[Biococoa-dev] peptides and proteins
Koen van der Drift
kvddrift at earthlink.net
Tue Sep 7 19:27:38 EDT 2004
On Sep 7, 2004, at 6:38 PM, Alexander Griekspoor wrote:
> I get it, and that works indeed fine. The problem here is that the
> moment you get an array with fragments, you loose all info about the
> digest. A digest object could encapsulate that. But indeed you're
> right and perhaps you're only interested in sequences. So maybe we
> should offer both options. A BCDigest could also be implemented as an
> encapsulated message, storing both the enzymes, the sequence, and the
> fragments. You then would have to options, either send the
> BCUtilDigester the individual items and get back an array with
> fragments, or send it a digest object and let the digester fill it's
> fragment array. Or do you think keeping the digest info around is
> something we should completely hand of to the app developer?
I never thought of keeping the digest object around, but if the
developer wants to keep it, why not?
BCProtease *protease = [[BCProtease alloc] initWithSequence: aSeq]
[protease setEnzyme: @trypsin]; // or based on a popup menu
NSArray *thePeptides = [protease digestResult];
[protease release]; // optional
> The other think I would like to add to a BCSequence is the info of
> which enzyme produced the 5' end and which the 3' end.
Yes, that's taken care of in the plist using the CleaveDirection key.
We have to add some code like:
[newPeptide setCleavedAt: cleavedAtN]; // or 5' or 3' or
> Therefore, I proposed the BCFragment class, which could be a subclass
> of BCSequence that stores these additional BCEnzyme variables (which
> can also be nil by default if the end is untreated).
The BCFragment would be similar to a separate BCPeptide class, correct?
Then let's create both classes if that makes it easier.
> The nice thing is that for the BCDigest story above, nothing changes
> still get an array of BCSequences returned, but as a convenience the
> digest object fills in which enzyme produced the ends.
> Very nice indeed, the plists are definitely the way to go. Still, for
> restriction enzymes instantiating 600 enzymes each time would be to
> expensive I think, so that's where it would be nice to instantiate
> once from the plist and keep the objects around in a static
I'm not familiair with restriction enzyms, can you explain why you have
to instantiate 600 enzymes if you're just using one?
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