Greg Landrum 2afeb3b086 Dev/cleanup bad confs (#973) ...

* passes all tests, but is still not 100 percent there

* generalize _centerInVolume for possible future use

* better testing of tetrahedral centers
update tests

* only test ring atoms

* handle 4-coordinate n too

* add a volume check; not all tests pass

* turn off debug printing

* rearrange the order of tests.
if this is not done, we get a seg fault when the github55 test runs.
the whole thing needs to be run under valgrind to track this down

* clear up a memory leak

* a bit more documentation
add a constant for one of the threshold values

* get more permissive on the energy tests.
Only do the extra tetrahedral tests for atoms in at least two rings.

* add a DEBUG_EMBEDDING option to make tracking down failures easier

* enable better debugging when the flag is set

* remove a FIX

* remove some debug printing from the tests

2016-07-25 14:26:19 -04:00

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