Hello. It would be nice if the Ward/JP APIs were modified to be more similar to the LibraryMCS API. I find the LibraryMCS API to be much more general and easy to use. The Ward/JP APIs are designed for easy use with files and direct connections to a database, but the functionality is difficult to incorporate into a Java program. Thanks.
many thanks for your comment, we admit that those are absolutely relevant.
We've been working on a unified clustering framework, sphere exclusion and k-means clustering, as well as Bemis and Murcko structures have been implemented within this new framework and we gradually move legacy clustering code in this framework (by re-implementing most of the old stuff). As part of this work we will provide more concise API, sg. similar to the LibraryMCS class.
The planned release of this new clustering is in 5.4 (Q3 2010).
Thank you for your suggestions, you'll be notified in this forum topic when the new Ward API is available.