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3dc1a220b7
* Test only commit for using enhanced stereo in substructure search
Adds some test cases to demonstrate what I'm planning.
When the test cases fail, the messages look like this:
-------------------------------------------------------------------------------
Enhanced stereochemistry
AND and OR match their enantiomer
-------------------------------------------------------------------------------
/Users/wandschn/Documents/src/rdkit/Code/GraphMol/Substruct/catch_tests.cpp:216
...............................................................................
/Users/wandschn/Documents/src/rdkit/Code/GraphMol/Substruct/catch_tests.cpp:218: FAILED:
CHECK_THAT( *opposite_mol, IsSubstructOf(*mol_and, ps) )
with expansion:
CC[C@@H](F)[C@@H](C)O is not a substructure of CC[C@H](F)[C@H](C)O |&1:2,4|
/Users/wandschn/Documents/src/rdkit/Code/GraphMol/Substruct/catch_tests.cpp:219: FAILED:
CHECK_THAT( *opposite_mol, IsSubstructOf(*mol_or, ps) )
with expansion:
CC[C@@H](F)[C@@H](C)O is not a substructure of CC[C@H](F)[C@H](C)O |o1:2,4|
* rename parameter to include q and m to reduce my confusion
* Don't keep recreating a map
This map is the same in every loop. And actually, the desired
information is slightly different than what was formerly stored
in the map.
* Fix tests after our discussion.
Also adds more exciting tests of disastereomers and structures
with multiple stereo groups.
* Use enhanced stereochemistry in substructure searching
Allows use of enhaced stereochemistry in substructure searching
if `SubstructMatchParameters.useEnhancedStereo` is set.
The matching rules are pretty obnoxious, but a synopsis is:
* An achiral query/substructure matches everything, because it
means "ignore chirality".
* An absolute query matches AND or OR, because they both include
the molecule with an absolute center
* An query with an OR matches either an OR or an AND, because
AND is more molecules.
* add info about matching to the documentation
* expose extended stereo matching option to python
* Some updates/tweaks to the documentation of enhanced stereochemistry
especially about searching.
* Code review comments.
Co-authored-by: greg landrum <greg.landrum@gmail.com>