Inconsistency in naming of items

[GoogleCodeExporter]

Some item names (i.e. molecules and regions) have a number appended onto them 
after they are created, which is incremented each time a new item is added, 
thus preventing duplicate names (unless the user attempts to explicitly give 
them duplicate names). Other item names (i.e. surface classes, release 
patterns, and release sites) do not have incremental numbers appended onto 
them, forcing the user to always manually rename them. 

Original issue reported on code.google.com by [email protected] on 14 Apr 2014 at 8:48