On Sunday 23 November 2003 21:08, [EMAIL PROTECTED] wrote:
> French translation
The French translation for the b6 branch please... That can be checked out
using:
cvs -d'bla' co -r b6 -d Jmol-b6 Jmol
The -r option defines the branch to check out. If omitted, it takes the
default, which is the HEAD branch. The -d option defines the directory name
that is locally created, and the last 'Jmol' is the module name...
> and porting 'old' stuff to the new tree sound both good to me.
We'll need to coordinate this with Micheal, who is currently doing most work
on HEAD... From his email to jmol-users this is the list of things to do:
> This release continues to have the following functional limitations:
> * Only supports .xyz, .mol, and .pdb files
These three file IO are Jmol specific IO classes... the rest of the IO is
covered by CDK. But not all Jmol IO in b6 is yet implemented in CDK...
All classes that subclass org.openscience.cdk.io.DummyReader need to be ported
from Jmol b6 branch to CDK cvs...
> * Does not handle animations
This is Jmol specific...
> * Does not handle crystal cells
This is both in Jmol as in CDK... Because Jmol is now based on CDK, the data
storage is on CDK, but rendering is still in Jmol. What needs to be done here
is:
1. org.openscience.cdk.Crystal needs a holder for symmetry operations
2. the Jmol 3D renderer needs to be extended so that it can display more than
one unit cell (called crystal box in b6), and apply the symmetry
operations mentioned in 1.
3. deal with special features like in case of molecular crystal, forcing all
molecule atoms to be placed inside the unit cell, thus breaking up the
molecules into fragments... as is the default in b6
> * Will not automatically recognize protein secondary structures
This is a bit of bioinformatics that needs to be implemented... Micheal has a
reference for this for an algorithm.
> * Will not render isosurfaces
HEAD can display dot surfaces, and this can be extended to isosurfaces too,
but two things need to be done:
1. calculation of the points on the surface
2. rendering using triangles instead of just dots
(Miguel, right?)
> * Does not handle nucleotide shapes
Not sure what Micheal means with this.
> Could you please include me to the developers team so that
> I could get the last CVS version?
I've just added you.
> In Eclipse I get a write access problem while trying to synchronize the
> project. So I will try to get an idea of the current version of the software
> and its source code. Thanks and cheers,
Though not as frequent as in the last year, Micheal and I tend to be online on
the #cdk IRC channel on irc.freenode.net network (see www.freenode.net)...
On that channel are several CDK developers often online too... Questions can
be asked there about CDK and Jmol, and on the email list too...
One last thing:
- if you want to work on file IO or on the Crystal bit, I need to make you a
CDK developer too, just let me know...
Ok, enough for now... have to go offline...
Egon
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