[Biococoa-dev] Re: BCProteinStructure

Philipp Seibel 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:

> 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?

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  
(Sequences, Structures,etc.)

> 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.



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