Using the API for generating the name of a molecule:
Molecule m = ...;
String name = MolExporter.exportToFormat(m, "name");
String traditionalName = MolExporter.exportToFormat(m.toFormat, "name:t");
The exact behavior of Structure to Name can be configured by including format options after the name
parameter and a colon, for instance name:common
.
See the Structure to Name User Guide for more information.