So in short. They do not have to have any database structure to convert
SMILES to 3D. I don't know the algorithm used.
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Ok thanks Bob.
I've written a force-directed layout mechanism to avoid any concerns over
sensitive data being transmitted from my application.
It calls JmolNode#set(x,y,z) to set the generated positions.
Could someone please tell me how I can display a JmolMolecule in a Viewer/
JmolViewer?
Digging further, it looks like loading as xyz is the way to go. I believe
this can be used with (Jmol)Viewer#loadInline(strXyz).
How can xyz format be output from a JmolMolecule instance programmatically?
David
On 3 February 2013 13:30, N David Brown hubd...@gmail.com wrote:
Ok thanks Bob.
I couldn't find a way to export a JmolMolecule as xyz unless it's in a
viewer already.
I've written a small function to do it, but there's a problem: there's no
way to get x,y,z coordinates out from a JmolNode instance.
Can a JmolNode instance be safely casted to some ..Atom.. type that
contains
Well, both Atom and SmilesAtom extend Point3f and Tuple3f and seem to be
the only implementations of JmolNode. So I'll cast to Tuple3f unless anyone
suggests a reason not to.
David
On 3 February 2013 14:14, N David Brown hubd...@gmail.com wrote:
I couldn't find a way to export a JmolMolecule as
I meant cast to a SmilesAtom then read from that.
On 3 February 2013 14:27, N David Brown hubd...@gmail.com wrote:
Well, both Atom and SmilesAtom extend Point3f and Tuple3f and seem to be
the only implementations of JmolNode. So I'll cast to Tuple3f unless
anyone suggests a reason not to.
This all seems to work well, the xyz is generated and loaded successfully.
On 3 February 2013 14:29, N David Brown hubd...@gmail.com wrote:
I meant cast to a SmilesAtom then read from that.
On 3 February 2013 14:27, N David Brown hubd...@gmail.com wrote:
Well, both Atom and SmilesAtom
Sorry, I did not notice that the first post of this note had Markus' slides
attached! Here's the note without the huge attachment.
This is still a bit long, but it might be useful to the list and David's recent
questions re Resolver. It's a brief email interview with Markus Sitzmann that I
did
I'm trying to add bonds explicitly to a structure loaded in .xyz format.
The structure intentionally has unrealistic atom positions.
The structure is loaded like so:
myAppConsole.execute(set autobond OFF);
myViewer.loadInline(molAsXyz);
The problem is that the viewer loads N atoms as N
Hi David
I don't know about doing this at the development level, but with scripting he
regular app or applet:
xyz format does not provide connectivity (bonds)
mol format is also quite simple and does include bond information
Hi Angel,
Yes I'm aware xyz doesn't provide connectivity information, that's why I
disabled autobond so non were predicted. I'm circumventing the CACTVS
system so SMILES structures can have positions generated locally instead
using a handcrafted method.
Maybe mol format will solve the problem
David, please switch to the developer list. This is the user list. Not a big
deal.
Sent from my stupid iPhone
On Feb 3, 2013, at 1:00 PM, N David Brown hubd...@gmail.com wrote:
Hi Angel,
Yes I'm aware xyz doesn't provide connectivity information, that's why I
disabled autobond so non
Apologies Bob, will do.
David
On 3 February 2013 20:44, Bob Hanson hans...@stolaf.edu wrote:
David, please switch to the developer list. This is the user list. Not a
big deal.
Sent from my stupid iPhone
On Feb 3, 2013, at 1:00 PM, N David Brown hubd...@gmail.com wrote:
Hi Angel,
Yes
The only thing I would add is that disabling java in firefox is no longer
necessary. The browser will simply wait to start it until you request it to do
so.
I now that this breaks frameless (hidden) applets.
Sent from my stupid iPhone
On Feb 2, 2013, at 7:50 PM, Eric Martz
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