* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* - fixed UFF/MMFF torsion constraints when the dihedral is set to 0.0
- removed some code duplication
- added relevant test and fixed existing ones
* - fix Windows exports
* - added PRECONDITION for RDGeom::Point3D pointers
- removed inline keywords
* Fixes atom documentation
* Fixes#1461
This is a complicated one. Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0. The standard operations is
to check
URANGE(num, size-1)
Which (for unsigned integers) obviously rolls over.
This fixes all usage cases to be
URANGE(num+1, size)
And fixes the bugs found. (addBond and the mmff tests)
* Fixes#1461 - Updates URANGE_CHECK to be 0<=x<hi
* add a test (currently fails, of course)
* backup, not really working
* Fixes#1240
* a bit more parameter tweaking to get some more structures to embed
* 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
This covers at least the specific instances from the bug report.
Still need to figure out a general way to identify these automatically
to make sure all are fixed.
