On 15/03/2012 00:01, Tony Cook wrote: > The Alias feature is for display. That is if you draw the structure from the > information in the SDF file (or any of the MDL formats) > you are supposed to use the alias name instead of the atomic symbol in the > drawing only. However for all other purposes you should use the real atomic > number/symbol > > For example this feature allows you to annotate the structure drawing with > labelled atoms "C1", "C2", "C3" etc > > Open Babel would do better to ignore the A records and just keep mum! unless > the intent is to convert to a graphical format (PNG etc), then the default > should be to use the Alias symbol unless explicity told not to > > This is all old hat standard stuff with MDL molecule/reaction formats. Sounds > like from the comments that this knowledge has been lost/confused in the > mists of time!
The specification document "CTFile Formats" gives no guidance on the use of the alias feature. It may have been intended only for display, but does seem to be used sometimes to convey essential chemical information, for instance in the sample sdf files provided with the InChI software (up to v1.03) by NIST. OpenBabel currently tries to interpret the alias information, so that the internal representation is a proper molecule (not a drawing), while retaining the alias information to be used (optionally) when output for SVG and PNG display, etc. There are differing views on whether OpenBabel should completely reject files with misused or malformed features. I prefer to be helpful if possible, but mistakes when interpreting other peoples mistakes are inevitable. Chris ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
