This all seems to work well, the xyz is generated and loaded successfully.
On 3 February 2013 14:29, N David Brown <[email protected]> wrote:
> I meant cast to a SmilesAtom then read from that.
>
>
> On 3 February 2013 14:27, N David Brown <[email protected]> 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.
>>
>> 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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