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 <[email protected]> wrote:
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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