Hi
The development version of our LICSS v3.2 program currently uses CDK 1.5.6.
To provide molecule input/editing facilities I have been using Stefan's
JChemPaint hotfix - jchempaint-hotfix-3.4.jar which works very effectively
with cdk-1.5.6.jar. I tried using the new CDK 1.5.8 release and found that,
whilst in general Smiles was generated correctly, there was an error for
all molecules containing Radium (which LICSS uses as a proxy R-Group
indicator for enumeration). To investigate this further, I ran the
JChemPaint hotfix as a standalone program using cdk-1.5.8.jar (in which I
had to include the apache commons cli jar to get it to run). I then tried
using the 'Create SMILES' command for a series of elements singly bonded to
Carbon. The following elements generated the expected Smiles: Li, Na, K,
Rb, Mg, Ca, Co, Cu, Zn, B, C, N, O, P, S, Ga, Ge, As, Se, In, Sn, Te, Tl.
However, the following all failed with the error: "Error while creating
SMILES: the number of hydrogens must be positive": Cs, Fr, Be, Sr, Ba, Ra,
Sc, Ti, V, Cr, Mn, Fe, Ni, Al, Si, Sb, Pb, Bi, Po. I must admit, I can't
see what distinguishes the successes from the fails chemically.
If it's any help, the error trace caught when calling JChemPaint from LICSS
includes the following:
Unexpected exception caught in CdkInterfaceDll -
getEditAsSmilesCdkInterfaceDll(const char * componentId):
java.lang.IllegalArgumentException: the number of hydrogens must be positive
at uk.ac.ebi.beam.AtomBuilder.hydrogens(AtomBuilder.java:220)
at org.openscience.cdk.smiles.CDKToBeam.toBeamAtom(CDKToBeam.java:203)
at org.openscience.cdk.smiles.CDKToBeam.toBeamGraph(CDKToBeam.java:149)
at
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:374)
at
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:330)
Incidentally,is there a JChemPaint release available/planned for use with
the CDK 1.6.x series?
Best regards
Kevin
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