jcsearch [old version 5. ?]

Hi chemaxon,

I use a jcsearch old version (5.??), and i reinstall all my computer (under fedora) but jcsearch doesn't work.

Can you help me please ?
Thanks,

Best regards,

Karim.

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I use command :

/jcsearch -q cc -f :Tcd_id DB:molecules --vaguebond:4 --cha
rge:i  -o /var/resultat/res.txt

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And i have errors :

 

Exception in thread "main" java.lang.NoClassDefFoundError: org/dom4j/DocumentExc                             eption
        at chemaxon.reaction.Standardizer.<init>(Standardizer.java:402)
        at chemaxon.jchem.db.TableInfo.getStandardizers(TableInfo.java:1343)

        at chemaxon.jchem.db.JChemSearch.initTable(JChemSearch.java:2904)
        at chemaxon.jchem.db.JChemSearch.init(JChemSearch.java:3639)
        at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2440)

        at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:2340)
        at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:2172)
        at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2199)

        at chemaxon.jchem.Search.searchInDatabase(Search.java:1026)
        at chemaxon.jchem.Search.convert(Search.java:796)
        at chemaxon.jchem.Search.run(Search.java:1338)
        at chemaxon.jchem.Search.main(Search.java:1383)

Caused by: java.lang.ClassNotFoundException: org.dom4j.DocumentException
        at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:205)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:266)____________________

 

Dear Karim,

It seems to be a classpath problem. Could you try a simple search without connecting to a database? E.g.

  jcsearch -q 'C1=CC=CC=C1' -t 'Nc1ccccc1'

Regards,
Peter

Peter,

 

It's OK without database, the result is  : Nc1ccccc1

It's a classpath problem ?

Hi Karim,

 

Please execute "jcsearch" without arguments, it should print the version.

Please also execute:

echo $CLASSPATH

and paste the result here.

Also:

echo $JCHEMHOME

This should not be set normally on Linux.

Please also list the "lib" directory in your jchem folder and look for dom4j*.jar files.

Best regards,

Szilard

 

Hi Szilard,

1) My $CLASSPATH is empty and $JCHEMHOME is empty too.

But i have $PATH :
/usr/lib/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/var/www/vhosts/xxxxx.com/httpdocs/jre1.6.0_11/bin:/root/bin:/var/www/vhosts/xxxxx.com/httpdocs/jre1.6.0_11/bin

(xxxx = my website)

2) In jchem/lib file dom* doesn't exist.
My backup is not good, so i use a good backup and now i have dom* file.

3) Now, i have this error :

Exception in thread "main" java.lang.NoClassDefFoundError: chemaxon/jchem/Search
Caused by: java.lang.ClassNotFoundException: chemaxon.jchem.Search
        at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: chemaxon.jchem.Search. Program will exit.

 
Thanks,

Best regards,
karim

Karim,

Obviously more jar files are missing from the lib directory.

I suggest to obtain a fully intact "lib" directory from an installation package and use that.

Make sure not to remove any files or subderectories from this lib directory.

Even if you do not want to upgrade for some specific reason you can download earlier versions in the "archives" section of the download page.

I hope this helps.

Best regards,

Szilard

 

Hi,

It's right, i have download the archive and it's OK now.

Thanks !