* Fixes#8379
* check in some working tests
* test passes
* test passes
* test passes
* test passes
* test passes
* ensure that the invariants flush the streams on failure
* tests pass
* test passes
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* Fixes#8391
* tests pass
* fix a test with legacy
not clear why this was not causing problems before
* make a test work
* Fixes#8396
* gcc builds work
* fingerprint tests pass
* mention backwards incompatible change
* fix a problem with FindMolChiralCenters
* more testing details
* enable the test status output
* Fixes#8432
fix a bug in double-bond stereo handling for template matching
* all depictor tests pass
* use the new-stereo chiral ranks in the depiction code
* always assign new-stereo chiral ranks
* make _ChiralAtomRank a computed property
This is analogous to _CIPRank
* tweak to the way the atom ordering is computed for 2D coordinate generation
* update two expected results
* backup
* response to review
* tests pass
* tests pass
---------
Co-authored-by: = <=>
* remove include from headers
* update implementation files
* completely remove BOOST_FOREACH (#7)
* convert those changes to use auto
* get rid of all usage of BOOST_FOREACH
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* Fingerprint generator first prototype
* Added some more details to the prototype
* Update based on comments
* Added additional outputs and return type changes
* FingerprintGenerator updated and placeholder implementation added
* Added getFingerprint implementation to FingerprintGenerator
* Added comments for FingerprintGenerator
* WIP: Atom pairs fingerprint implementation for FingerprintGenerator
* Removed templates and added comments
* Fixed AtomPairEnvGenerator creating duplicate environments
* Added a atom pair old version compatibility test
* Moved the FingerprintGenerator related tests to a new file
* Added new comments and changes from the PR comments
* using int types from std instead of boost and remove cleanUpEnvironments
* Minor refactoring for atom-pair atom code generation
* Added more tests for AtomPairGenerator
* Removed additional clean up method from FingerprinGenerator
* Added additional output for atom-pair fingerprint and a test
* Removed leftover code
* Default argument changes
* Removed leftover include
* Default invariant generation logic seperated from env generation logic for AtomPairs
* Implemented fingerprint as bit vector type and added the test for it
* Folded fingerprint implementation and a test case added
* String representation for fingerprint generator is added
* Python wrapper for fingeprint generator added with a simple test
* Removed unused linked libraries
* AtomPair related wrapper code moved to its own file
* Python wrapper methods for different fingerprint output types added
* Wrappers for invariants generators and tests are added
* Added more comments and tests
* Changed python side names for FIngerprintGenerator and removed extra wrappers used for invariant generators on python
* Fixed object lifetime problems for invariant generators in Python
* Fixed typo
* Added a list of test molecules and made fingerprint generator related classes noncopyable
* Morgan fingerprint python wrappers
* Removed argument helper class for wrapper
* Morgan Fingerprint simple implementation
* Added more invariants generators for Morgan
* Fixed a bug in Morgan bond invariant generator
* Added invariant generator combination tests
* Added atom pair generator to the invariant generator combination test
* Fixed a problem in morgan feature invariant generator
* Overriding invariants without generators is made possible
* Added comments and documentation
* Radius changed for morgan fingerprint test
* RDKit fingerprint generator implementation with cpp tests
* 32 bit and 64 bit fingerprint support for FingerprintGenerator
* Common utilities moved to FingerprintUtil.h and code duplication reduced
* Solved undefined reference issues for FPGenerator templates
* Topological torsion fp generator added
* Fingerprint notebook added
* Python wrappers updated
* Morgan tests added
* Tests expanded and reduced excess amounts of collision in folded output
* Expanded tests
* More documentation
* Python docs for atom pair
* Updated fingerprint generator notebook
* Python wrapper documentation added
* Seperated FingerprintGenerator implementations into seperated file again
* Python wrapper names updated to reflect new naming
* getCountFingerprint now returns 32 bit output and count simulation does not affect count fingerprints
* Python 3 compatibility for fingerprint generator tests
* a bit of ABC cleanup
* some comment formatting got screwed up
* <sigh>
* fix an uninitialized memory problem
* Added copyright statement to new files
* Corrected some comments and docs according to the latest changes
* Bulk fingerprint generation and tests
* Convenience function wrappers and size limiting for getSparseFingerprint
* Copyright text fixed
* Info string added to python wrappers
* Some changes to get the swig wrappers building again
