* updated atomic radii to follow the Blue Obelisk Data Repository
Ubuntu package bodr version 10-1; radii are from file
/usr/share/bodr/elements.xml
* typo
* use 2.0 as default VDW radius instead of 1.7
for elements missing from the Blue Obelisk Data Repository
* Document the atomic_data
* update expected test results
* update java tests
* allow a bit more slop when comparing confs
For cross-platform stability
* remove all of the "from __future__" imports
* remove the first batch of rdkit.six imports/uses
* next step of rdkit.six removal
* removing xrange, range, and some maps
* next round of removals
* next round of cleanups
* fix inchi test
* last bits of "from rdkit.six" are gone
* and the last of the six stuff is gone
* strange importlib problem
* trying to add shape tversky
* alpha and beta no defaults, added more tverskyIndex tests to testGrid
* added python function ShapeTverskyIndex to call tverskyMolShapes
* rebasing
* add python test for ShapeTverskyIndex
* changing to aassertAlmostEqual in testShapeHelpers
* 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
* trying to add shape tversky
* alpha and beta no defaults, added more tverskyIndex tests to testGrid
* corrections to GridUtils.h and ShapeUtils.cpp
* corrections to GridUtils.h
remove const specifiers from return values in DataStructs
add initial pass at query-query matching for Atoms and Bonds
fix and test for sf.net issu 2738320
add Mol.AddRecursiveQuery() method to Mol
the horrible cross-library exception handling mess on linux. This may well break things on windows, which
might want these things static. Regardless, even as it is, this should be considered experimental
- Remove a few confusing and unnecessary SD file handling functions from FileParsers (better functionality is available in the SDMolSupplier)
- Support not removing Hs in the Mol file handlers (C++ and Python)
- Remove requirement that boost be in $RDBASE/External on windows (the BOOSTHOME environment variable is now required)
- fix dependencies
This builds on windows in debug mode now and most tests pass. There's a problem with PySVD in debug mode and for some reason the rdAlignments wrapper test fails; but these don't seem super important.
https://sourceforge.net/tracker/index.php?func=detail&aid=1485703&group_id=160139&atid=814650
