* 3D MCS
* Move test data to dedicated directory
* 3D MCS: changes based on code review
* Replace conformer generation code in MCS 3D test with mol blocks
* 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
* a round of cleanups courtesy of PVS studio
* add a test to make sure that a warning is a false alarm
* bug fix
* Fix a UFF bug
* more PVS studio cleanups
* next round of PVS studio cleanups
* completely remove the chances for that bug
* changes in response to review
* add an additional test
+ a bit of reformatting that snuck in
Fixes#2420
Tests updated to reflect changes.
The existing CompleteRingsOnly code wasn't actually guaranteeing CompleteRingsOnly at all, it was just causing #2420.
The updated code actually makes sure that bonds that were ring bonds in one of the queries are ring bonds in the final MCS.
This is done via a relatively simple DFS.
* spelling
* Allow types.h to be included in applications that set _USE_MATH_DEFINES
Our application defines _USE_MATH_DEFINES on the visual studio
compiler command line, so every compilation includes the macro
definition. Including types.h (or anything other RDKit header,
basically) causes compilation to fail with a "doubly defined
macro" error message.
This commit defines the macro locally and only if it is not already
defined
* very basics of charge checking in
* add the new parameters to the python wrapper. more testing please
* Additional testing.
* update which unittest methods are used
* 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
