Obtaining image from a Molfile

Hi,

I am trying to get image from a molfile. Here is my codes;

 public static byte [] getStructureImage(String molfile, String format){
MolHandler mh=null;
try{
System.out.println("molfile="+molfile);
mh=new MolHandler(molfile);
System.out.println("molhandler established");
}catch(MolFormatException me){
return null;
}
Molecule mol=mh.getMolecule();
return mol.toBinFormat(format);
}

The error message is:

Jun 2, 2011 10:04:51 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [jsp] in context with path [/erms] threw exception [javax.servlet.ServletException: java.lang.NoClassDefFoundError: chemaxon/formats/MolFormatException] with root cause
java.lang.ClassNotFoundException: chemaxon.formats.MolFormatException
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1676)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1521)
at org.apache.jsp.jsp.structureImage_jsp._jspService(structureImage_jsp.java:119)
at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:419)
at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:390)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:333)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:304)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:240)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:164)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:462)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:164)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:563)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:399)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:317)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:204)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:311)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)

 

I also attached my mol file.

Please advise!

Ben

 

I think, the marvinbeans.jar, and the files from the lib directory of marvinbeans package are not in the classpath of the used webcontainer, are they?

Would you please be more specific how I should deal with it? Do you mean MarvinBeans.jar and marvinbeans directory in JChem package should be copied to context (in may case erms)/WEB-INF/? I am confused.

I use Tomcat as my web server and the project called erms. I have chosen all the jars in JChem package as my library in Eclipse project.

Hi,

We figured it out. It was not marvinbeans.jar. The jchem.jar needs to be in classpath in tomcat. Once we add the jchem.jar, it worked.

Ben Li