* move detectBondStereoChemistry() into MolOps
* switch more code over to using the new function
* add an addStereoChemistryFrom3D() function. Needs testing still.
* add some tests
* cleanups and rename
* Wrap Chem.FindPotentialStereoBonds into Python.
* findPotentialStereoBonds now sets the Bond.GetStereo property of the double bond to Bond::STEREOANY.
Some of the doc strings indicated this as the desired behavior, but
some others also indicated otherwise. So I've cleaned up and
refactored those doc strings as well to be consistent. Pulled all the
doc string comments from the .cpp file up to the .h file and merged
all the necessary prose, including adding some about the fact rings
are ignored.
Previously, users would have to test the size of the GetStereoAtoms
vector to determine whether this function found potential double bond
stereo. Testing for Bond::STEREOANY instead is way more straight
forward.
* 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
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.
o rdkit gains a RDKit::common_properties namespace that contains common string value properties
o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
true/false on success or failure. This is used to optimize access.
o rdkit learns how to pass property keys by reference, not value.
A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties. This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values. All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.
Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
