* Fixes#8379
* check in some working tests
* test passes
* test passes
* test passes
* test passes
* test passes
* ensure that the invariants flush the streams on failure
* tests pass
* test passes
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* Fixes#8391
* tests pass
* fix a test with legacy
not clear why this was not causing problems before
* make a test work
* Fixes#8396
* gcc builds work
* fingerprint tests pass
* mention backwards incompatible change
* fix a problem with FindMolChiralCenters
* more testing details
* enable the test status output
* Fixes#8432
fix a bug in double-bond stereo handling for template matching
* all depictor tests pass
* use the new-stereo chiral ranks in the depiction code
* always assign new-stereo chiral ranks
* make _ChiralAtomRank a computed property
This is analogous to _CIPRank
* tweak to the way the atom ordering is computed for 2D coordinate generation
* update two expected results
* backup
* response to review
* tests pass
* tests pass
---------
Co-authored-by: = <=>
* remove no-op macros and dead code (pt 2)
* test failures due to whitespace changes?
* actually run the testFeatures tests
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Fixes for canonicalization, and stereochemistry
* chnages from code review
* test that was omitted for canon correction
* PR review changes
* changes as per PR review
* missed file checkint to make PR tests compile
* PR conflict resolution
* change to fix PR buld errors (hopefully)
* line delete to force re-running of tests
* changes as per PR review
* resolve merge conflicts with master
* some suggestions
* revert chirality modifications when sanitization isn't being done
* addl changes: no stereo percept when no sanitize
* missing test expected files added
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Fixes#6138
* If we aren't initialize, don't dump AllProps
* Save atom props for agents as well
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* stop using CIP codes in the atomic canonicalization
this will change results in some cases, so lots of tests need to be updated.
* stop breaking string literals... ARGH
* tests now pass
* update double bond canonicalization
* update a python test
* some cleanup
* update expected results for cartridge
* clean up in testDatastructs
* avoid jump on unassigned mem in rxns
* set valgrind error exit code
* update suppressions
* clean up RDValue in testDict
* don't leak mol if parsing Maestro file fails
* don't leak mol if parsing PDB block fails
* cleanup leftover rxns in testReaction
* cleanup mol if CX extensions cannot be parsed
* cleanup leftover mols in smiTest1
* cleanup leftover mols in moldraw2DTest1
* cleanup leftover mols in testSubstructMatch
* make testEnumeration go easier on valgrind
* reduce R counts
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* backup
* output bond stereoAtoms in debugMol()
* stop removing STEREOCIS/STEREOTRANS markers in setDoubleBondNeighborDirections()
* Re-establish bond dirs in reaction products.
* test all that
(the first set of tests, should do more)
* cleanups
* add SetDoubleBondNeighborDirections() to python API and test it
* add more tests
* changes in response to review
* add another c++ test, fix the java tests
* Enable getStereoAtoms() for E/Z stereo bonds
* do not copy reactant bond directions to product & refactor
* new bond stereo mechanism
* update tests & add some more
* fix problems in E/Z getStereoAtoms()
* use make_iterator_range in Bonds.cpp
* backwards match, refactor, +1 test
* Apply suggestions from code review
Co-Authored-By: Greg Landrum <greg.landrum@gmail.com>
* Apply more suggestions, clang-format
* add comments, mixed pair stereo forwarding, tests; fix bug
* make Bond::getStereoAtoms threadsafe
* Revert "make Bond::getStereoAtoms threadsafe"
This reverts commit c5902d9dfb.
* Revert "Enable getStereoAtoms() for E/Z stereo bonds"
This reverts commit 9ef8c4d1f8.
* add back findStereoAtoms() to ReactionRunner
* add missing brace in conflict resolution
* Add tests for #1868
* Fix github bug number
* Fix#2 for correcting issue number
* Fixes#1868
The primary problem here was that when v3K reactions were being processed,
a bunch of "finalization" steps were being skipped for the reactants and products.
