* add option to track atoms involved in each bit for morgan FP
Needs test still
* support similarity maps using fingerprint generators
* support RDKit, AP, and TT
still need tests
* add some testing
* response to review
* FingerprintGenerator improvements
1. simplify construction by adding ctors taking FingerprintArguments
2. remove inexplicable boost::noncopyable from FingerprintArguments
* Switch FingerprintType to be an enum class
* Fixes#7521
* dumb mistake
* initialize everything
* get the defaults right
* Update Code/GraphMol/ChemReactions/ReactionFingerprints.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* 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
* 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
* 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>
* 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
* unused vars in bison parser cleanup
* initialization order in TopologicalTorsionGenerator
* unused params in SLN bison
* sln flex unused params
* throwing destructor in TDTWriter
* signed comparison in substructmethods
* unused input param in smiles/smarts bison
* unused ms param in sln bison
* signed comparison in FingerprintGenerator
* store return of fscanf in StructCheckerOptions
* unreferenced var in catch
* uninitialized value in FileParserUtils
* avoid override overload warning in MolDraw2DSVG
* non-final overrides in Validate.h
* unused static var in Avalon
* unused vars in catch blocks
* make AvalonTools avalonSimilarityBits & avalonSSSBits const int
* assert fscanf result in StructCheckerOptions
* rm names of unused params in Code/GraphMol/Fingerprints/AtomPairGenerator.cpp
* correct some compilation warnings
mostly unused parameters and one unsigned Vs signed comparison
* 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
