* speed up scoring of permutations by clever caching of already settled
matches rather than recomputing scores for all matches every time
process() is called
* changes in response to review
* changes in response to review
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* Fixes#3924
The scoring function was not taking into account empty rgroups which biased certain
arrangements of rgroups that didn't have an rgroup at every position.
* Change in response to review
* Rigger the no_rgroup into EMPTY_RGROUP
* Remove Fix Me label from the geminal rgroup test
* add testUserMatchTypesDefaultScore to test default score on user types
* Fix scoring RGroups with split attachments [*:1]O.[*:1]N.
* Test both scoring functions for testMutipleCoreRelabellingIssues and testUnprocessedMapping
* Update testRGroupInternals.cpp
remove a couple obsolete comments as suggested in review
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Tests for default function failures
* Revert tests
* Fix linker matches in the case that they span multiple rgroups
* Change to test required by linker fix
* Update based on Brian's changes
* get windows dll builds working
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Exploration
* Initial work on GA fro Rgroup Symmetry
* GA for rgroup decomp and fingerprint rgroup symmetry scoring
* Continuing development
* Exploration
* Initial work on GA fro Rgroup Symmetry
* GA for rgroup decomp and fingerprint rgroup symmetry scoring
* Continuing development
* Further development
* Continued tweaks
* Function rename
* Continued tweaks
* Bug fix for variance calculation
* Copyright notices. Remove Eigen dependency. RdKit logging. Clock fix.
* Changes to fix build failures
* Fixes for Windows dynamic DLL build
* Included GA export.h file
* Fixed RGroupDecomp CMakeLists.txt
* Notebooks working, GGroup labelling bug fixed
* Fix windows build. More options for example GA program
* More bugs found and tests adjusted
* Fixed Python rgroup test
* Trivial change to trigger CI
* OSX java and windows build fixes
* Windows DLL fix
* Fix segmentation error
* proposed change
* Possible fix for segmentation fault
* CR fixes
* CR fixes
* CR fixes
* Recreates molecules from rgroups where possible
Co-authored-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: Brian Kelley <fustigator@gmail.com>
