* add MolOps::expandAttachmentPoints, along with tests
* support expandAttachmentPoints in the mol file parser
* switch the v2 stuff in the guts of the reaction parser
* add collapseAttachmentPoints()
add addAsQueries option to expandAttachmentPoints()
lots of testing
* an edge case and some cleanup
* add python wrapper for those two functions
* Update Code/GraphMol/FileParsers/FileParsers.h
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* changes in response to review
- support addCoords in expandAttachmentPoints()
- support the new attachment point stuff to/from CXSMILES
- add MolOps::details::addExplicitAttachmentPoint() and MolOps::details::isAttachmentPoint() utility functions
---------
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* basic approach to v2api
* does not work, backup commit
* well, that now compiles
* cleaner
* more cleanup and testing
* get the SWIG wrappers to build
* swig wrappers now build
* switch back to using references to default values
* adjust to new catch version
* move the implementation to v2 and call it from v1
* update the parameter object too
* move debugParse down
* a couple of review changes
* make v2 naming consistent with Python
* first pass at v2 for the ctab parsers
* move a the writing functionality to a different header
this is just an organizational thing at the moment; we still import the writers header in the parsers header so as to not break code
* do v2 of the tpl parser
* fix missing dependency
* Mol2 parser
* move over the XYZ parser
* switch over the PDB parsers too
* get mac and java builds working (hopefully)
* add v2 API for the reaction parsers
Fixes#7075
* v2 of the fileparser API about done
This cannot be completed until the CDXML changes are merged
* 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>
* move replaceAtomWithQueryAtom() and completeMolQueries() to QueryOps namespace
* support ring bonds from cxsmiles
* add a test that is still failing
* update nonHydrogenDegree query, add SMARTS extension for that
* some cleanup
* unsaturation and substitution count
* fix typo in test
* update expected result
* add linknodes
* add variable attachment points
* improve documentation of supported cxsmiles features
* clarifying the docs
* support leaving out the outer atoms in LN specs
* Deprecation: planned removal of .message() and .getMessage() methods
* Deprecation: planned removal of old MolHash code
* document deprecations
* output the diffs when the psql tests fail
* remove .message() from SWIG wrappers
note that the KeyError doesn't work properly. We should clean up the the exceptions here anyway
* typo
* 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
* 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
* 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
* add a SmilesParserParams object to prepare for this
* add a SmilesParserParams object to prepare for this
* add tests for the SmilesParseParmas
* support name parsing, should it be the default?
* rename CXNSmiles to CXSmiles;
add a spirit parser for CXSmiles coordinate that is at least syntax correct
* abandon boost::spirit for now; crude atom token parser
* support params in smiles parser (not tested, may not build)
* can read coords and atom labels along with mol names; crude, but works
* read coordinate bonds
* remove some compiler warnings with VS2015
* remove a bunch of compiler warnings on windows
* remove more warnings on windows
* remove more warnings on windows
* backup commit: first pass at parsing query features
* radical spec parsing
* handle attachment points using atom mapping
* switch to a named property for atom labels
* fix handling of the "A" atom query
* add functions to construct A and Q queries (needs more work)
* fix a problem created while cleaning up warnings earlier
* add some additional convenience functions for making generic atoms.
Still need M and to recognize these while writing CXSMILES
* add M queries; update some tests
* fix a linux compile problem
* get the cxsmiles stuff working in python; basic testing
* support "M" in CXSMILES
- Module to generate reaction fingerprints: structural FP for screening,
difference FP for similarity search
- Add some utility functions to simplify handling of reactions
- Add new functionality to include agents in the reactions, some adaptions
to parsers and writers had to be done
- Supports intra-bond breaks in products now
- Molecules with rxn role (atom property) can be parse as reaction now
