* Properly cleanup Dict::Pair when serializing HasPropWithQueryValue
* Make sure pickling doesn't change original molecule
* Fix bad cut and paste
* Add PairHolder utility class for memory management of non Dict Dict::Pairs, fix mem leak in pickler
* Edit comment to force a rebuild
* Ignore PairHolder from Java/Swig builds
* Ignore PairHolder API from swig
* Reponses to review
* Add backward incompatible change
* Make release note a bullet point
* Fixes#6017
* a bit of cleanup work
* remove unused variable
* change in response to review
switch to using std::max(maxMatches,maxRecursiveMatches)
* test the case where maxSubstructMatches<maxMatches
* suppress a bunch of warnings from third-party code
get rid of one warning in RDKit code
* corrections
* fix the maeparser flags
* remove some more inchi warnings with clang
* do not throw in desctructor
* remove unused var; reserve
* provide operator= for DiscreteValueVect
* provide operator= for SparseIntVect
* remove unknown 'omp' #pragmas; refactor loop
* remove unused var
* remove unused variables
* give EmbeddedAtom a default constructor & early exit on self assignç
* handle unused vars/args
* catch exception by ref
* address unused args
* fix signed type comparison; refactor extra checks
* remove unused variable
* suppress switch fallthtough warning
* handle signed type comparison
* handle signed type comparison
* potentially uninitialized vars
* fix abs() of bool
* unused vars in catch statements
* remove unused variables
* python::list returns will be copied
* give ValidationMethod constructor & virtual destructor
* remove extra semicolon
* 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>
* backup, does not work
* working on the C++ side
* backup
* fix the API
* document the new functionality
* improve that example
* final bit of cleanup
* switch to std::function
* first pass at adding a SubstructMatchParameter struct
* start moving the rest of the backend to use the parameters
* backend at least mostly moved over
* add aromaticMatchesConjugated
add tests
* switch over the MolBundle too
Add templates to reduce duplicated code
* support older compilers
let's see if it works...
* add SubstructMatchParameters to Python wrapper
* remove some deprecations and warnings
* damn compilers
* parameter support for bundles in python wrapper
* add the parameters to the java wrappers
* response to review
