XML_PARSING ERROR

Hi Chemaxon,

I had installed Chemaxon
academic license user version installed on Linux 64 bit system. Whenever
I am trying to use fragmenter from the bin of Jchem but I am getting
stucked with the error ( pasted below).  I am not clear about the XML
parser that is showin here. Pease help me to fix this. THANK YOU


[lalitk@cadd3 ILSTGFB1]$ frag -c TGFB1.sdf -x 10 -f sdf /home/lalitk/PROJECTS/CoETB/FBDD/ILSTGFB1 TGFB1frag.sdf
org.dom4j.DocumentException: Error on line 1 of document file:///home/lalitk/PROJECTS/CoETB/FBDD/ILSTGFB1/TGFB1.sdf : Content is not allowed in prolog. Nested exception: Content is not allowed in prolog.
        at org.dom4j.io.SAXReader.read(SAXReader.java:482)
        at org.dom4j.io.SAXReader.read(SAXReader.java:264)
        at chemaxon.fragmenter.FragmenterConfig.readConfig(FragmenterConfig.java:271)
        at chemaxon.fragmenter.FragmenterConfig.<init>(FragmenterConfig.java:105)
        at chemaxon.fragmenter.Fragmenter.main(Fragmenter.java:1261)
Nested exception:
org.xml.sax.SAXParseException: Content is not allowed in prolog.
        at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
        at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
        at org.dom4j.io.SAXReader.read(SAXReader.java:465)
        at org.dom4j.io.SAXReader.read(SAXReader.java:264)
        at chemaxon.fragmenter.FragmenterConfig.readConfig(FragmenterConfig.java:271)
        at chemaxon.fragmenter.FragmenterConfig.<init>(FragmenterConfig.java:105)
        at chemaxon.fragmenter.Fragmenter.main(Fragmenter.java:1261)
Nested exception: org.xml.sax.SAXParseException: Content is not allowed in prolog.
        at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
        at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(Unknown Source)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
        at org.dom4j.io.SAXReader.read(SAXReader.java:465)
        at org.dom4j.io.SAXReader.read(SAXReader.java:264)
        at chemaxon.fragmenter.FragmenterConfig.readConfig(FragmenterConfig.java:271)
        at chemaxon.fragmenter.FragmenterConfig.<init>(FragmenterConfig.java:105)
        at chemaxon.fragmenter.Fragmenter.main(Fragmenter.java:1261)
java.io.IOException: Error occured during XML parsing.

Regards,
Lalith Kumar K

lalith wrote:

[lalitk@cadd3 ILSTGFB1]$ frag -c TGFB1.sdf -x 10 -f sdf /home/lalitk/PROJECTS/CoETB/FBDD/ILSTGFB1 TGFB1frag.sdf

After the "-c" command line option an XML config file should be specified, not an SDF. Please try it with a config file and let us know if it works.

Example:

$ fragment -c fragmenter_config.xml -x 10 -f sdf input_file.sdf  

See also: http://www.chemaxon.com/jchem/doc/user/fragment_recap.html#config

The error message is not really informative, we should improve that.

Zsolt

Thank you solt,

As I am a newbie to chemaxon I am unable to do that. Meanwhile I got up with one more problem where I am unable to create result as output(sdf/cxsmiles) file. Anyhow I am getting the results got displayed in the running terrminal, but i need that to be as output file to easy handling of multi mol files. This is the error I am stopped with:

 

[lalitk@cadd3 ILSTGFB1]$ frag -c fragmenter.xml TGFB1.sdf -x 10 -f sdf "/home/lalitk" out.sdf
Exception in thread "main" java.io.IOException: Could not read file or structure string: /home/lalitk
/home/lalitk (Is a directory)
    at chemaxon.util.ConfigUtils.getMolImporter(ConfigUtils.java:462)
    at chemaxon.util.ConfigUtils.getTargetMolImporter(ConfigUtils.java:378)
    at chemaxon.util.ConfigUtils.getTargetMolImporters(ConfigUtils.java:498)
    at chemaxon.util.ConfigUtils.getTargetMolImporters(ConfigUtils.java:478)
    at chemaxon.fragmenter.Fragmenter.main(Fragmenter.java:1332)
[lalitk@cadd3 ILSTGFB1]$ frag -c fragmenter.xml TGFB1.sdf -x 10 -f sdf /home/lalitk out.sdf
Exception in thread "main" java.io.IOException: Could not read file or structure string: /home/lalitk
/home/lalitk (Is a directory)
    at chemaxon.util.ConfigUtils.getMolImporter(ConfigUtils.java:462)
    at chemaxon.util.ConfigUtils.getTargetMolImporter(ConfigUtils.java:378)
    at chemaxon.util.ConfigUtils.getTargetMolImporters(ConfigUtils.java:498)
    at chemaxon.util.ConfigUtils.getTargetMolImporters(ConfigUtils.java:478)
    at chemaxon.fragmenter.Fragmenter.main(Fragmenter.java:1332)

Please help me out. Thank you

 

Regards,

Lalith.k

 

lalith wrote:

[lalitk@cadd3 ILSTGFB1]$ frag -c fragmenter.xml TGFB1.sdf -x 10 -f sdf "/home/lalitk" out.sdf

The syntax is not correct. Try something like this:

$ frag -c fragmenter.xml -x 10 -f sdf "/home/lalitk/TGFB1.sdf" -o out.sdf

In this case
 - "/home/lalitk/TGFB1.sdf" is the input file
 - out.sdf is the output file
 - fragmenter.xml is the configuration file.

I hope this helps.
Zsolt

yes yes...! I got it Thank you lot....