHydrogens is expected to retain Hs with > stereo-info. > > Regards, > Martin > > > > Am 22.11.2016 um 13:09 schrieb John M: > > Martin, > > Do you have the compound, this should be handled... but there may be a > corner case. Can you add an issue to GitHub with the molecule, thanks. > > [image: Inline images 1] > > [H]/C(C)=C(\[H])C > > [image: Inline images 2] > > [H]/C(C)=C(/[H])C > > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > Cdk-user mailing > [email protected]https://lists.sourceforge.net/lists/listinfo/cdk-user > > > -- > Dr. Martin Gütlein > Phone:+49 (0)6131 39 23336 (office)+49 (0)177 623 9499 (mobile) > Email:[email protected] > >
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