Problem using JChemManger

Hello


I'm new to this software and Chem computing too. I installed the JChem, marvin and Instant jchem following the documentation of each.


I tried to setup jChem example as an starting point for me.


When I start the JchemManager, it starts OK, connect to mysql db OK


The property table is created OK. When I try to create the structure table, the software doesn't go through the steps described in the documentation, the table doesn't get created and the dialog box disappears.





Any help will be appreciated.





Thank you.

Hello Abayazid,





the topic was moved to the "Structure search and chemical databases" forum, my colleagues will answer you soon.





Kind regards,


Judit

Hi Saif,





can you post us your JChem, mysql and JDBC driver version numbers?


It also should be good to see the stack trace if it is available.





Regards, Edvard

Hello Ebuki


Thank you for your respond.


I'm using MySQL: Server version: 5.0.51a


JChem jchem-5_0_03-linux


For the connection I have three of them in the lib directory of JChem:





mysql-connector-java-3.1.14-bin.jar


mysql-connector-java-5.1.6-bin.jar


mysql-connector-java-5.0.8-bin.jar





Fopr the stack trace, I don't know where does JChem store it.





Thank you.

Hello Edvard ,


I removed the unused MySQL connectors, leaving only one which is:


mysql-connector-java-5.0.8-bin.jar.


But that didn't change any thing.





Thank you.

Please check which driver is in you Classpath. If it is 5.0.8, try to chage it to 5.1.6. (I have already met with incorrect 5.0.x driver for MySql)


Waiting for your response,


Edvard

Edvard,


I replaced the connector mysql-connector-java-5.0.8-bin.jar with


MySQLl-connector-java-5.1.6-bin.jar, set the CLASSPATH and exported it,


when I start the JchemManager, it doesn't connect to MySQL DB giving an error of java.lang.NoClassDefFoundException, which I assume it's the mismatch of Driver because when I put this (mysql-connector-java-5.0.8-bin.jar) one back it connects but still having the problem of NOT creating the structure table.


I went further and created the structure table manually and tried to use import file from the GUI, it doesn't work too.





Thank you.

Hi Saif,





if you start JChem Manager from command line with jcman script, the stack trace will be available in that command line window. I need the stack traces for next steps. Note, I have already tested JChem Manager with JChem 5.0.3 and MySql driver 5.1.6 and it worked fine for me.





it doesn't require to copy database driver to JChem lib (We don't use this directory as a path of drivers), but it have to be in the Classpath with correct file system path.

Quote:

I went further and created the structure table manually and tried to use import file from the GUI, it doesn't work too.

I recommend to never create a structure table by hand unless you want further problems for own. ;) Moreover we cannot support your problems in that case.





Regards, Edvard

Hi Edvard,


I created the structure tables using the command line mentioned in the doc http://www.chemaxon.com/jchem/doc/admin/


The error.log file doesn't log any record when I try to use the GUI to create structure table.





The CLASSPATH: If I point my CLASSPATH to the DB Driver residing in tomcat/lib, JChem doesn't work or connect to MySQL db. The only way I manage to make JChem to connect to MySQL DB when I place the Driver in the lib directory of JChem and point the CLASSPATH to that driver.


If you can could you please post you configuration so I can follow it.


Because using my setting the example doesn't display any of the molecule I imported to the structure table created using command line.





Regard, Saif

Hi Saif,





If I understand well, you could create a structure table and import structures with command line tool, but GUI didn't work good for you. It is strange because they use same connection settings which you can find in the .jchem file in <user home>/.chemaxon directory.


We haven't got error.log file for JChem Manager, you can catch the stack trace if you start it from a command line window.


You can check your database tables in command line with 'jcman t' command.





An important question: what like JVM do you use? Can you post me the output of java -version?





Regards, Edvard

Hi Edvard,


Yes you are right, I'm able to use jcman from the command line. I got the example working OK using my created tables. The issue I'm having now is Maximum number of searches allowed per minute. Is that something to do with the academic version?


