On 7 May 2010 05:32, Egon Willighagen <[email protected]> wrote: > moving to: cdk-user > > Hi Rajarshi, > > On Fri, May 7, 2010 at 4:07 AM, Rajarshi Guha <[email protected]> wrote: >> Take an SDF file with no H's and then call >> AtomContainerManipulator.convertImplicitToExplicitHydrogens and no H's >> are added. > > SD files do not have info on the number of implicit hydrogens, making > the field set to UNKNOWN (null). The > convertImplicitToExplicitHydrogens has nothing to convert yet; I'd > guess you simply have to calculate the number of implicit hydrogens > first? > >> But if the corresponding SMILES form is read in, and implcit H's are >> converted to explicit, H's are added. > > SMILES on the other hand *does* specify the number of implicit > hydrogens (implicitly, of course), but it's part of the standard... so > the SmilesParser does atom type detection, calculate number of > implicit hydrogens, and actually aromaticity detection too... The > values now being set, the convert() method has something to convert... > > Rajarshi, can you please verify this hypothesis?
My 2c. It's common for 2D SD files in particular to not include implicit hydrogens. - Noel > Egon > > -- > Post-doc @ Uppsala University > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > ------------------------------------------------------------------------------ > > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
