So you kind of need to bake it into the layout algorithm. A colleague has been looking at implementing principles the Alex Clark / MOE paper ( but it’s quite involved. There was discussion about issues with the SDG circulated last year (I still have the google docs from Nina).

Otherwise, I would say reset the test to fail - that way it's a
permanent reminder of a task to do! :)

A cardinal sin :-) - tests aren’t feature requests. I tend to be of the philosophy if it can’t be done well it shouldn’t be done.

Yeah I did see Noel’s post - we can actually do stereo layout now (or rather, I have a patch for that).


On 11 Dec 2013, at 17:38, gilleain torrance <> wrote:


Hmm. How difficult would it be to implement some code to try all
orientations around rotatable bonds? There is a descriptor in:
o.o.c.qsar.descriptors.molecular called the
RotatableBondsCountDescriptor that contains some logic for finding
these bonds…

Otherwise, I would say reset the test to fail - that way it's a
permanent reminder of a task to do! :)

(oh, and Noel O'Boyle had a blogpost on roughly this area :


On 12/10/13, John May <> wrote:
Hi All,

As we all know the structure diagram generation in the CDK has some quirks
one of which is dealing overlaps (it doesn’t). The existing generator lays
out the atoms and then invokes OverlapResolver which previously did nothing
due a tiny threshold value which was adjusted 3 months ago (resolving a
failing test). With a better threshold value overlaps are detected and the
bonds are now moved. Unfortunately how it resolves the overlaps is not ideal
(see attached).

Should we change the threshold back so it doesn’t nothing -> dead code,
failing unit test or perhaps remove this class completely and just stick
with the overlaps?

Many thanks,

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