* 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
* 3D Descriptors Dragons
* stripped down, not yet working
* get this building on a non C++-11 compiler
* move the python test to the python directory
* move the python test to the python directory
* add the python test
* now at least those tests runn
* warning comment
* some basic refactoring and cleanup
* get python wrapper "working" (completely untested)
* fix Name
* fixing AutoCorr & RDF
* AutoCorr test added
* RDF reviewed based on AutoCorr comments
* fix Morse code
* Morse reviewed
* Correct Morse & start Getaway
* correct MORSE test
* start Getaway clean up
* simplification of Whim
* better
* fix Getaway
* fix RCON
* merge repaired
* adding Dragon 2D autocorrelations descriptors
* fix the 3D autocorrelation descriptors based on the modification in
Dragon.
* Adding the 2D autocorrelation descriptors (no need of Eigen
dependency for this one)
* Adding 2D test case
* IState … no idea for the moment
* there is an error in 2D computation (memory error ???)
* fix the IState for molecules with Hs
* need to use getTotalNumHs(true) not getTotalNumHs()
* also need to remove Hs in both dv and d!
* fixing Rcov values
I fix the Rcov values
* fix Getaway
* remove push_back
* remove call to sum
* improve tests
* fix getaway
* adding precision parameter to GETAWAY
* adding rouding (1e-3)
* fix WHIM
* use void in declarations of function
* update MolDescriptors link
* remove print option in WHIM
* fix python wrapper to 3D descriptors.
- all modifications reduce computation time by a factor of 3!
* final fix for Getaway
* all output are fixed except the 2 first values due to clustering
approach.
* cluster cannot be fixed du tu float precision issue between Java &
c++
* best fix of ITH and ISH
* use the same algorithm as in Dragon 6 but there is still a deviation
* remove std::move
* std:move only works on c++ 11
* fixing issue based on Greg Comments
* auto2D still not working on my env
* update 3d test.py
* auto 2D not working after the first loop test
* tighten up the tests
* change name
* update, but still does not pass
* make this run (though it does not work)
* re-enable test3D
* some cleanup
* add GETAWAY test data. Note that the tests fail
* fix the ATS and ATSC autocorrelation 2D
Broto Moreau and Geary autocorrelation are not correct again a specificity of Dragon to compute them. The result are not consistant with Padel because we use the relative weigth not in Padel.
* one minor change to get things to compile
* fix the M & G matrix computation
fix inversion in the computation of the equations for both M & G matrixes
* update autocorr2d tests
* 192 examples
* fix issue in cluster 0.01 0.009 case
this is not correct all the cases
* update GETAWAY expected values to reflect the fact that we cannot reproduce the literature values exactly
fix a leak in GETAWAY
* fix the negative values in gamma
this is strickly the implementation that we find in the book molecular descriptors for chemoinformatics (except the case where an atom is already in the axis in this case it should be added in the symetric list which is not the case in this implementation)
* Update WHIM.cpp
adding the axis atoms to the symetrical list
* update WHIM tests
* add AUTOCORR2D to MolDescriptors and the python wrappers
* start adding tests
* test the python versions of the new descriptors
* update list of descriptors
* update .gitignore
* foundation for 3D descriptors
move PBF into core
* cleanup work
* a bit more cleanup
* move the principal moments calc to MolTransforms
* cleanup
* cleanups
* add caching of the principal moments and values
* do not include the 3D descriptors in MolDescriptors.h
* the properties are computed
* add PMI descriptors and tests
* add tests for NPR descriptors
* return 0 when the largest PMI is zero
* PMI edge case tests
* NPR edge case tests
* PBF edge case tests
* PBF edge case tests
* more edge cases
* add a few more 3d descriptors
* add defns to docs
* tests for the new descriptors
* add versions to new descriptors
* add 3d descriptors to python wrapper
* add eigen support to the travis build
* try to get non-windows builds working
* remove computeCovarianceMatrix() from java wrapper
* make pmi property names "private"
