Aleix Lafita

After looking a bit more into these methods, it seems that the main problem is their documentation, as they seem to be differently used when parsing from PDB or mmCIF...

Steps to be made: 1. All classes that are **Jmol** specific should be moved to **structure-gui** module and must contain the word **Jmol** in their name. 2. All methods and...

Yes, it is currently what we are using for symmetric repeats in internal symmetry. For alignments it would be a bit more involved to include gaps in the **Identifier Ranges**,...

I already implemented a test for the `Structure` serialization and it is working. You might want to take a look at it (https://github.com/biojava/biojava/blob/master/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java). Note that your Test Class is not...

Related to #673, #676 and #693

Ok @lukeczapla, you are right! It seems that the `StackOverflowError` occurs when the `Structure` is parsed from an MMCIF or MMTF file format, but not from a PDB file format...

Yes you should try to use mmCif where possible, PDB format is now legacy and should be avoided. The default in BioJava is MMTF, and apparently that is the one...

For the moment, to avoid the problem you can set the parsing file format as mmCif (not MMTF) and you should be able to serialize the Structure objects without problem....

I have been looking into what might be causing the `StackOverflowError` when calling the `writeObject()` method and it seems that objects referring to one another (recursively) is the most probable...

@pwrose you are right, the bonds are creating the `StackOverflowError`. If I set the bond parsing as true for the MMCIF or PDB formats the error appears, as for MMTF....