CFParameters construction failure under jython

Hi,

I'm on ubuntu 11.10, with jchem-6.1.3, java version "1.7.0_25" and Jython 2.2.1.

I'm trying to calculate a tanimoto but it doesn't work anymore. (It worked under Jchem_5.11)

 

It sends me this error:

File "tanimoto_min.py", line 21, in ?
File "tanimoto_min.py", line 18, in main

at chemaxon.descriptors.MDParameters.initParameters(MDParameters.java:225)
    at chemaxon.descriptors.CFParameters.initParameters(CFParameters.java:192)
    at chemaxon.descriptors.CFParameters.setLength(CFParameters.java:141)
    at chemaxon.descriptors.CFParameters.<init>(CFParameters.java:73)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
    at java.lang.reflect.Constructor.newInstance(Unknown Source)

java.lang.RuntimeException: java.lang.RuntimeException: Failed to create default XML configuration.

 

I can obtain this error with a code as small as:

#!/etc/jython
 
import sys
import os
 
sys.path.append('/home/florent/ChemAxon/JChem/lib/chemaxon-core.jar')
sys.path.append('/home/florent/ChemAxon/JChem/lib/jchem.jar')
sys.path.append('/home/florent/ChemAxon/JChem/lib/jchem-descriptors.jar')
sys.path.append('/home/florent/ChemAxon/JChem/lib/jchem-reaction.jar')
sys.path.append('/home/florent/ChemAxon/JChem/lib/jchem-sss.jar')
 
from chemaxon.formats import *
from chemaxon.descriptors import *
 
def main():
 
    cfparams = CFParameters()
 
if __name__ == '__main__':
    main()

I tried to replace the cfparams line by :

cfparams = CFParameters('<Parameters Length="1024" BondCount="7" BitCount="2"/>')

And it gives me this error:

File "tanimoto_min.py", line 21, in ?
File "tanimoto_min.py", line 18, in main

at chemaxon.descriptors.CFParameters.processDocument(CFParameters.java:283)
    at chemaxon.descriptors.MDParameters.readFromXmlString(MDParameters.java:915)
    at chemaxon.descriptors.CFParameters.<init>(CFParameters.java:97)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
    at java.lang.reflect.Constructor.newInstance(Unknown Source)

chemaxon.descriptors.MDParametersException: chemaxon.descriptors.MDParametersException: Parameter configuration error.

So my question is: is this normal ?

Is there a new way to call CFParameters ? (Or you don't need to call CFParameters at all anymore ?)

Thank you for any light you can shed on the subject,

Florent.

Dear Florent,

The imported JAR files in your scripts are incorrect. These files are changed in the current JChem version.
I have tested the CFP Tanimoto dissimilarity calculation with merged jchem lib (6.1.3) and the below script was running correctly.

#!/etc/jython
 
import sys
import os
 
sys.path.append('lib_jchem_6.1.3/jchem.jar')

sys.path.append('lib_jchem_6.1.3/com.chemaxon-core.jar')
sys.path.append('lib_jchem_6.1.3/com.chemaxon-io.jar')
sys.path.append('lib_jchem_6.1.3/com.chemaxon-io-smiles.jar')
sys.path.append('lib_jchem_6.1.3/com.chemaxon-common.jar')
sys.path.append('lib_jchem_6.1.3/com.chemaxon-concurrent.jar')
sys.path.append('lib_jchem_6.1.3/com.chemaxon-license.jar')

sys.path.append('lib_jchem_6.1.3/dom4j-1.6.1.jar')
 
from chemaxon.formats import *
from chemaxon.descriptors import *
 
def main():
    print 'Molecules: ' + sys.argv[1] + ' ' + sys.argv[2]
    
    m1 = MolImporter.importMol(sys.argv[1], 'smiles')
    m2 = MolImporter.importMol(sys.argv[2], 'smiles')
    param = CFParameters()
    cfp1 = ChemicalFingerprint(param)
    cfp1.generate(m1)
    cfp2 = ChemicalFingerprint(param)
    cfp2.generate(m2)
    
    dissimilarity = cfp1.getTanimoto(cfp2)    
    print 'Tanimoto dissimilarity:', dissimilarity
 
if __name__ == '__main__':
    main()

Example usage:  $ jython script.py CC CN

Best regards,
Laszlo