Dear CDK developers,

I tried to import a PDB format file created with GaussView containing the structure of alanine (attached).
This raised an exception:

java.lang.StringIndexOutOfBoundsException: String index out of range: -4
at java.base/java.lang.String.substring(String.java:1841)
at org.openscience.cdk.io.PDBReader.readChemFile(PDBReader.java:397)
at org.openscience.cdk.io.PDBReader.read(PDBReader.java:198)

After looking into it, I think the problem is line 3 in the file that has the property key "COMPND". In the class PDBReader line 396 and following, the functionality tries to parse the rest of the line as a title for the imported compound. But it is not checked whether there is actually something more than just "COMPND" in the line. Maybe, you can add a check for the line length before it is parsed (as it is done above for "REMARK").

If I can be of any further help, please let me know!

Kind regards,
Jonas Schaub

Ala_PDB.txt