This remedies that.
* update the python test so that it tests the actual problem
* 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
* 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: #1988
This just handles the atomic number part. Still need to think about the bond types
* update the tests
This includes adding UnitTestSaltRemover.py to the list of tests to be run
* fix bug from interacting PRs
* initial pass at pickling reaction properties
* move more of the property handling functions to props.hpp
Wouldn't be bad to rename these at some point.
* add reaction properties to python wrappers
* auto generate coords in mol block writer if includeChirality = True
* default to include chirality when writing mol blocks/files
* make isomeric smiles the default; note that not all tests are passing at the moment
* update a reaction test
* update expected cartridge search results
at this point all python, c++, and cartridge tests pass
* docs
* update incompatibility docs
* update doctests
* these now build
* minor example update
* update expected c++
* typo
* make allowCXSMILES=true the default
* add auto perception of chirality when reading 3D structures from mol blocks
* explain changes in release notes
* further doc update
* backup
* Fixes#1387
this passes the bug tests, but needs the full tests run
* all tests pass
* remove some droppings left from an earlier attempt at a fix
* remove some additional printing
* cleanup
* Fixes exceptions to use correct functionName
* Deprecates ChemDrawAdjustParams name sciquest integration/eln searching
doesn’t map to this behavior. renamed MatchOnlyAtRgroupAdjustParams
* Python wrapper for deprecated API
* fixHs now is more intelligent about merging hs.
The only cases where hs can’t be merged is if they are mapped
to a non hydrogen in the product.
* Updates deprecated ChemDrawAdjustParams
* Adds C++ Enumeration Engine to the RDKit
* Adds Sanitization helpers, wrappers and tests
* Clang format
* Remove unused enumerationStateOnly flag
* Fixes docStrings to current API
* Adds doc strings
* Removes RGroupPosition, adds getPosition to EnumerationBase
* Fixes readability.
* Adds EnumerateLibraryBase::reset and getReaction
* Added getReagents method to EnumerateLibrary
* Make the tests have the same naming
* Need to save the initial state for resetting.
* Stupid case-insensitive file systems
* Moves ResetState to EnumerateLibraryBase
* Adds removeNonmatchingReagents helper
* Renames currentPosition to getPosition
* Adds Enumeration Toolkit tutorial
* Fixes Python3 serialization and enumerators
* Verified to run on python2 and 3
* Fixes integer issues on windows
* The number of enumeration should be unsigned.
* Adds deserialization constructor
* Moves boost_serialization to the end
* Deprecates Clone in favor of copy
* Update tests to use copy.copy not Clone
* Move RGROUPS and BBS into an EnumerationTypes namespace
* Make sure old pickles work
* Adds pickle for backwards compatibility
* Moves to uint64_t from size_t for public api
* Whups, accidentally used the binary archiver.
* Commits boost 1.55 serialization
* Makes serialization turnoffable Like Filter Catalog
* Fixes tests when serialization not available. Adds more enumeration strategy tests
* Fixes a syntax error on some versions of python
* Fixes sanitizeRxn to actually make proper RGroup atoms
* Updates SanitizeRXN python API
* Updates Enumeration API to a parameter class - fixes reagent removal
* Adds a mess of tests
* Change stats to return a string.
* Exposes EvenPairSamplingStrategy Stats to python
* Fixes a crash bug in SanitizeRxn
* Adds better testing of the even pair sampling
* Fixes namespace
* One more try to fix gcc
* Enum classes are c++11 and a microsoft extension.
* Fix typo
* Fixes np.median for python3
* Fixes atom iterators
* Adds virtual tags to derived virtual functions (for clarity)
* Fixes size comparison issues
* Adds doc string
* Small cleanup (has no effect since flags aren’t used)
* fixes crash bug on windows
* get the tests working on windows
* Updates tutorial
* Adds Glare implementation to Contrib
