Greg Landrum e625c58bab Add cis/trans tags to double bonds (#1316) ...

* add cis and trans to bond stereo

* compiles, does not work

* tests all pass

* Whitespace cleanup to recent changes.

* C++ test case for Bond::setStereo using Bond::STEREOCIS and Bond::STEREOTRANS

* Adding a PRECONDITION to Bond::setStereo to make sure the stereo atoms
are already specified if CIS or TRANS is being specified.

E/Z is technically defined by the topology of the molecule so the
stereo atoms are redundant (easier to understand and use!), but
ultimately redundant with the graph. However, CIS and TRANS is _only_
defined in this usage as the orientation of the atoms in the
getStereoAtoms vector.

* Exposing Bond::setStereo to Python and adding test cases to make sure
it can be used to set CIS/TRANS stereochemistry.

* verify substructure matching works

* Adding Bond::setStereoAtoms to C++ Bond class.

This allows setting the atoms to be considered for CIS or TRANS
directly without a much more costly determination of ranking that E/Z
requires.

* Wrap Bond::SetStereoAtoms into python with a new type of test case.

* docs

2017-02-26 08:15:44 -05:00

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