Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

[Geoffrey Hutchison]

> So I was just taking another look, and I think all you need assuming
> you have the QtGui::Molecule, and the Atom object you want to access:
> 
> RWAtom rwAtom = molecule->undoMolecule()->atom(atom.index());

No, no. It's the reverse. I want the Atom from an RWAtom..

-Geoff

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Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

[Marcus D. Hanwell]

On Fri, May 27, 2016 at 11:22 AM, Marcus D. Hanwell
 wrote:
> On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison
>  wrote:
>>> I thought that ideally HydrogenTools would operate on the RWMolecule,
>>> but RWMolecule is now a lightweight class. There is not currently a
>>> way to get the Atom from an RWAtom, but the code would be very simple
>>> so if we want to add it we can.
>>
So I was just taking another look, and I think all you need assuming
you have the QtGui::Molecule, and the Atom object you want to access:

RWAtom rwAtom = molecule->undoMolecule()->atom(atom.index());

If you have an example where that doesn't seem to work I can take a
better look. The call to undoMolecule on molecule is cheap, no object
creation/destruction, and the rwAtom object creation should also be
really cheap. There is also atomByUniqueId if you want it, but the
index version should be faster and safe in the context you want it.

Marcus

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Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

[Marcus D. Hanwell]

On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison
 wrote:
>> I thought that ideally HydrogenTools would operate on the RWMolecule,
>> but RWMolecule is now a lightweight class. There is not currently a
>> way to get the Atom from an RWAtom, but the code would be very simple
>> so if we want to add it we can.
>
> Just a follow-up.. Can you point me in the direction here?
>
Sorry, I knew I owed you something. I will take a look at it, too much travel...

Marcus

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Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

[Geoffrey Hutchison]

> I thought that ideally HydrogenTools would operate on the RWMolecule,
> but RWMolecule is now a lightweight class. There is not currently a
> way to get the Atom from an RWAtom, but the code would be very simple
> so if we want to add it we can.

Just a follow-up.. Can you point me in the direction here?

Thanks,
-Geoff

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[Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

[Geoffrey Hutchison]

Hi Marcus,

I'm trying to fix up the draw tool so that it does automatic hydrogen 
adjustment on the atoms in the edit, etc.
(The new catch is that it will "snap to" standard bond lengths and ideally 
angles as well.)

But I keep coming back to the pain of the hydrogentools code operating on Atom 
classes and Editor having RWAtom.

Is there a way to get the Atom that corresponds to an RWAtom, or does the 
hydrogen tools code need to be updated to only work on RWAtoms - or something 
else?

Thanks,
-Geoff
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