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 this information?
David
On 3 February 2013 13:56, N David Brown <[email protected]> wrote:
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 <[email protected]> wrote:
>
> 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?
>>
>> I've been looking through the code API but can't see a means to do so.
>>
>> Equally I haven't spotted a script command that'll enable this.
>>
>> A solution would be to output the molecule in xyz format and load it I
>> suppose. But is there a neater way?
>>
>> Many thanks.
>>
>> David
>>
>> On 3 February 2013 08:27, Bob Hanson <[email protected]> wrote:
>>
>>
>>> 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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