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
The documentation notes that SMILES layouts are generated remotely via HTTP.
Is the service providing the force-generated layout storing any information
about these structures?
I wouldn't want sensitive data to be accessed by others.
Many thanks,
David
What is a layout? Jmol uses the CACTUS server at NIH/NCI to translate
SMILES strings to 3D.
On Sat, Feb 2, 2013 at 7:44 PM, N David Brown hubd...@gmail.com wrote:
The documentation notes that SMILES layouts are generated remotely via
HTTP.
Is the service providing the force-generated layout
A force-directed
layouthttp://en.wikipedia.org/wiki/Force-directed_graph_drawing .
It's useful if you don't need the accuracy of molecular dynamics, and
instead just want a semi-realistic layout for interaction with a 3D
molecule.
I'm not familiar with CACTUS. A quick google suggests the service
David,
On InChI, SMILES, and most common IUPAC, the Resolver structure is calculated
by CATVS. Name is look-up.
http://www2.ccc.uni-erlangen.de/software/cactvs/whatis.html
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Feb 2, 2013, at 4:07 PM, N David Brown wrote:
A
Nice concise summary in that link, Otis. Thank you for elucidating.
David
On 2 February 2013 21:34, Otis Rothenberger osrot...@chemagic.com wrote:
David,
On InChI, SMILES, and most common IUPAC, the Resolver structure is
calculated by CATVS. Name is look-up.
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