Hi Egon,
the graphical image for the BioJava data model in that blog is not
completely correct. It is true that it follows the
Interface/Implementation approach,but the data model is more
hierarchical than shown on that image.
Structure
|
Models(s)
|
Chain(s)
|
Group(s)
|
Atom(s)
There are different iterators and utiliy classes that allow to access
arrays of Atoms or iterate over all amino acids, do calculations etc.
It can deal with ATOM vs SEQRES issues and a couple of other things.
For more docu on what you can do with the BioJava structure modules
see here:
http://biojava.org/wiki/BioJava:CookBook#Protein_Structure
Andreas
On Thu, Aug 21, 2008 at 4:37 AM, Egon Willighagen
<[EMAIL PROTECTED]> wrote:
> Hi all,
>
> the PDBReader of Jmol is of high quality, and certainly much better
> than the CDK one. There is also the BioJava PDBReader, and the
> question was popped if the CDK should adopt the BioJava or Jmol
> reader, both better, though I am not familiar with the BioJava one...
> now, that would involve conversion of data model, which Gillean just
> blogged about the data models, but still has questions (so do I):
>
> http://gilleain.blogspot.com/2008/08/on-models.html
>
> Anyone who can share some experiences between the differences in
> quality between the BioJava and the Jmol PDB readers?
>
> Egon
>
> --
> ----
> http://chem-bla-ics.blogspot.com/
>
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