Greg Landrum 19bdd21de1 Updated code for chirality perception (#3324) ...

* add new test (it fails, of course)

* isAtomPotentialTetrahedralCenter() there and tested
tests cases for molecular stereo written (but failing, of course)
create new_chirality.cpp, we will probably want to change this at some point
new StereoInfo structure

* more infrastructure
- isBondPotentialStereoBond()
- two getStereoInfo() functions
- associated unit tests

* backup

* oops

* backup

* switch to always using four atoms for bonds

* backup

* add new test (it fails, of course)

* isAtomPotentialTetrahedralCenter() there and tested
tests cases for molecular stereo written (but failing, of course)
create new_chirality.cpp, we will probably want to change this at some point
new StereoInfo structure

* more infrastructure
- isBondPotentialStereoBond()
- two getStereoInfo() functions
- associated unit tests

* backup

* oops

* backup

* switch to always using four atoms for bonds

* backup

* this now actually works

* doc update

* add a test to demo that ring stereo is not working

* more testing

* add a fun CIP test

* add review note

* debugging

* remove extraneous debugging
turn off tests for ring-double bond stereo

* disable the ring-stereo fix... this breaks a few tests, but we will recover

* works, needs cleanup, chirality code needs re-testing

* nothing works

* Fixes #3322

* Python and C++ tests now pass

* clang-format

* first pass at python wrappers

* improve doctest

* basic optimization...
stop with the copying

* rename

* all tests passing again

* optimization

* fix the sort in the tests

* looks like this might fix the windows-dll build problems

* update tests

* the fun never ends

* comment cleanup

* handle deliberately unspecified atoms/bonds

* add cleanIt option

* add flagPossible

* add option to use the new code to the SMILES parser

* additional testing

* additional testing

* a bit of additional testing never hurts

* changes in response to review

* fixes a bug with potential parastereo not being cleared

other changes in response to review

* update docs

2020-09-02 15:00:29 +02:00

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