* 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
* Fixes#1021, kind of.
The test for the bug passes, but there are other failures
* all tests except hanoi pass
* passes all tests
* remove some vestigial code
* remove debug-droppings
* minor documentation
* 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
* first pass
* Fixes#623
* fix a merge problem
* move the aromaticity perception to a helper fn
* python doc update
* replace setSimpleAromaticity() with a parameter to setAromaticity()
* add simple test for the custom aromaticity function
- rename RDLog::AddTee()->RDLog::SetTee()
- remove a leak when RDLog::SetTee() (formerly AddTee()) is called twice
- add RDLog::ClearTee() method to allow RDLog::SetTee() to be safely used with a stream that goes out of scope.
This changes the CIPCode and CIPRank atom properties to no longer be computed properties.
Note: under linux I was unable to actually get the bug to manifest (converting the uint property to an int didn't cause problems), but that doesn't mean it shouldn't still be fixed.
