* 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
* this is a rough first pass, needs to be finished and is a strong argument for changing the names of some of the #defines that are currently used
* rationalize the rest of the #defines
add something to the release notes about this
* Fixes#1810
There's still a problem with stereo atoms (see the commented out test),
but this takes care of the basics and that's up next.
* clean up that last problematic bit.
Still needs all tests to run
* this seems to be a necessary workaround for problems with VS2017.
It's a bit ugly, but shouldn't have any performance impact, so I'm not
going to get too worked up.
* This set of changes alters what we get for some of the InChI test cases.
Adjust for that.
* boost::thread mostly gone... still need to get rid of once
everything compiles
* replace boost::call_once
* remove link-time dependency on boost::thread
* first pass at using async
* switch to using async everywhere
* clean up the header a bit
clang-format
* clang-format
* add test for #1286
* backup
* fixes the specific failure, but needs more looking
* add an additional test
* update the inchi code to explicitly include queue
* fix a typo identified during the review
* add cis and trans to bond stereo
* compiles, does not work
* tests all pass
* Whitespace cleanup to recent changes.
* C++ test case for Bond::setStereo using Bond::STEREOCIS and Bond::STEREOTRANS
* Adding a PRECONDITION to Bond::setStereo to make sure the stereo atoms
are already specified if CIS or TRANS is being specified.
E/Z is technically defined by the topology of the molecule so the
stereo atoms are redundant (easier to understand and use!), but
ultimately redundant with the graph. However, CIS and TRANS is _only_
defined in this usage as the orientation of the atoms in the
getStereoAtoms vector.
* Exposing Bond::setStereo to Python and adding test cases to make sure
it can be used to set CIS/TRANS stereochemistry.
* verify substructure matching works
* Adding Bond::setStereoAtoms to C++ Bond class.
This allows setting the atoms to be considered for CIS or TRANS
directly without a much more costly determination of ranking that E/Z
requires.
* Wrap Bond::SetStereoAtoms into python with a new type of test case.
* docs
* - this should fix the problem with "Inchi" being hardcoded into PostgreSQL
* - moved the InChI check code out of the main CMakeLists.txt
into FindInchi.cmake
* Remove a bunch of warnings
The biggest change here is to treat the boost includes as system libraries.
This causes g++ to ignore warnings from boost.
This change still needs to be tested with clang and on Windows
* suppress a bunch of warnings on clang