From my reading about this issue in the example documentation and the forum, I should contact the tech support for license that allow more searches per minute.





I'm using


tomcat 6


java jdk 1.6


MySQL 5.0.51a


Apache 2.2.8














Regards, Saif

HI Saif,





Just to check - you do have an academic package license? Also do know that the academic package license is limited to 3 searches/min.





If you need more searches/min please tell me more about what you are doing. Normally this limit is fine for academic package users. For other uses there may be another free license available, find out about free licensing on this page





Cheers


Alex

Hi Alex,





Yes we have the academic version license.


We are trying to develop a web-based application to perform cheminformatics-based search from our database, including similarity search, substructure search, etc. The project is planned to be hundred percent free service to the whole computational community, so we are expecting the usage will be significant. One example is ZINC database, and thus, small number of searches/min will not be enough. We anticipate at least 100 searches/min, even many more.





Waiting for your advice.





Regards, Saif

Hi Saif,





If you can confirm that there is no login for any functionality we provide and no commercial aspect then I expect we can freely license this under our FreeWeb package. You will need to load a logo on those pages which use our functionality to generate content and link this to "http://www.chemaxon.com/"





Do respond here but if you can confirm then also send an email to me (aa__at__chemaxon__.__com) and I can forward the FreeWeb license





Cheers


Alex

I confirm that this will be a free service. As you may know I work for MD Anderson Cancer Center which is part of University of Texas, based in Houston, TX USA.





If you need more confirmation you can directly contact Dr.Shuxing Zhang at his email address: shuzhang _at_ mdanderson.org


Dr. Zhang is the scientist I work with.





Best regards, Saif

Hi Alex,


Thank you for your help with license. Even though I imported the new license into the installed JChem, I'm still getting the error of "Maximum number of search allowed is exceeded"


Is there any other steps I'm missing more than importing the new License?


Should I reinstall the Jchem?


Please note that I restarted the service too.





The Stack Trace is bellow:





Stack trace:


------------


chemaxon.jchem.db.MaxSearchFrequencyExceededException: Maximum number of searches allowed per minute is exceeded. Please try it later.


at chemaxon.jchem.db.JChemSearch.checkLicense(JChemSearch.java:5191)


at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2437)


at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:2333)


at chemaxon.jchem.db.JChemSearch.access$2000(JChemSearch.java:126)


at chemaxon.jchem.db.JChemSearch$SearchThread.run(JChemSearch.java:535)

Hi Saif,





You have to import the license file for JSP on behalf of the user which runs the tomcat.


The documentation of licensing was improved in JChem 5.0.5 (it was released yesterday) see: http://www.chemaxon.com/marvin/help/licensedoc/install.html , I hope it can help you.





Regards, Edvard

Hi Edvard,


Thank for the hint. The issue of the search limitation is solved.


Still the first question I asked about creating structure table using GUI remains. As I mentioned the dialog box of creating table disappears, the table doesn't get created. The error.log file is blank, i.e nothing get logged into it.


More over JchemManger GUI doesn't allow to do more than one task, I mean if I choose to create table for example, I can't perform different task like import or export. To do that I have to exit completely and launch the JchemManger again, this doesn't sound like normal.





Any help will be appreciated.








Regards, Saif

Hi Saif,





please send me the output of 'java -version' command.


Do you start JChem Manager gui with command line or icon?





Regards, Edvard

Hi Edvard


Here is my java -version command result:





java version "1.7.0"


IcedTea Runtime Environment (build 1.7.0-b21)


IcedTea 64-Bit Server VM (build 1.7.0-b21, mixed mode)





I start the JChem gui with command.





Thank you.





Saif

Hi Saif,





JChem should only be used with Sun Java. Please add the installed Sun JRE bin directory to your PATH variable, and it should appear before the IcedTea Java.





Regards, Edvard

Thank you Edvard.


That solved the problem.





Regards, Saif