Is Fragmenter available for JChem eval?

All,

I just downloaded the eval copy of JChem (download link is on the Fragmenter page) but I don't see any evidence of Fragmenter.  I tried the examples, etc but have gotten nowhere.  What am I missing?

Thanks,

Elliot

Fragmenter is currently available in the form of API (chemaxon.fragmenter) and some command line tools (fragment, fragmentstatistics, molfragment).

Gyuri,

Thanks for your response!

Unfortunately I do not see chemaxon.fragmenter.  I am on windows and only see ChemAxon.NET.Base.dll, ChemAxon.NET.dll, ChemAxon.Net.IKVM.dll, and ChemAxon.NET.Windows.Forms.dll (in addition IKVM dll's, Examples folder, JDBCDrivers folder, PublisherPolicies Fodler, x64 folder, and x86 folder).

My attempts to call fragmenter all met with unknown errors.

Did I download the wrong eval?  This seems odd.

Thanks again!

Elliot

Dear Elliot,

Please try to refer jchem.dll, it contains the original JChem API including the fragmenter.

Best regards,

Gabor Vasko

The .NET API installer just gives you the pure API, desktop applications and command line scripts are included with the Java version only.

Dear Gyuri,

I'm a new user for this software Fragmenter (in Jchem 5.8 version). 

When i gave "fragment -c Fragmenter.xml input.mol -f sdf:-a -o fragments1.sdf" windows command line.... the output file gives errror of access denied...

but when i give "fragment -c Fragmenter.xml input.mol" i can see the results... there is some conflict happening in windows. Can you please help me with his?

I'm also attaching the screenshot of this error message... hope you know abou this? For your info I'm Using vista OS.

Regards,

Ankit

Ankit, I think you don't have the rights to write the output file on that partition/directory.

Zsolt

Hi Zsolt thanx for reply..

I did following things

1) Installation of JChem 5.8 in C drive of my computer... and it lies in the program files directory..

2) I followed the instructions given in the user guide where it asked me to use the command line for fragment examples..

so if you say that i dont have rights to write output file in the partition/directory..

then what you suggest me to do?

I mean do i have to un unistall and reinstall in other drive? or can you suggest me some command line to wirte the result file in other directory?

Waiting for your reply

Regards,

Ankit

No need to reinstall anything.

Write the result file to your user home directory.

Zsolt

Dear Zlot,

My problem with windows app is working okay now... I was trying to automate the fragmentation activity using linux system. I encountered following problem. 

Please help if you can 

Waiting for your reply

Regards,

Ankit

Try this:

cd ChemAxon/JChem/bin
./fragment -c FragmenterAll.xml input.mol 

 I hope this helps.

Zsolt

cd ChemAxon/JChem/bin
./fragment -c FragmenterAll.xml input.mol 

[root@utlab3 bin]# ./fragment -c ./../examples/fragmenter/Fragmenter.xml ./../examples/fragmenter/input.mol
Exception in thread "main" chemaxon.license.LicenseException: No license file found.
Product name: Structure Search
License path:
Please contact sales _at_ chemaxon.com to obtain the corresponding license.
Students and academic researchers are entitled of free use
through our Academic Package, for more information
please visit: http://www.chemaxon.com/acpack_conditions.html />        at chemaxon.license.LicenseHandler.checkLicense(LicenseHandler.java:514)        at chemaxon.sss.search.MolSearch.checkLicense(MolSearch.java:1762)
        at chemaxon.sss.search.MolSearch.setQuery(MolSearch.java:373)
        at chemaxon.fragmenter.Fragmenter.createCBS(Fragmenter.java:898)
        at chemaxon.fragmenter.Fragmenter.init(Fragmenter.java:404)
        at chemaxon.fragmenter.Fragmenter.<init>(Fragmenter.java:387)
        at chemaxon.fragmenter.ExhaustiveFragmenter.<init>(ExhaustiveFragmenter.java:204)
        at chemaxon.fragmenter.Fragmenter.main(Fragmenter.java:1293)
[root@utlab3 bin]#

it seems i need some license to run it... so I have to apply for new license or can i use my academic license for windows for this purpose... because while using the windows version i did not gave any license but it worked autometically by changing the directory as you had suggested...! can you comment upon this?

You can find help on license file installation here: http://www.chemaxon.com/marvin/help/licensedoc/install.html

Vikoria