problem with MolImporter

Hi,


I'd like to load an sd file into Molecule objects using MolImporter (JChem 3.2.7) with the following code:

Code:

MolImporter oSDFileImporter = new MolImporter(sInputFile); while(!oSDFileImporter.isEndReached()){     Molecule  oMolecule = oSDFileImporter.read();     System.out.println(oMolecule.toFormat("smiles")); //for test }

When I run it I have a NullPointerException not on the read() function but on the print line. It seems that the isEndReached() doesn't find the end of the source file or I just missed something?


Thank you,


peter

Hi Peter,





Could you send the SD file?





Tamás

Please find attached my sample file.


peter

Hi Peter,





There's no problem with your file, the error is in our system.


The isEndReached() method is misleading: it is not designed for checking the end of the file. You should check whether the molecule given back to you is null or not:

Code:

MolImporter oSDFileImporter = new MolImporter(sInputFile);    Molecule  oMolecule = oSDFileImporter.read();    while(oMolecule != null){        System.out.println(oMolecule.toFormat("smiles")); //for test        oMolecule = oSDFileImporter.read();    }

This way I could read your file.





Tamás

Hi,


Thank you to clarify this point!


Now, I'm curious: what is the purpose of this function?


regards,


peter

It's used in estimating the number of records (see MolImporter.estimateNumRecords() in the API-doc: "If the end of file is already reached ...").


Probably should be a private method.





Tamás