* Issue #2403: Speed up SSSR symmetrization
For my horrible example molecule (a highly symmetric
nanotube with 2400 atoms and > 1000 rings), this speeds up
symmetrizeSSSR() from 5s to about 0.002s. findSSSR() takes
another .4s or so.
* Refactor after Ricardo's suggestions
* Greg's review comments. use std::vector
* 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
* not quite done yet
* Fixes#2244
* Fixes#2148
This fixes a few of the knock-on effects of the actual fix.
* Test that we still write SMILES properly
* Fixes#2266 (#2269)
* Fixes#2268 (#2270)
* Improve interactivity of output SVG (#2253)
* Add clickable atoms when tagAtoms() is called
* add python tests
* add class tags for atoms and bonds
* add marker to allow easy insertion of extra text
* 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
* Modify removeHs so that it does not remove degree 0 atoms
Update the docs at the same time.
* include a warning when not removing some Hs
* clear up a problem with the warning log
* 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
* 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.
* This makes assignStereochemistry cleanIt=True not remove CIS/TRANS
bond stereo chemistry that was manually added as described in issue #1614.
Incorrect CIS/TRANS stereochemistry will still be removed by
'cleanIt=true' if symmetry is detected. However, this symmetry
detection doesn't work in more complex pseudo-stereo chemistry cases:
bond stereo that depends on other bond stereo to break symmetry; and
bond stereo that depends on other atom stereo centers to break
symmetry. Test cases for these cases have been added ifdef'd in based
on USE_NEW_STEREOCHEMISTRY.
However, getting USE_NEW_STEREOCHEMISTRY to work in a copacetic way is
not trivial, I tried a little bit here to no avail. I'm leaving the
test cases checked in as they should be useful when we decide to make
the plunge into using Canon::chiralRankMolAtoms for symmetry detection
instead of the CIP ranks.
So this fixes at least the glaring issue of STEREOCIS and STEREOTRANS
being incorrectly removed by 'cleanIt=true' when it is indeed valid
stereo. The checks made for symmetry are rudimentary, but don't feel
complete.
* add another test; make what's being tested explicit
* test smiles generation and function when Hs have been added
* add a test that fails
* I think that it's ok to remove this
* backup
* At this point all tests pass.
Bond wedging is now handled even if sanitization is turned off when mol files are read
* adjust to code changes
* fix a couple problems caused by rebase
* update docs
* Fix for issue #1730
setAromaticity() now works even if there are aromatic atoms present and the relevat test case is added
* Removed setaromaticity flag
* Fixes#1735
I’m unsure if this is the correct solution, it appears
empty molecules never initialize their rings.
* Return immediately when ranking empty molecules
* Make github issue the correct one
* Always resize results to the number of atoms
* backup
* Add a couple of more tests and an exclusion for triple bonds.
* expose the MDL aromaticity model to python and test it.
* exocyclic bonds should not “steal” electrons in the MDL model
* backup (partial) update for aromaticity model documentation
* add examples to testGithub1622 for aromatic and nonaromatic compounds
* updates to aromaticity model and docs based on additional information from @bannanc
* some additional examples from @bannanc
* add rule to allow exocyclic multiple bonds to disqualify an atom.
* minor doc update
* address some review comments
* handle the heavy-atom degree queries differently
* Fixes#1563
* add a test for the heavy atom degree option
* Support (and test) adjustHeavyDegree in the cartridge too.
* test results
This actually just causes the molecule processing to fail in a reasonable amount of time; it is not an actual fix to the underlying ring-finding problem
* Adds RDProps updateProps API point
* AdjustQuery now copies over original atom data to the query ato
* Preserves existing data on the replacing atom
* Exposes preserveProps to Python replaceAtom/Bond
* Adds RDProps updateProps API point
* AdjustQuery now copies over original atom data to the query ato
* Preserves existing data on the replacing atom
* Exposes preserveProps to Python replaceAtom/Bond
* 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
* first pass at RWMol::replaceBond()
* get ready for the changes
* rename some options
add bond options (not doing anything with them yet)
update tests to reflect new options
* backup
* re-enable the rest of the tests
* Fixes#1021, kind of.
The test for the bug passes, but there are other failures
* all tests except hanoi pass
* passes all tests
* remove some vestigial code
* remove debug-droppings
* minor documentation
* backup commit
* Change the names and meanings of MolOps::AdjustQueryWhichFlags
What was there before was not flexible enough and was extremely confusing. This should clear that up.
NOTE: this does break backwards compatibility with code that uses this enum, but given that this is new and has not been
widely promoted, I suspect it should not affect that many people. The default behavior of MolOps::adjustQueryProperties()
remains the same.
* adjust to the new AdjustQueryWhichFlags
* add mol_adjust_query_properties tests to the cartridge
* first pass
* Fixes#623
* fix a merge problem
* move the aromaticity perception to a helper fn
* python doc update
* replace setSimpleAromaticity() with a parameter to setAromaticity()
* add simple test for the custom aromaticity function
