* Compile time and runtime deprecation warnings
* Used [[deprecated]] attribute to mark deprecation on cpp side
* Used RDLog to escalate deprecation warnings to python
* deprecated non fingerprint generator fingerprint generation functions
* Address build errors
* suppress deprecation warnings in cpps and tests
* experiment with new SWIG versions in the mac azure pipeline
* More deprecation suppression
* revert mac java experiment
* Fix SWIG syntax errors
* Attempt to fix windows unit test
* Remove test because of logging behavior
* Change linux java build to SWIG 4.1
- removes the need for preprocessor interaction
* Change mac java build to SWIG 4.1
* try updating the CI buid
* lock cmake version
needed to find JNI correctly
* update compiler versions
needed for the boost
* Fix typo and unavailable version
* Fix version conflict
* update mac build
* get linux build working?
---------
Co-authored-by: Patrick Penner <patrick@ppenner.com>
* 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 modernize-use-default-member-init
* results from modernize-use-emplace
* one uniform initialization per line
otherwise SWIG is unhappy
Co-authored-by: Brian Kelley <fustigator@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
* do not use new on loggers
* del pointers in testDistGeom
* Update Dict hasNonPOD status on bulk update
* delete new Dicts in memtest1.cpp
* fixes in MolSuppliers and testFMCS
* PeriodicTable singleton as unique_ptr
* fix EEM_arrays leak
* fix leaks in testPBF
* fix ParamCollection leak in test UFF
* fix leaks in MMFF
* clear prop dict before read in in pickler
* fix leaks in testFreeSASA
* fix leaks in test3D
* modernize Dict.h & SmilesParse.cpp
* fix leaks in testQuery
* fix leaks in testCrystalFF
* fix leaks in cxsmilesTest
* fix leaks in Catalog & mol cat test
* fix leaks in ShapeUtils & tests
* fix leaks in testSubgraphs1
* fix leaks testFingerprintGenerators
* fix leaks in Catalog/FilterCatalog
* fix leaks in graphmolqueryTest
* these changes reduce bison parse leaks
* fixed leaks in testChirality.cpp
* fix leaks + 2 tests in testMolWriter
* fix 4m leaks in substructLibraryTest
* small improvements to molTautomerTest; still leaks
* fix leaks in testRGroupDecomp
* fix leaks in test; parser still leaks
* fix leaks in itertest
* fix 4m leaks in testDepictor
* fixes in smatest; still leaking due to parser
* fixes in testSLNParse; still leaking due to parser
* flex/bison: always add atoms with ownership; smarts error cleanup
* fix leaks in testReaction
* fix leaks in testSubstructMatch
* fix leaks in resMolSupplierTest
* fix leaks in testChemTransforms + bug in ChemTransforms
* fix leaks in testPickler
* fix leaks in testMolTransform
* fix leaks in testFragCatalog
* fix leak in testSLNParse. Still leaks due to Smiles
* fixed most leaks in testMolSupplier
* pre bison fix
* fix some atom & bond parse problems; others still fail
* bison smiles & smarts, atoms & bonds more or less fixed
* fix leaks in molopstest.cpp
* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp
* fix leaks in moldraw2Dtest1
* fix leaks in testDescriptors
* fix leaks in testInchi
* fix leaks in testUFFForceFieldHelpers
* fix leaks in hanoiTest & new_canon.h
* fix leaks in testMMFFForceField
* fix leaks in graphmolTest1
* fix leaks in testMMFFForceFieldHelpers
* fix leaks in testDistGeomHelpers
* fix leaks in testMolAlign
* initialize occupancy & temp facto with default values
* fix leak in TautomerTransform
* updated suppressions
* fix testStructChecker
* fix logging & py tests
* fix TautomerTransform class/struct issue
* remove misplaced delete in testSLNParse
* deinit in testAvalonLib1
* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp
* fix random testMolWriter/Supplier fails
- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.
* use reset in FFs Params.cpp
* comments on testMMFFForceField
* unrequired 'if's added to mol suppliers
* correct cast in FilterCatalog.h
* use unique_ptr in MACCS Patterns
* remove unrequred if in new_canon
* update & move suppressions
* Changes to Python bulk FP convenience functions
- Change the default fingerprint to Morgan
- Change the method of specifying fingerprints to use an enum instead of a string
- Pluralized the name of the bulk functions to make it obvious that they return more than one FP
* Use Morgan radius=2 for the bulk convenience functions
* 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
