* 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
* Allow creation of Enhanced Stereo groups from Python
This wraps creation of Enhanced Stereo groups from Python. It
also allows setting enhanced stereo groups on an RWMol from
Python.
Additionally, this provides a little function to allow C++
vectors to be wrapped for Python, but allow Python list objects
or wrapped C++ vectors to be used as arguments to functions
that take vectors as inputs. I added it only to
Wrap/StereoGroup.cpp, but I _think_ that I should add this
logic to RegisterVectorConverter in RDBoost/Wrap.h. If I
did that, I'd be able to remove a couple of lines in Wrap/Mol.cpp
* enforce atom ownership in SGroups
Some cleanups to make sure you can't add an S group with bogus atoms
to a molecule
* Remove constructor for StereoGroup.
I tried very hard to convince boost Python to allow me to use
with_custodian_and_ward_postcall on an init, and it just never
worked. I've removed the constructor - folks will need to
use the factory function "CreateStereoGroup" if they want
a StereoGroup.
* add a couple test files
* backup
* first pass at some theory documentatin
* it's a draft
* Update enhanced stereochemistry documentation
Adds initial target use case and caveats about the tentative
nature of the current implementation.
* Support read/write of molfile enhanced stereochemistry
This includes reading and writing of enhanced stereochemistry
from v3000 molfiles (sdf). Enhanced stereochemistry encodes
the relative configuration of stereocenters, allowing
representation of racemic mixtures and compounds with
unknown absolute stereochemistry.
It does not include:
* Python wrapping
* invalidation of the enhanced stereochemistry
* use of enhanced stereochemistry in search
* depiction of enhanced stereochemistry.
* Update to reflect changes from #1971
* change names of enum elements to allow compilation in VS2017
I think it's also clearer to do things this way
* Addressed most review comments.
* Run missed test "testEnhancedStereoChemistry"
* In tests, added size checks to group equality checks
* Updated copyright statements
* Deleted mol created for a test
* Use perfect forwarding in RWMol::setStereoGroups()
* use references for stereo groups that are checked in write and pickle
* Updated stereogroup.h in hopes of fixing compilation on Windows.
* clang-format
* try allowing a switch to boost regex and requiring it for g++-4.8
* do a better job of that
* typo
* Code review comments. Updated Copyright notice.
* When an atom is deleted, delete stereo groups containing it.
Also updates StereoGroup toUse accessors instead of
constant member attributes. This allows move of StereoGroups.
* RDKit style guide
* Add header required on Windows.
* get the SWIG wrappers to build
