nice. A few comments:
you can just use
monomers[i].getProteinStructure() == monomers[iNext].getProteinStructure()
instead of all these:
( (isHelix(i) && isHelix(iNext)) || (isSheet(i) && isSheet(iNext)) ||
(isTurn(i) && isTurn(iNext)) )
and it's a bit more accurate, since your definition of "isTurn" as (not
Helix and not Sheet) is not quite correct.
Why the removal of the eccentricity/variable radius business?
Bob
On Sat, Oct 6, 2012 at 4:49 PM, Alexander Rose
<alexander.r...@weirdbyte.de>wrote:
> Hi,
>
> better images...
>
> https://www.dropbox.com/s/o5vdr88ebwqqf6o/1CRN_seams.jpg
> https://www.dropbox.com/s/vcqxh6w0fh9ik7s/1CRN_noSeams.jpg
>
> Am 06.10.2012 um 23:44 schrieb Alexander Rose:
>
> Hi,
>
> I created an initial patch that aims to fix the seams between cartoon mesh
> elements of consecutive residues. Attached are two images to illustrate the
> seams. The seams occur because the (lighting) vertex normals are calculated
> for each cartoon mesh elements individually without considering the
> adjacent elements. The patch includes a helper function that smoothes the
> vertex normals for the overlapping vertices two consecutive cartoon meshes.
> I also needed to slightly change the way by which the mesh of turn/loop
> elements is created so that the start/end vertices of two turn/loop
> elements always overlap.
>
> The patch is against revision 17624.
>
> There are problems. I adjust the normals between two consecutive elements
> when constructing the second element's mesh, so the first element's mesh
> has been already created (needed to adjust the normals) and also once
> rendered/drawn. Therefor to see the adjusted normals the meshes need to be
> rendered/drawn again. Just interacting with Jmol, e.g. zooming, naturally
> triggers a redraw. However its not nice initially. An idea. I could trigger
> a redraw in Jmol after cartoon mesh constructions. How? Or do you have
> other suggestions?
>
> Also I need to carefully check if the code works also when individual
> residues are (randomly) displayed/hidden one after the other.
>
> Please let me know what you think!
>
> Best
> Alexander
>
>
> <patch_seams_r17624.txt>
>
> <1CRN_seams.jpeg><1CRN_noSeams.jpeg>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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