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139d2bdb83
* 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