In high-symmetry cases where the symmetric SSSR does not find all
possible rings, substructure searches can fail because of this check.
Removing it fixes those cases, but is likely to decrease the performance
of substructure matching.
Also, adds a unit test where the old code fails
Co-authored-by: Franz Waibl <waiblfranz@gmail.com>
* revert duplicate chunk in release notes
* replace deprecated ifdefs
This one gets rid of USE_BUILTIN_POPCNT and RDK_THREADSAFE_SS
use RDK_OPTIMIZE_POPCNT or RDK_BUILD_THREADSAFE_SSS instead
* get rid of BUILD_COORDGEN_SUPPORT from ROMol.i
* fix a stupid typo
* update release notes
* suppress a bunch of warnings from third-party code
get rid of one warning in RDKit code
* corrections
* fix the maeparser flags
* remove some more inchi warnings with clang
* backup commit
This is mabye heading in the right direction and at least passes the basic tests which are there.
* some progress
* more tests and refactoring
* additional aliases
add carboaryl
* add CYC and ACY
* add ABC
* add AHC
* CBC and AOX
* add CHC and HAR
* add CXX
* cleanup: remove a bunch of nullptrs
* initial tagging support
* remove atom labels/sgroups after using them
* docs
* start handing writing
NOTE: this does not currently work: the generic code needs to move out of SubstructSearch
* move the generic groups to their own library
Signed-off-by: greg landrum <greg.landrum@gmail.com>
* make sure the generic groups end up in ctabs
* add forgotten CMakeLists.txt
* fix includes
* expose this stuff to Python
* CYC needs to initialize rings
* renaming
* add docs
* change in response to review
* - fix non-threaded *nix builds that currently fail because
boost flyweight introduces a dependency on pthreads
- make sure that mutexes and futures are only used when
RDK_BUILD_THREADSAFE_SSS is ON
- fix SubstructMatch failing test when RDK_BUILD_THREADSAFE_SSS is OFF
due to misplaced #ifdef's
- rename RDK_TEST_MULTITHREADED to RDK_THREADSAFE_SSS in inchi.cpp
(which is not a test)
* - the limitexternal Linux build is now single-threaded so we make
sure single-threaded builds do not break in the future
(suggestion from Greg)
* reverted unnecessary change to Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* make sure that ResonanceMolSupplier subtructure matches are uniquified consistently
* Fixes github #4311 (#4312)
* a bit of simple refactoring
* Fixes#4311
- adds getValenceContrib() to QueryBond
- adds hasBondTypeQuery() and hasComplexBondTypeQuery() to QueryOps namespace
- atoms with complex bond type queries now have explict and implicit valences of 0
- adds tests for the above
* add a test
* Support using SubstructMatchParameters in RGD (#4318)
* support substructure search parameters in RGD.
Still needs testing/verification of the enhanced stereo stuff
* test enhanced stereo
* add support to python wrapper
unfortunately some python reformatting got mixed in there.
* addressed comments in review
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Most tests working
* All tests working
* Fixed tests after merge with master
* Create header and implementations for RCore
* Updated comments
* Removed old code
* DLL export for MolMatchFinalCheckFunctor
* Information line for failing Mac test
* Log replace core behaviour
* Ordering fix for OSX
* Possible fuzzer fix
* Removed debug output
* Fix unmatched user R group bug
* Code review changes
* Bug fix and ChemTransforms test
* hello world works
* more
* more
minimallib needs to be tested
* parse substructure parameters from JSON
* add substruct search and parameters
* add descriptors
* register more descriptors
* fingerprints, first pass
* stop outputting tiny coord vals
* support generating 2d coords
* coordgen testing
* return nulls
* initial 3d support; add/removeHs; cleanup
* Embedding parameters from JSON
* update
* pattern fp, fps as bytes
* use json to configure MFP
* use json to configure rdkit and pattern fps
* aligned 2d coords
* parsing options
* options for writers
* rename remove_hs
* get this working on windows (kind of)
* silence some msvc warnings
* cmake updates
* update python tests
* add the CFFI code to CI builds
* cleanup line ending mess?
* a couple small fixes
* make this work with URF
* support coordMap in the 3D coordinate generation
* updates in response to review
* - generateDepictionMatching2DStructure can be used with referencePattern smaller than reference
to only use part of a scaffold
- adds generateDepictionMatching2DStructure overload to pass a matchVect instead of doing a substructure match
- adds allowRGroups parameter to enable using a scaffold bearing R groups as reference
* changes in response to review
* added comments
* fixes failing doctest
* - reverted change committed accidentally
- fixed get_sss_json for the case where R groups are not included in the match
- added tests for the return value of generate_aligned_coords
* Documented the value returned by GenerateDepictionMatching2DStructure (Python)
* changes in response to review
* - changes in response to review
- fixed sortMatchesByDegreeOfCoreSubstitution that was not working
- added Python wrappers for sortMatchesByDegreeOfCoreSubstitution and getMostSubstitutedCoreMatch
- added C++ and Pyhon unit tests for the above
* added missing variable initialization
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* remove include from headers
* update implementation files
* completely remove BOOST_FOREACH (#7)
* convert those changes to use auto
* get rid of all usage of BOOST_FOREACH
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* TautomerQuery class
* working test
* Comment header
* Merge with master. Greg's suggestions. More tests. Python wrapper
* Updated Pattern Fingerprints to merge with master. Reset email
* Java/C# wrappers. Java test
* Java/C# wrappers. Java test
* Java/C# wrappers. Java test
* Greg suggestions of 6_2_2020
* Explicit types in Java TautomerQueryTests class
* Update Code/GraphMol/QueryOps.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* get windows dll builds working
* Removed tautomer query wrappers from RDKit namespace
* Fixes from evaluation
* Template molecule identification fix. Greg's suggestion
* Final check search functor for evaluating template matches as they are found
Co-authored-by: Gareth Jones <gjones@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* run clang-tidy with modernize-use-default-member-init
* results from modernize-use-emplace
* one uniform initialization per line
otherwise SWIG is unhappy
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* 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
* do not throw in desctructor
* remove unused var; reserve
* provide operator= for DiscreteValueVect
* provide operator= for SparseIntVect
* remove unknown 'omp' #pragmas; refactor loop
* remove unused var
* remove unused variables
* give EmbeddedAtom a default constructor & early exit on self assignç
* handle unused vars/args
* catch exception by ref
* address unused args
* fix signed type comparison; refactor extra checks
* remove unused variable
* suppress switch fallthtough warning
* handle signed type comparison
* handle signed type comparison
* potentially uninitialized vars
* fix abs() of bool
* unused vars in catch statements
* remove unused variables
* python::list returns will be copied
* give ValidationMethod constructor & virtual destructor
* remove extra semicolon
* change minimal cmake version to a consistent 3.5
* progress towards a cleanup
* get the basic python deps working
* two more libs
* another round of changes
all tests pass at this point
* next round of changes
all tests pass at this point
* close to done
all tests pass
* very close
* almost done
* shift the RDBoost dependencies around a bit
* remove an extraneous python linkage
this is trying to get the mac builds working again
* Only link to python if it was built shared (#3091)
* change in response to review
Co-Authored-By: Ric <ricrogz@users.noreply.github.com>
* move that suppression of the maybe-uninitialized warning to BoostStartInclude.h
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* Test only commit for using enhanced stereo in substructure search
Adds some test cases to demonstrate what I'm planning.
When the test cases fail, the messages look like this:
-------------------------------------------------------------------------------
Enhanced stereochemistry
AND and OR match their enantiomer
-------------------------------------------------------------------------------
/Users/wandschn/Documents/src/rdkit/Code/GraphMol/Substruct/catch_tests.cpp:216
...............................................................................
/Users/wandschn/Documents/src/rdkit/Code/GraphMol/Substruct/catch_tests.cpp:218: FAILED:
CHECK_THAT( *opposite_mol, IsSubstructOf(*mol_and, ps) )
with expansion:
CC[C@@H](F)[C@@H](C)O is not a substructure of CC[C@H](F)[C@H](C)O |&1:2,4|
/Users/wandschn/Documents/src/rdkit/Code/GraphMol/Substruct/catch_tests.cpp:219: FAILED:
CHECK_THAT( *opposite_mol, IsSubstructOf(*mol_or, ps) )
with expansion:
CC[C@@H](F)[C@@H](C)O is not a substructure of CC[C@H](F)[C@H](C)O |o1:2,4|
* rename parameter to include q and m to reduce my confusion
* Don't keep recreating a map
This map is the same in every loop. And actually, the desired
information is slightly different than what was formerly stored
in the map.
* Fix tests after our discussion.
Also adds more exciting tests of disastereomers and structures
with multiple stereo groups.
* Use enhanced stereochemistry in substructure searching
Allows use of enhaced stereochemistry in substructure searching
if `SubstructMatchParameters.useEnhancedStereo` is set.
The matching rules are pretty obnoxious, but a synopsis is:
* An achiral query/substructure matches everything, because it
means "ignore chirality".
* An absolute query matches AND or OR, because they both include
the molecule with an absolute center
* An query with an OR matches either an OR or an AND, because
AND is more molecules.
* add info about matching to the documentation
* expose extended stereo matching option to python
* Some updates/tweaks to the documentation of enhanced stereochemistry
especially about searching.
* Code review comments.
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* backup, does not work
* working on the C++ side
* backup
* fix the API
* document the new functionality
* improve that example
* final bit of cleanup
* switch to std::function
* 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
* a round of cleanups courtesy of PVS studio
* add a test to make sure that a warning is a false alarm
* bug fix
* Fix a UFF bug
* more PVS studio cleanups
* next round of PVS studio cleanups
* completely remove the chances for that bug
* changes in response to review
* add an additional test
+ a bit of reformatting that snuck in
* disable builds of the StructChecker code by default
* operator"" _smarts() doesn't need to catch sanitization errors
* remove unused function
* turn back on some tests that shouldn't have been disabled
* Remove unused code from SMARTS parser and simplify a bit
SmilesParseOps::AddFragToMol is now used only from the SMARTS parser, so we can simplify the API
* Removes obsolete special case code for SMARTS
This was relevant when organic atoms in SMARTS queries were stored as two-part queries.
* improve SMARTS testing
make sure we can generate SMARTS from all the examples and then parse that again.
* Fixes#2814
* Fixes#2815
* some additional smarts tests to improve coverage
* test copy ctor and getPos
* remove obsolete test_list files
* include tests for the morgan invariant generators
* more cleanups and coverage improvements
* remove files that were mistakenly added
* forward doIsomericSmiles
* added test for #2565
* fix for my snippet
* update test with Greg's comments
* add braces for readability to MolMatchFinalCheckFunctor
* small refactors: abstract label checking, while/size, final check
* merge loops reading order of bonds -- all tests pass
* fix chiral-lead fragments, allow frags w. degree < 3
* add new test, update old
* add test, update old
* fix (inocuous) bug with ranks assignment in MolToSmarts
* start SMARTS with first non-chiral atom
* use smart pointers in test
* reenable doIsomericSmiles
* update patch for #2594
* remove faulty fragments matching
* review tests, remove wrong flip
* Remove out_1 and out_2, only need for directed graphs.
* Variable renaming, no other changes.
* Fix a couple things that were forgotten during the rename
* Only one of these counts is updated now.
* Add ifdef to enable/disable VF2Pruning
* Add degree bound check, could be pushed down to the generic VertexCheck predicate.
* The stack knows at each point what was added, by passing these into the Backtrack call the clone allocation can be removed.
* Indent and rename added_node1 to node1.
* Now the clone is removed we can add a member function to handle the recursion cleanly.
* Also make for MatchAll a member function.
* Set lim=0 to mean infinity.
* VF2Plus optimisation, when candidate is in the terminal set select from a mapped neighbours adjacency list.
* Optimisation hint.
* Use a struct for the Pair removing the need for double pointer and heap alloc/delete of the iterators.
* disable pruning by default (it's a bit quicker to not do this)
* update expected test results
The updated VF2 code can return symmetric results in a different order
than we were getting previously. The results are still correct, but they
change some of the downstream things that don't do symmetrization
* update expected java results
* first pass at adding a SubstructMatchParameter struct
* start moving the rest of the backend to use the parameters
* backend at least mostly moved over
* add aromaticMatchesConjugated
add tests
* switch over the MolBundle too
Add templates to reduce duplicated code
* support older compilers
let's see if it works...
* add SubstructMatchParameters to Python wrapper
* remove some deprecations and warnings
* damn compilers
* parameter support for bundles in python wrapper
* add the parameters to the java wrappers
* response to 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
