Following pull request #376 there is an issue with how the structure identifier string is detected to be a file. If a file happens to be present in working dir with a name coinciding with a PDB id, then StructureIO.getStructure(pdbId) tries to read the file instead of going to the actual PDB id. We've just seen this (unlikely) issue happening in real life and it was very confusing.
A better behavior would be to try first if the string matches a pdb id and only if it doesn't try to see if a file with that name is present.
I've added a test to demonstrate the issue here: josemduarte/biojava@f4a86f2
Following pull request #376 there is an issue with how the structure identifier string is detected to be a file. If a file happens to be present in working dir with a name coinciding with a PDB id, then
StructureIO.getStructure(pdbId)tries to read the file instead of going to the actual PDB id. We've just seen this (unlikely) issue happening in real life and it was very confusing.A better behavior would be to try first if the string matches a pdb id and only if it doesn't try to see if a file with that name is present.
I've added a test to demonstrate the issue here: josemduarte/biojava@f4a86f2