* Deprecation: planned removal of .message() and .getMessage() methods
* Deprecation: planned removal of old MolHash code
* document deprecations
* output the diffs when the psql tests fail
* remove .message() from SWIG wrappers
note that the KeyError doesn't work properly. We should clean up the the exceptions here anyway
* typo
* 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
* StructChecker changes. Initial commit. First implementation. Added some tests.
* StructChecker: add GoodAtoms and AcidicAtoms. new updates
* StructChecker: add new tests
* StructChecker: added TransformAugmentedAtoms()
* StructCheck: add structCheck to GraphMol. Fix compilation errors.
* StructChecker: add stereo verification and some utilities.
* StructChecker: function FixDubious3DMolecule was added
* StructChecker: checkStereo added. done with stereo.
* StructChecker: add StripSmallFragments()
* StructChecker: add AtomClash() function. Some cosmetic + tests
* StructChecker: checkAtoms() was started
* StructChecker: checkAtoms is ready
* StructChecker: user RingInfo from RDkit. Start regarge
* StructChecker: ReCharge molecule method prototype
* StructChecker: updates for ReCharge. Almost finished
* StructChecker: all ReCharge is done except external data tables loading
* StructChecker: add path tables into API. ReCharge completed
* Adds augmented atom data
Signed-off-by: Brian Kelley <brian.kelley@novartis.com>
* Removes extra files
Signed-off-by: Brian Kelley <brian.kelley@novartis.com>
* Adds path to test data via RDBASE environment
Signed-off-by: Brian Kelley <brian.kelley@novartis.com>
* Revert "Struct checker apr15"
* StructChecker: add missing tautomer tests
* Updates test to use RDBASE
* Adds initialization of data from data section
* Adds Python API and tests
* Fixes namespace for enum
* StructChecker: update/imporve strip small fragments
* StructChecker: fix acidic atoms (but logic does not work)
* StructChecker: fix match issue for CheckAtoms
* Adds macro guards
* Adds loading API and proper constructor
* Fixes tests, adds stereo test
* Fixes crash bug, matches[0] was being accessed from an empty match vector
* Reverts crash fix - conflicts with previous
* Adds the rest of the structure checker options
* StructChecker: fix atom matching for aromatic rings
* StructChecker: add tautomers checks. Update some tests
* StructChecker: stereo fixes. Add some tests
* StructChecker: fix check atoms. Start ligand symbol list
* StructChecker: fix some check atoms validation. Add Tranform to query lists. Start correct loading augmented atoms
* update
* another set of fixes
* StructChecker: fix loadDefaultAugmentedAtoms. Some changes in CheckAtom + tests + debug conditional breakpoints (TEMP operators)
* StructChecker: rewrited RecMatch() to sequential. Changed bond matching algorithm. small bug fixes
* Adds better logging of mismatched atoms
* Removes duplicated negative charge
* Fixes charges
* Adds nitro group test
* StructChecker: add better logging
* remove double logging
* Reformats code using RDKit's clang-format style
* StructChecker: Fix charge reformat using RDKit format.
* StructChecker: compilation restore after merge
* restore bond matching
* Removes the same fragments that strucheck does in case of ties
* Don't resanitize - this adds aromaticity which mucks things up
* Adds empty molecule checks
* Fixes atom clashes.
* Removes debug printing
* Removes debug logging info
* First pass at stereo fixes
* Fixes off by one error for dubious stereo fix
* Fixes more off by one errors
* Fixes more off by one errors
* More off by one fixes.
* Another off by one
* Fixes chiral flag set in molfile check
* Copies chiral flag over to largest fragment if necessary
* Poor man’s parity check.
* Find unspecified chiral centers ala Avalon.
* StructChecker: fix recursive match. Fix transformations
* StructChecker: fix transformation for atom list (using query atoms)
* Fixes checks && to &
* StructChecker: fix carboxylic acids tranform issue. Atom list is changed only if different
* StructChecker: documentation was updated
* Fixes snprintf and silences some warnings
* Adds Get/Set StructCheckerOptions
* Adds default AugmentedAtomTransforms
