[Biococoa-dev] BCProteinStructure

[Koen van der Drift]

Hi,

Just noticed a set of new classes have been added by Philipp to 
represent protein structures. Nice work! I assume these are to 
facilitate the reading of PDB files? Although I can see a wider use as 
well. What I really like is that the introduction of a BCAtom class 
will allow the definition of modifications and features on the 
atom-level (think oxidation, deamidation, di-sulfide bridges, 
DNA-damage). So it might be useful to incorporate the BCAtom class in 
BCSymbol.

A few small comments (also see the 'new files' entry in the BioCocoa 
dev docs):
All headers should be public in the Target (I already fixed this in cvs)
BCFoundation should only import the Foundation headers, not all Cocoa 
headers (also fixed)
@class declarations are enough in headers, unless you subclass another 
class, then you need to use #import (also fixed)

One last question, since BCResidue is basically an amino acid, why not 
subclass BCAminoAcid? Or even, make BCResidue a subclass of BCSymbol, 
and make BCAminoAcid and BCNucleotide subclasses of BCResidue. Also, 
BCChain seems to be a replication of BCSequence so I am not sure yet 
what its added value can be.

Other then that, I think it is an excellent addition to BioCocoa.

cheers,

- Koen.