Dear CDKers,
I'm facing several errors happening when writing (because of wrong
reading?) a SDF file.:
- When a Group Abbreviation is used for a molecule, well it seems the
CDK set this abbreviation as atomic symbol when writing back the
molecule to MDL format, eg:
(...)
2.1012 -2.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
(...)
G 15 10
Ph
(...)
Becomes the following when using SDF writer:
2.1012 -2.6351 0.0000 Ph 0 0 0 0 0 0 0 0 0 0 0 0
- When the bond stereochemistry is set to 4 (either up or down), a CDK
exception occurs when writing back the molecule. Here is the exception:
org.openscience.cdk.exception.CDKException: Exception while writing
MDL file: Exception while writing MDL file: null
at org.openscience.cdk.io.SDFWriter.write(SDFWriter.java:171)
at sa2.core.CDKReaderBugTest.testCDK(CDKReaderBugTest.java:76)
at sa2.core.CDKReaderBugTest.main(CDKReaderBugTest.java:95)
Caused by: org.openscience.cdk.exception.CDKException: Exception while
writing MDL file: null
at org.openscience.cdk.io.MDLWriter.write(MDLWriter.java:184)
at org.openscience.cdk.io.SDFWriter.writeMolecule(SDFWriter.java:201)
at org.openscience.cdk.io.SDFWriter.write(SDFWriter.java:165)
... 2 more
Caused by: java.lang.NullPointerException
at org.openscience.cdk.io.MDLWriter.writeMolecule(MDLWriter.java:297)
at org.openscience.cdk.io.MDLWriter.write(MDLWriter.java:178)
... 4 more
I think the stereo is in cause because the NullPointerException
occures here in the MDLWriter:
297 switch(bond.getStereo()){
I've used the following code snippet which read a file containing 5
molecules that illustrate the problem:
public class CDKReaderBugTest {
public static void testCDK(File f) throws Exception {
FileInputStream ins = new FileInputStream(f) ;
IteratingMDLReader reader = new IteratingMDLReader(ins,
DefaultChemObjectBuilder.getInstance());
CDKHydrogenAdder hAdder = null ;
IMolecule mol = null ;
while (reader.hasNext()) {
mol = (IMolecule) reader.next() ;
// Clean molecule
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
if(hAdder == null) {
hAdder = CDKHydrogenAdder.getInstance(mol.getBuilder()) ;
}
hAdder.addImplicitHydrogens(mol);
// Show SDF
StringWriter sw = new StringWriter() ;
SDFWriter mw = new SDFWriter(sw) ;
try {
mw.write(mol) ;
}
catch(Exception e) {
System.out.println("Error while writing MDL:
"+e.getMessage()+" "+n);
e.printStackTrace(System.out);
}
mw.close() ;
String mdl = sw.toString() ;
System.out.println("Atom count: "+mol.getAtomCount());
System.out.println("MDL: "+mdl);
}
reader.close();
}
public static void main(String [] args) {
File f = new File("/home/vince/Desktop/testLMA.sdf") ;
try {
testCDK(f);
}
catch (Exception ex) {
Logger.getLogger(CDKReaderBugTest.class.getName()).log(Level.SEVERE,
null, ex);
}
}
}
Please, let me know if I'm doing something wrong or if these issues
are actual bugs.
Cheers ;)
Vincent
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