Re: [Jmol-users] Are SMILES communications private?

2013-02-03 Thread Bob Hanson
So in short. They do not have to have any database structure to convert SMILES to 3D. I don't know the algorithm used. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download

Re: [Jmol-users] Are SMILES communications private?

2013-02-03 Thread N David Brown
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?

Re: [Jmol-users] Are SMILES communications private?

2013-02-03 Thread N David Brown
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.

Re: [Jmol-users] Are SMILES communications private?

2013-02-03 Thread N David Brown
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

Re: [Jmol-users] Are SMILES communications private?

2013-02-03 Thread N David Brown
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

Re: [Jmol-users] Are SMILES communications private?

2013-02-03 Thread N David Brown
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.

Re: [Jmol-users] Are SMILES communications private?

2013-02-03 Thread N David Brown
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

[Jmol-users] Are SMILES communications private?

2013-02-02 Thread N David Brown
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

Re: [Jmol-users] Are SMILES communications private?

2013-02-02 Thread Robert Hanson
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

Re: [Jmol-users] Are SMILES communications private?

2013-02-02 Thread N David Brown
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

Re: [Jmol-users] Are SMILES communications private?

2013-02-02 Thread Otis Rothenberger
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

Re: [Jmol-users] Are SMILES communications private?

2013-02-02 Thread N David Brown
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.