* WIP - Substruct Library Serialization
* Add serialization to SubstructLibrary
* Add SubstructLibraryDefs
This holds the definition of whether the substruct
library is serializable
* Wrap serialization in python
* Remove .h file, add .h.in file
* Configure header file into source dir
* Use RDConfig.h to configure serialization
* Move serialization code to seperate header file
* Fixes for review comments
* Removes some code redundancy
* Make pickling mols less memory intensive
* Check if molholders come back as the right types
* 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
* Adds substruct library documentation
* Adds testing of (fixed) documentation code
* Fixes typos and emphasizes the speed of trusted smiles
* Removes colons from parameters in docstrings, was causing warnings
* First entry of the SubstructLibrary module
* Switch to shared_ptrs for memory safety
* run clang-format and add a test
* only build when threadsafe_sss is enabled, only test when test_multithreaded is enabled
* Adds PRECONDITION
* Adds exceptions for out of range errors
* Changes getQueryBits to makeQueryBits for clarity
* Adds API point to add Binary and Smiles directly
* Replaces 0 with NULL for clarity.
* Removes debugging code.
* Makes endIdx non-inclusive
* Adds substruct searching options
* Adds preconditions
* Small documentation cleanup and removes a line of code.
* Add DataStructs library dependency
* Actually uses passed in parameters
* Adds TrustedSmiles/Binary inputs
* Adds more api testing options/trusted smiles and binary inputs
* Finalizes API adds docs and doctests
* Minor copyright fixes and such
