Hi,

I'm getting the follow warning when reading a PDB file:

[main] WARN  org.biojava.nbio.structure.io.BondMaker - Could not find atoms specified in SSBOND record: [SSBOND:
Atom 1:
	Chain: I
	Residue #: 24
	Ins. Code: 
Atom 2:
	Chain: I
	Residue #: 56
	Ins. Code: 
]

Looking at the code it seems that PDBFileParser::triggerEndFileChecks is being called before PDBFileParser::formBonds. The method triggerEndFileChecks calls assignAsymIds which changes the ID's of the chains and, then the method BondMaker::formDisulfideBonds can't find the chains of the SSBonds, since it has changed by assignAsymIds.

I will try to do a pull request to fix it, but before I need to know what is the best approach to fix it.

thanks.