InChi and InChiKey by Ajax/JSP

API Java - Jchem 15

 

I can calculate the InChI and InChiKey with Java, but I can't calculate InChI and InChiKey through Ajax with a JSP page. How should I proceed?

 

java.lang.NoSuchMethodError: net.sf.jniinchi.JniInchiWrapper.loadLibrary(Ljava/lang/String;)V

at chemaxon.marvin.io.formats.inchi.Inchi.loadNative(Inchi.java:172)

at chemaxon.marvin.io.formats.inchi.Inchi.install(Inchi.java:75)

at chemaxon.marvin.io.formats.inchi.Inchi.<clinit>(Inchi.java:246)

at chemaxon.marvin.io.formats.inchi.InchiExport.<clinit>(InchiExport.java:35)

at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:264)

at chemaxon.formats.MFileFormat.createExportModule(MFileFormat.java:1123)

at chemaxon.formats.MFileFormatUtil.createExportModule(MFileFormatUtil.java:783)

at chemaxon.formats.MolExporter.init(MolExporter.java:514)

at chemaxon.formats.MolExporter.<init>(MolExporter.java:406)

at chemaxon.formats.MolConverter.init(MolConverter.java:712)

at chemaxon.formats.MolConverter.<init>(MolConverter.java:550)

at chemaxon.formats.MolConverter$Builder.build(MolConverter.java:341)

at MolConvert.MolConvert.gera(MolConvert.java:94)

Hi,

Could you please clarify your usage, in what circumstances would you like to call that function? It seems that the inchi library is not found on the Molconvert's host machine. For some reference: Chemaxon InChI Documentation.

Regards,
Domi

In Java the code below works:

public static void main(String[] args) {


        String smiles = "CCC";



        OutputStream fs = new ByteArrayOutputStream();



        MolConverter.Builder mcbld = new MolConverter.Builder();
        mcbld.addInput(new ByteArrayInputStream(smiles.getBytes()), "smiles");
        mcbld.setOutputFlags(MolExporter.TEXT);
        mcbld.setOutput(fs, "inchikey");


        try {
                MolConverter mc = mcbld.build();
                mc.convert();
                mc.close();
        } catch (IOException e) {
                e.printStackTrace();
        }



        System.out.println(fs.toString());
}

OUTPUT: InChIKey=ATUOYWHBWRKTHZ-UHFFFAOYSA-N

 

But in JSP the same code does not work:

<%
	String smiles = "CCC";



        OutputStream fs = new ByteArrayOutputStream();



        MolConverter.Builder mcbld = new MolConverter.Builder();
        mcbld.addInput(new ByteArrayInputStream(smiles.getBytes()), "smiles");
        mcbld.setOutputFlags(MolExporter.TEXT);
        mcbld.setOutput(fs, "inchikey");


        try {
                MolConverter mc = mcbld.build();
                mc.convert();
                mc.close();
        } catch (IOException e) {
                e.printStackTrace();
        }



        out.write(fs.toString());
%>

OUTPUT: 

Exception in thread "main" java.lang.NoSuchMethodError: net.sf.jniinchi.JniInchiWrapper.loadLibrary(Ljava/lang/String;)V
	at chemaxon.marvin.io.formats.inchi.Inchi.loadNative(Inchi.java:172)
	at chemaxon.marvin.io.formats.inchi.Inchi.install(Inchi.java:75)
	...

Find out where was the bug!

 

My team was also using the API Chemistry Development Kit (CDK version 0.99.1) containing another version of Chemaxon net.sf.jniinchi package containing the JniInchiWrapper class. This conflict was generating the NoSuchMethodError.

 

I removed the .jar package of CDK and began to work.

 

But...

 

When I use MolConvert to generate InChiKey, it creates a directory and a .dll file in C:\Users\{username}\chemaxon\lib\inchi-1.3\inchi64.dll

 

Everything works normally, but if I restart Tomcat, gives the following error: Native Library C:\Users\{username}\chemaxon\lib\inchi-1.3\inchi64.dll already loaded in another classloader

 

Why does it happen? How to fix it?

 

I am using:

Windows 10

Tomcat 7.0.61

Java 8

API Jchem 15.9.7.0

Dear Silasyudi12!

   Unfortunately I could not reproduce you problem. Could you provide us a stacktrace? Or could you send what processes use the dll? (For example with this tool: https://technet.microsoft.com/en-us/sysinternals/bb896653.aspx )

   It is also possible that the resource is used by multiple class loaders in tomcat, and for that there might be a workaround by adding the required library to the /lib folder and this way this library is shared between all the classloaders of tomcat.

   I hope we can move forward with your issue.

Regards:
Balázs 

Hi Silas!

Do I understand correctly that you moved to Linux and you do not need a solution on Windows? If not, please, provide the stacktrace of the exception thrown (that Balázs asked in his earlier reply).

Regards,

Zsuzsa