I recently created a Bioclipse feature to filter chemical structures in a StructureDB database (the new database for chemical structures in Bioclipse). The new plugin is called VScreen, and aims at being a future Virtual Screening feature. Currently the feature is in very early proof-of-concept state with only two simple filters, Molecular Weight and XlogP. Plans include to create an extension point for filters that plugin can extend to contribute new filters.
Currently, the only way of interacting with the plugin is via Bioclipse scripts. A sample usage is available below in a Gist:
A screenshot from Bioclipse is shown below: