* add test making sure that multiple bits per feature works with other fp types
* simplification
* expose base options class
* remove redundant df_includeChirality from TT generator
* expose the fingerprint arguments (i.e. options) to python
* typo
* remove deprecated useCountSimulation argument
* remove the mol_from_smarts() function from the cartridge
* remove the balabanj
* a couple final cleanups to the countSimulation thing
* document changes
* Fixes a variety of problems with simulating counts using the FingerprintGenerators from Python
1. the countBounds arguments were not working
2. the GetXXXGenerator() functions used inconsistent naming for the countSimulation argument
3. there were no tests to make sure that the changing countBounds actually did something
* typo
* Split bonds to per-atom parts for interaction
* It would help to commit test fixes also
* Update Code/GraphMol/MolDraw2D/MolDraw2D.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Refactored code
* bit info works for Morgan fps and is tested
get the stubs in place everywhere else
* add RDKitFP bit info too
* expand atom pair info
* add info for TTs
* atom pairs
* enable shared_ptrs for SparseBitVects in python
* fix core leaks in the bulk operations
* simplify the AdditionalOutput API
* first pass at a useable AtomOutput from Python
needs "a bit" more testing.
* documentation
* response to review
Co-authored-by: SPKorhonen <samuli-petrus.korhonen@iki.fi>
* 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
