Support for Nicknames

[BobHanson]

One of the most powerful aspects of the CDX and CDXML formats is that they allow for compact depiction of over 500 recognized "nicknames" (Ph, Ac, THP, etc.)

Nicknames are in the form of simple CDXML files that register the fragment information as well as its connectivity. When incorporated into a depiction, the convention is to hide the nickname's node/edge information and only display the nickname's label.

It seems to me that JME-SwingJS and OCL-SwingJS could both utilize these effectively, and openchemlib itself could incorporate the idea easily enough with a subclasssing of StereoMolecule, perhaps. (Jmol-SwingJS already handles CDXML reading, allowing conversion to SMILES, InChI, 2D depictions, or 3D models.)

Ph.cdxml.txt