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recently there was a nice post-10.00 feature development request:
support for multiple molecular models
- including reading multiple files into one AtomSetCollection
- rotation of individual AtomSet's in the Collection
- alignment in general
Some comments (picked for supporting my suggestion in this email :):
"The answer: It depends on the user and the task they're performing."
"What happens to the scaling factor? Do things get moved off the screen? Wh=
becomes the new center of rotation? What happens to the 'camera' for=20
perspective depth calculations?"
"Jmol is a component"
"I'm a computer engineer not a chemist"
Some applications of support for multiple molecular models:
=2D - manual/algorithmic docking
=2D - superposition of molecules
=2D - fun
=2D - ...
I've had an discussion with Miguel about this, and will now explain a few=20
PLUGINS FOR JMOL
Jmol has a plugin mechanism. This mechanism is aimed to extend the=20
functionality of Jmol 'The Viewer' to do certain things... we all know the=
DirBrowser plugin. Another plugin that has been around for about a year now=
is the RSSViewer plugin. Both these extend the core functionality of Jmol=20
with specific features, dir browsing and browsing chemistry enhanced Rich=20
Site Summery feeds, respectively.
A full list of plugins is available from: http://www.woc.science.ru.nl/cdk/
The name CDK plugin is used there, as the interface is principally CDK base=
but can be used without CDK at all too...
Now, the plugin has access to the data classes, and can 'order' Jmol to=20
display new data (the last e.g. used by the DirBrowser).
Thus, an alignment plugin could have a button "SuperImpose Molecules in=20
AtomSetCollection" which go through all AtomSet's in the Collection, and=20
align them according to some rules.
Thus, 'us' chemistry-pros, would write alignment plugins for certain specif=
tasks. Plugins that come to mind:
=2D - a super impose the molecules in a SDF file
=2D - place ligand in protein active site with method X
=2D - etc
Each plugin would expect certain features of the contents of the=20
AtomSetCollection, but that's all something the Jmol engine need not take=20
Only Jmol has to do, is display the active AtomSetCollection.
The current plugin API does not have a script functionality, but this is=20
something we could add quite easily, and, actually, something I have on my=
TODO list for some time.
(off topic: yes, we could thus with this script feature in the plugin API,=
also make a plugin that will download info from some biochemical database,=
and use script commands to highlight certain features in the PDB file shown=
in Jmol... many possibilities come to mind here (e.g. high light of active=
site)... since a plugin is a self contained component, it can do whatever i=
want, have custom IO for parsing database specific formats and whatever it=
needs to do more...)
Merging of more than one file can be covered by a plugin too.
The big advantage of this setup is that we don't impose many difficult=20
requirements upon the core Jmol development team (aka. Miguel).
2. JMOL AS A JPANEL
A second option would be to write a custom application for a certain tasks,=
but I have a tendency for the above solution, and would like discuss that=20
Ok, so please have a look at one or more plugins, and ask me questions on t=
above, and let's discuss if the suggested setup would work in the settings=
you had in mind for multiple models and alignment.
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