Success! I have gotten it all to work. Thanks to Rajarshi and Egon for
their suggestions. I will update the web page as soon as possible.
Move everything to Java 1.5 (aka 5.0):
$ java -version
java version "1.5.0_03"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_03-b07)
Java HotSpot(TM) Client VM (build 1.5.0_03-b07, mixed mode, sharing)
$ echo $JAVA_HOME
/home/no228/Tools/Java/jdk1.5.0_03
$ jython
Jython 2.2a1 on java1.5.0_03 (JIT: null)
Compile the latest CDK from CVS using Java 1.5 and add to the CLASSPATH:
$ echo $CLASSPATH
.:/home/no228/Tools/CDK/cdk-cvs-java15.jar
Update pycalculateBCUT.py to reflect recent changes in the CDK API:
"""
from org.openscience.cdk import *
from org.openscience.cdk.qsar.descriptors.molecular import
BCUTDescriptor
from org.openscience.cdk.io.iterator import IteratingMDLReader
from java.io import InputStreamReader
import sys
try:
sdfile=open(sys.argv[1],"r")
except (IOError,IndexError):
print "You need to give the name of an existing .sd file"
sys.exit(1)
bcut=BCUTDescriptor()
bcut.setParameters([1,1])
for mol in IteratingMDLReader( InputStreamReader(sdfile)):
BCUTvalue=bcut.calculate(mol).getValue()
# Create list of values in BCUTvalue
BCUTlist=[str(BCUTvalue.get(i)) for i in range(6)]
# Concatenate BCUTlist around tabs
print "\t".join(BCUTlist)
"""
Regards,
Noel
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