* Fixes#7533
Fixes problem with SparseIntVect and SparseBitVect where the intention is to
be able to store all possible values of the index type: in these cases
you could not store (or access) the final element.
* increase the verbosity of the DataStructs tests
so that we can see what's going on
* add FingerprintFuncArguments() to simplify things
* getFingerprintHelper() also uses FingerprintFuncArguments
* port atompairs and tts to use new code
* not working yet
* all tests pass
* move the includeChirality flag to the global arguments
ensure stereochemistry is assigned when calculating fingerprints using chirality (#1993)
* migrate legacy morgan fp code to use generators
* refactoring the way bit info is handled
* all tests pass
* all tests pass
* expose getArguments()
* rename getArguments->getOptions
* copyright updates
* update a test
* remove template from FingerprintArguments
some other refactoring and cleanup
* hopefully fix the windows dll builds
* partial docs update
* improve docs and API
* more docs
* more docs
* a bit of modernization
* more doc tweaks
* changes in response to review
* 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>
