This is expanding on one of the points that Rajarshi made in his blog (which he followed up here) on the PDB file handling capabilities of the CDK. There are two related topics : reading of PDB format files (the ancient, fixed column-width ATOM files) and the model that these are read into.
The old PDB format is being replaced with mmCIF and/or PDBML formats. Only there are lots of programs that write out this format, so it makes sense to still support it for a while at least.
However, it is a quite nasty format, in some ways. Not so much the fixed column width, but the fact that crystallographers abuse the file format in all sorts of ways. Even simple things like expecting that atom numbers will always increase, may not be true.
So it is not easy making a good reader for PDB files. The current CDK one won't read a file with just ATOM records, for example. Think that's reasonable? Well, tough luck for people that made programs that produce simple files like this.
A more serious problem is the fact that you can't get properly connected ligands from a PDB file. Or easily get at the disordered regions. Or get at the waters. Well, sort of - I suppose that many of these things can be done after reading, with CDK classes.
In some ways - so long as the atoms are read in - anything can be done to the model post-reading. However, the point of having data model classes like Polymer and BioPolymer is to capture some of the complexity of the macromolecule's organisation.
BioPolymer and the PDBReader do a good job of reading and storing the information in the header files (except that it is not always right!). Apart from calling chains 'Strands', some things are done reasonably well. I don't think that ligand atoms should be stored 'loose' as they are, but probably in referenced atom containers.
The real difficulty with modelling proteins lies with representing the hierarchy. One way is 'PMCA' - protein, model, chain, atom. This misses out secondary structure, but it may be too literal to have objects for every concept; the CDK stores the secondary structure given in the header file as IPDBStructure objects - with insertion codes, which is good to see.
However, there are more secondary structures than helix, turn, and strand. I'm never quite sure what the best way to model the more flexible situation, though.
Integration with biojava
It seems a shame that several open source java projects have very little in the way of integration (that I can see). At least on this topic. Of course, Egon (among others) has done work on both both CDK and Jmol, but it concerns me that incompatible ways of doing things lead to projects drifting apart, that should work together.
For example, here is a class I wrote today (for someone else) that uses both biojava and the CDK. It is very much a hack, but the key point is the method makeLigandsFromGroups that takes both a List of biojava.Group objects and a List of IMolecules, along the way converting biojava Atoms to CDK Atoms.
Clearly, biojava has a better interface to its model as you can get a List of the hetatm groups. The CDK, on the other hand, has better support for determining atom types and setting properties on them.