* 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
* unused vars in bison parser cleanup
* initialization order in TopologicalTorsionGenerator
* unused params in SLN bison
* sln flex unused params
* throwing destructor in TDTWriter
* signed comparison in substructmethods
* unused input param in smiles/smarts bison
* unused ms param in sln bison
* signed comparison in FingerprintGenerator
* store return of fscanf in StructCheckerOptions
* unreferenced var in catch
* uninitialized value in FileParserUtils
* avoid override overload warning in MolDraw2DSVG
* non-final overrides in Validate.h
* unused static var in Avalon
* unused vars in catch blocks
* make AvalonTools avalonSimilarityBits & avalonSSSBits const int
* assert fscanf result in StructCheckerOptions
* 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
* move _embedPoints over to use EmbedArgs structure
* move _embedWithExpTorsions over
* a few pointer cleanups
* step by step
* more
* wrap the ETKDG paramaters into a struct
* fix a typo
* additional cleanup
* more
* simplify the embedargs struct
* pass embedParams instead of having them in embedargs
* a bit more cleanup
* response to code review
* 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
* Fixes#2057
docs still need to be updated
* docs update
* Update getting started doc.
This still needs to have the doctests run and should probably be
proofread and tweaked
* some doc updates
* change in response to review
* Fixes#1990
makes sure we don't destroy a double bond's StereoAtoms just because a bond connected to one of its atoms is removed
* change in response to review
* 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
* first pass, does not yet actually work
* pass2, same problems
* pass2, same problems
* another test
* new tests; bugfix
* move the code out to a header
* add a double bond example
* enable auto-downloads of the code
* move the function to its own namespace
* first pass at a basic python wrapper
* change coordgen commit used
* try supporting bond stereo; does not currently work
* cis/trans seems to now work.
* first pass at templates; needs testing
* use the fixed flag too
* need mol align
* expand test
* initial pass at python wrapper for template
* simplify tests
* add an option to directly use a substructure match for alignment
* scaling
* add #define
* Define a cache setting for RDK_COORDGEN_LIBS to allow these to be used in other packages
* return the conformer id from addCoords
* Make CoordGen the default when it’s available.
This is a backup commit… the tests don’t even come close to passing.
* add some debugging options for a bit
* add alignment step to testing when using non-fixed coords
* Add global to allow use of CoordGen to be disabled
get the basic depictor tests working
* make coordgen the default when it is available
* make sure things continue to work when coordgen is disabled
* get windows builds working
* mods to get this building on windows.
something is screwy with the fileParsersTest1
* no need to generate coords for the 1K C string
* fix java wrappers
* works on linux
* update the (stupid) way dependencies were handled on windows.
this allows a lot of cleanup of cmake files (still more to do)
the linux build is unlikely to work due to the way _statics aren't handled
* docs
* extend forceRDKit applicability
* switch coordgen version
* try using templates
* try to get the template dir finding reasonably robust w.r.t. conda install
* continuing to iterate on the way the template file is installed
* fix a problem caused by the merge
* remove test that should never have been checked in
* update expected results for cartridge tests
* switch back to using the RDKit as the default coordinate generator
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
* Actually delete atoms and bonds...
* RWMol::clear now calls destroy to handle atom/bond deletion
* Changes broken Atom lookup for windows/gcc
* Adds tests for running with valgrind
* Adds test designed for valgrind and molecule deletions
* Removes RNG, actually tests bond deletions
* update swig wrappers
* deal with most recent changes on the main branch
* Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0.
Fixing two distinct bugs:
- A randomSeed of 0 didn't use '0' as the seed even though the
documentation said that it should.
- Very large seeds could overflow the 'int' representation during
calculation of a new internal seed. This would make
EmbedMultipleConfs non-deterministic even though the user provided a
valid seed.
* Adding a C++ test for case pull request #1635.
* version 2 of ETKDG
* setting default and changing to unsigned int
* ETversion 2 only via EmbedParams available
* Some refactoring so that the DG functions that take the parameter object are the primaries.
This should allow new parameters to be added without having to modify the API
* test and wrapper changes to go along with that
* update cookbook to use etkdg
* regression test for ETKDG version 2 improved
* version 2 of ETKDG
* setting default and changing to unsigned int
* ETversion 2 only via EmbedParams available
* Some refactoring so that the DG functions that take the parameter object are the primaries.
This should allow new parameters to be added without having to modify the API
* test and wrapper changes to go along with that
* update cookbook to use etkdg
* add a test (currently fails, of course)
* backup, not really working
* Fixes#1240
* a bit more parameter tweaking to get some more structures to embed
* 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
* Fix a bug in the python DistGeom tests.
* test new features
* add simple parameter objects for ETDG, ETKDG, and KDG
* Update conformation generation documentation to use the new parameter objects.
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* yapf
* document the parameter object;
introduce pre-defined const objects for ETDG, ETKDG, and KDG
* this is why we write tests
* swig did not like the initialization in the header file
* passes all tests, but is still not 100 percent there
* generalize _centerInVolume for possible future use
* better testing of tetrahedral centers
update tests
* only test ring atoms
* handle 4-coordinate n too
* add a volume check; not all tests pass
* turn off debug printing
* rearrange the order of tests.
if this is not done, we get a seg fault when the github55 test runs.
the whole thing needs to be run under valgrind to track this down
* clear up a memory leak
* a bit more documentation
add a constant for one of the threshold values
* get more permissive on the energy tests.
Only do the extra tetrahedral tests for atoms in at least two rings.
* add a DEBUG_EMBEDDING option to make tracking down failures easier
* enable better debugging when the flag is set
* remove a FIX
* remove some debug printing from the tests
* enforce planarity
* increase the force constant for the impropers
* force constant adapted
* reduced tolerance for planarity and force constants changed for some torsions
* tolerance for planarity increased a bit again
* cerr outputs removed
* planarity tolerance increased
* boost log added in planarity check
* - made Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp and Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py
more robust against very small coordinate variations which may induce UFF energy variations in the 1-kcal/mol range.
This was observed in a single case using the MinGW 32-bit g++ compiler. The check for identity of conformations
between single- and multi-threaded runs is now complemented by a 3D coordinate MSD check
* - lowered the energy tolerance to 1.0 kcal/mol
* - added rdkitBuild string with compile-time information
- added runtime check in Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
and Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py
to use more lenient tolerances with MinGW compilers
