moving to: cdk-user Hi Rajarshi,
On Fri, May 7, 2010 at 4:07 AM, Rajarshi Guha <rajarshi.g...@gmail.com> 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? 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 Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
