* get fileparsers catch tests building faster
should use this same approach across all of the catch2 tests
* Fixes#2916
* support parsing of STBOX for atoms and bonds in v3K mol files
add molStereoCare to common_properties
STBOX is translated to the molStereoCare property
* add stereocare support to adjustQueryProperties
make building the catch2 tests faster for the GraphMol package
* copy in AdjustQueryParameters JSON parsing from adapter.cpp
(That still needs to be ported to use the new code)
* get the cartridge using the new parsing code
* update test to reflect new parser behavior
* add a v2000 test
* changes in response to review
* 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
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
* Actually delete atoms and bonds...
* RWMol::clear now calls destroy to handle atom/bond deletion
* Changes broken Atom lookup for windows/gcc
* Adds tests for running with valgrind
* Adds test designed for valgrind and molecule deletions
* Removes RNG, actually tests bond deletions
* update swig wrappers
* deal with most recent changes on the main branch
* handle the heavy-atom degree queries differently
* Fixes#1563
* add a test for the heavy atom degree option
* Support (and test) adjustHeavyDegree in the cartridge too.
* test results
* Adds RDProps updateProps API point
* AdjustQuery now copies over original atom data to the query ato
* Preserves existing data on the replacing atom
* Exposes preserveProps to Python replaceAtom/Bond
* Adds RDProps updateProps API point
* AdjustQuery now copies over original atom data to the query ato
* Preserves existing data on the replacing atom
* Exposes preserveProps to Python replaceAtom/Bond
* first pass at RWMol::replaceBond()
* get ready for the changes
* rename some options
add bond options (not doing anything with them yet)
update tests to reflect new options
* backup
* re-enable the rest of the tests
* backup commit
* Change the names and meanings of MolOps::AdjustQueryWhichFlags
What was there before was not flexible enough and was extremely confusing. This should clear that up.
NOTE: this does break backwards compatibility with code that uses this enum, but given that this is new and has not been
widely promoted, I suspect it should not affect that many people. The default behavior of MolOps::adjustQueryProperties()
remains the same.
* adjust to the new AdjustQueryWhichFlags
* add mol_adjust_query_properties tests to the cartridge
