* RGD code cleanup
- made an effort to give more meaningful names to variables (e.g., renamed most instances of attachment (point) to avoid ambiguity as attachment may be interpreted as either the R-group atom or its neighbor atom on the core, which are two different things)
- replaced the old school removeAtom() method with begin/commitBatchEdit()
- added std::move and std::make_move_iterator where relevant to avoid potential unintended copying
- replaced instances of container.size() == 0 and !container.size() with container.empty() for better clarity
- replaced std::map::find() with std::map::at() where the key was not needed
- replaced expensive std::find_if with more efficient alternative
- added some missing const keywords and added references to avoid copying where appropriate
- replaced for loops with modern implicit looping alternatives where convenient
- avoid calling MolToSmiles when VERBOSE is not defined as the result is anyway not used
- removed "oops, exponential is a pain" code snippet as I believe 1. it is never executed 2. it is not tested 3. I do not think it is correct
- removed check for data->matches.size() > 1 as I do not believe it is correct
- Use std::unique_ptr::reset instead of defining a new std::unique_ptr and moving it to the original one
* changes in response to review
* change in response to review
* replaced std::set with boost::dynamic_bitset to save time on std::set::insert and std::set::find
* make sure we do not go out of bounds
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Support tautomer queries in RGD
* Continuing RGD and tautomer development
* Python and C# tests
* Python and C# tests
* C# test
* Typo fix
* For cire tautomer query update properties instead of full sanitization
* Added query comment
* Code review change
* Support Enumeration of input cores
* Mol enumeration test
* Remove useNormalMatch from RGroupDecomp
* Added comments for handling tautomeric core
* Added comments for handling tautomeric core
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Initial development and test
* Sort of working tests
* Copy corodinates to new core
* Clear stereochemistry on core atoms with unlabelled rgroups
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Continuing development
* Updated development
* Fixed Chirality Issues
* All tests working
* Remove some unused code
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Working tests
* Tidy test code
* Adjust catch_rgd for stereochemistry in output cores
* Build ring info in output cores
* Fix Mac OS bug
* Fix for MCS and onlyMatchAtRGroups
* Brian's optimization suggestion
* Fix core group coordinate bug
* Test for replaceCore and multiple core bonds to chiral atom
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Changes in response to Greg's code review
* R group stereo bond attachment fix
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* support substructure search parameters in RGD.
Still needs testing/verification of the enhanced stereo stuff
* test enhanced stereo
* add support to python wrapper
unfortunately some python reformatting got mixed in there.
* Most tests working
* All tests working
* Fixed tests after merge with master
* Create header and implementations for RCore
* Updated comments
* Removed old code
* DLL export for MolMatchFinalCheckFunctor
* Information line for failing Mac test
* Log replace core behaviour
* Ordering fix for OSX
* Possible fuzzer fix
* Removed debug output
* Fix unmatched user R group bug
* Code review changes
* Bug fix and ChemTransforms test
