GNF - HierS: clustering for analyzing HTS results

HierS of Genomics Institute of the Novartis Research Foundation (GNF)





Hiers: An exhaustive ring-based algorithm to provide an intuitive approach to compound clustering for analyzing high-throughput screening results.





Download Hiers:


http://www.gnf.org/publications/hiers/





More details: http://www.chemaxon.hu/forum/viewpost2596.html#2596

Hello All,





I am trying to use HierS algorithm. I have followed the instructions by installing Tomcat, JChem ... when submitting a list of smiles and IDs, I have an exception error :





java.lang.NoClassDefFoundError: org/gnf/db/ConFactory


hiers.Data.ScreenWrapper.findCompoundsBySmiles(ScreenWrapper.java:157)


hiers.struts.action.CpdAction.execute(CpdAction.java:81)


org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:484)


org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:274)


org.apache.struts.action.ActionServlet.process(ActionServlet.java:1482)


org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:525)


javax.servlet.http.HttpServlet.service(HttpServlet.java:709)


javax.servlet.http.HttpServlet.service(HttpServlet.java:802)





I will be very grateful if you can assist me in running the program.


Many Thanks.





Best regards,





IsI

Sorry, we don't provide support for contributed stuff. You will find a contact address at the HierS site.

It appears that the HierS servlet application developed and freely distributed by the Genomics Institute of the Novartis Research Foundation is built using a JChem version (perhaps 2.2.1) which has a now-deprecated class chemaxon/sss/search/SearchException and is no longer available via the ChemAxon archives. We have tried to contact hiers _at_ gnf.org as instructed via http://public.gnf.org/publications/hiers/ but received no reply. The website advises: "Acquire jchem.jar from Chemaxon (version 2.2.1 or later should work)".





So I wonder if jchem.jar v2.2.1 is available anywhere.

Hi,





The class chemaxon.sss.search.SeachException is still included in jchem.jar, and will not be removed in the foreseeable future.


The class is not deprecated.





It might have been misleading for you that it's not listed in the API documentation for some reason - we will fix this soon.





An example where we are throwing it:





http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/MolSearch.html#isMatching()





So it must be a configuration issue, I suggest to go on and use the latest jchem.jar.





Best regards,





Szilard