* backup
* Add a couple of more tests and an exclusion for triple bonds.
* expose the MDL aromaticity model to python and test it.
* exocyclic bonds should not “steal” electrons in the MDL model
* backup (partial) update for aromaticity model documentation
* add examples to testGithub1622 for aromatic and nonaromatic compounds
* updates to aromaticity model and docs based on additional information from @bannanc
* some additional examples from @bannanc
* add rule to allow exocyclic multiple bonds to disqualify an atom.
* minor doc update
* address some review comments
* 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
This actually just causes the molecule processing to fail in a reasonable amount of time; it is not an actual fix to the underlying ring-finding problem
* 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
* 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
* 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.
