[Biococoa-dev] Re: BCProteinStructure
biococoa at bioworxx.com
Wed May 11 06:34:07 EDT 2005
sorry not mentioning the addition yet, but my diploma thesis is
coming to an end and i'm very busy. Perhaps you noticed the time i
checked the new classes in ;-), i needed some time to relax in the
evening, so i did something productive ..... programming new biococa
structures ;-) .....
Am 11.05.2005 um 04:13 schrieb Koen van der Drift:
> 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?
thats what i want them for.
> 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.
i completly agree. we just have to specify how to make annotations in
general. really important for nearly every structural class
> 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
> 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.
> - Koen.
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