Greg Landrum 95613b6279 Allow SubstanceGroups to survive molecule edits (#3170) ...

* Progress on #3168

* Fixes #3167

* Fixes #3169

* deal with CBONDS too

* test PATOMS

* Fixes #3175

* a bit of code simplification and test updates

still needs more testing

* more testing

* handle s-group hierarchy
also a couple of other changes in response to the review

* add forgotten test file

* changes in response to review

2020-05-19 17:35:08 +02:00

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