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I'm writing kLayout DRC-check-rules
Can I select polygons in Layer-A that contains at least 2 polygons of layer-B?
Not now. But there is such a feature in the next version, 0.27. I target end of April for the release.
You can try that now with the beta version from here: https://www.klayout.org/downloads/master/
The feature is "covering" ("enclosing" was used for the enclosing distance check already):
l1 = input(1, 0)
l2 = input(2, 0)
l1.covering(l2, 2..2).output(10, 0)
# new "universal DRC"
l1.drc(covering(l2) == 2).output(11, 0)
Wow, this will be cool!!! It will make it easy to flag overlapping polygons inside a (non-merged) layer itself... Is there an easy way to do the latter right now???
No need to answer my question.
Just found out it can be done using the merged(2) method on raw layers.
And I just published 0.27 which has this feature