Re: [Cdk-user] [Cdk-devel] [discuss] GeometryTools.has2DCoordinates(IAtomContainer)

[Rajarshi G. <raj...@gm...>]

I agree - the 2D and 3D cases should behave similarly, and I think
modifying the 2D case to be true if all atoms have 2D coords is
sensible

On Wed, Jul 18, 2012 at 5:47 PM, John May <joh...@gm...> wrote:
> Hi all,
>
> I got stung for not fully reading some doc today and thought I would share
> to get some opinions on whether the method behaviour should/could change.
> I'll explain more in a bit but here's what I was doing.
>
> The following snippet (https://gist.github.com/3139004) checks if the the
> container has coordinates for it's atoms and will invoke the renderer if it
> does. If we don't have coordinates we handle appropriately.
>
> if (GeometryTools.has2DCoordinates(container)) {
>     renderer.paint(container, new AWTDrawVisitor(g2), bounds, true);
> } else {
>     // can log or invoke g2.drawString() to display "no coordinates"
> }
>
>
> This will work for the majority of cases however if can cause the paint
> method to throw an exception. In my mind the 'has2DCoordinates' tells me
> whether we have coordinates for all atoms in our container/molecule. However
> what it will actually tell you is whether any of your atoms have 2D
> coordinates. As I said this was my fault for not fully reading the doc and
> assuming 'Determines if this AtomContainer contains 2D coordinates' means
> all atoms. There is the method 'has2DCoordinatesNew' which we can use to get
> an integer and determine full (2) or partial coordinates (1). In my mind a
> method like  'has2DCoordinates' would be mainly used to check an input is
> valid (as above) and not fail.
>
> It should be noted that equivalent 'has3DCoordinates' will return true only
> if all atoms have 3D coordinates as I had presumed with the 2D method.
>
> It would be good to unify the 'has2DCoordinates' and 'has3DCoordinates' to
> behave the same way. Personally I would opt to change 'has2DCoordinates' as
> I can see the use cases for such a method being used more for preventing
> errors then checking molecules with partial atoms.
>
> Please let me know your opinions.
>
> Many thanks,
> John
>
>
>
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-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science