* Remove Dict::getData() for a strict abstraction boundary
Replace direct access to Dict's internal std::vector<Pair> with
encapsulated methods: size(), empty(), const iteration via
begin()/end(), appendPair(), markNonPOD(), and getRawVal().
This enables future changes to Dict's internal representation
without breaking callers.
Ref: rdkit/rdkit#9112
* Harden Dict::appendPair to take a populated Pair by move
appendPair(Pair&&) now auto-detects non-POD status via
RDValue::needsCleanup(), eliminating markNonPOD() and the
risk of dangling references or uninitialized entries.
needsCleanup() is placed next to destroy() on RDValue to
keep the POD/non-POD distinction in one place.
* Remove vestigial dictHasNonPOD param from streamReadProp
Both callers ignored the output. Non-POD detection is now handled
by Dict::appendPair via RDValue::needsCleanup().
* unbork java build
* Address PR review: bulk append, rename getRawVal, add custom data test
- Add Dict::append(vector<Pair>&&) for bulk insertion with reserve
- Use bulk append in streamReadProps to restore pre-allocation
- Rename getRawVal -> getRDValue per reviewer preference
- Add test verifying custom AnyTag data is destroyed through Dict lifecycle
* heed self-review
* don't manually implement vec.insert
* Add test: ExplicitBitVect round-trip through Dict serialization
Exercises the full streamWriteProps/streamReadProps path with an
ExplicitBitVect in an RDProps Dict, confirming the custom handler
is invoked and no memory is leaked (verified under valgrind).
* in anyTag test, assert destructors ran a specific number of times.
---------
Co-authored-by: bddap (Coding Agent) <andrew+bot@dirksen.com>
* When building RDKit as a static library, Ricardo found that the externs aren't
being resolved correctly causing a number of bad std::any casts. This is his
patch (which we apply in the context of the sketcher build) which moves the
definitions up from the types.cpp file, and make them static.
* Use inline keyword to avoid duplication overhead; this still allows the
use of the static keyword to resolve the issue with static libs
https://en.cppreference.com/w/cpp/language/inline.html
* static inline doesn't work in my static builds; inline only does though
* inline constexpr std::string_view
* casting
* inline-constexpr
* add string_view to python converter
* propagate string_view after static types
---------
Co-authored-by: Ric <ricrogz@gmail.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Properly cleanup Dict::Pair when serializing HasPropWithQueryValue
* Make sure pickling doesn't change original molecule
* Fix bad cut and paste
* Add PairHolder utility class for memory management of non Dict Dict::Pairs, fix mem leak in pickler
* Edit comment to force a rebuild
* Ignore PairHolder from Java/Swig builds
* Ignore PairHolder API from swig
* Reponses to review
* Add backward incompatible change
* Make release note a bullet point
* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* fix for CI build
* attempt to fix java build in CI
* attempt to fix java build in CI #2
* New routine to remove non-explicit 3D-geneated chirality
* changed to use pair for atrop atoms and related bonds
* Changes as per PR reviews
* PR review respnses
* PR review reponse - more
* Fix merge from master
* fixing java ci after merge
* Updated the help doc for atripisomers
* update the atropisomer docs
* improve the images
* add the source CXSMILES
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* store more bond properties (if present) when pickling
* store the attachpts stuff more efficiently in pickles
* better error reporting in the cartridge
* updated cartridge use cases
* switch from boost::any to std::any
* changes in response to review
* handle the slightly different error messages from different compilers
* document changed error message
* try to use g++10 for the linux builds
* remove those CXX defns
* another spelling
* stupid typo
* bump all linux builds to g++-10
* some day this will be done
* small steps
* increase mac ci builds runtime
* backup
* fixes#6312
all tests pass
needs tests for atoms
* more optimization; tests pass
* get rid of the global variables so that the cartridge works with this
sooooooo weird
* 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
* resolves oss-fuzz #24399
* clean up some undefined behavior
* fix some UB in mergeQueryHs
* be more defensive
* defensive programming
* fix a _cxsmilesBondIdx bug
* more defensive programming
* start refactor query pickling
* further query pickling refactoring
* bit of modernization
* partial implementation of query writing
* serialize recursive queries
* new tests
* support QueryAtom and QueryBond with null queries
* more query cleanup
* tests pass
* switch from std::variant to boost::variant
* update clang version for CI
* explicit instantiation of templates
* get dll builds working on windows
* optionally skip h counts on parsing; more query tests
* change in response to review
* changes in response to review
* make sure atom and bond bookmarks survive replaceAtom/Bond
* fixes oss-fuzz #30572
* fix possible memory-access error in error reporting
* more defensive deserialization
* switch that recursive smarts error handling to not use an exception
* 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
* allow CXSMILES generic query atoms to be parsed from mol;
need more tests here
* remove vestigial directory
* Add d_queryType to Query
This opens up additional flexibility with customizing the way queries are handled
Also includes some assorted cleanups in the Query directory
* remove the MolFileSymbol hack added in #3235
We don't need it anymore
* Add support for additional ChemAxon extensions and document them
Signed-off-by: greg landrum <greg.landrum@gmail.com>
* bump pickle version
* add an additional test
* 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>
* 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
* 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
* first round of cleanups based on PVS-studio suggestions
* a couple more
* a few more cleanups
* another round of cleanups
* undo one of those cleanups
we want the integer rounding behavior here
* add a comment to make that clear
* Fix for filter catalog PRECONDITION redundancy
* Fixes#2311
at least I hope it does
* Stop using deprecated boost functionality
* allow the Murtagh module to import even if the code isn't built
update the associated tests
* update release notes
* typo
* fix integer division
* Implementation of SGroups
* remove sample files test
* update gitignore with test outputs
* fix RevisionModifier
* re-enable tests
* backup commit; things seem to work so far
* some refactoring; obvious s group tests pass now
* more refactoring
* everything now out of the public API
* not sure why this was still in there
* rename functions; all tests now pass
* remove getNextFreeSGroupId; readd comment in copy SGroups
* clang-format
* squash-merge current master
* squash merge master
* Address comments on PR
- Update to current master.
- Move SGroup parse time checks to SGroupChecks namespace.
- Store SGroups in ROMOl as vector<SGroups>.
- SGroup methods return referenes instead of pointers.
- Use atom/bond/sgroup indexes for properties instead of pointers.
- Have SGroups inherit from RDProps; move properties to RDProps.
- Remove trivial/unused methods.
- Add a link to the SD specification atop SGroup.h
* add a couple test files
* backup
* first pass at some theory documentatin
* it's a draft
* Update enhanced stereochemistry documentation
Adds initial target use case and caveats about the tentative
nature of the current implementation.
* Support read/write of molfile enhanced stereochemistry
This includes reading and writing of enhanced stereochemistry
from v3000 molfiles (sdf). Enhanced stereochemistry encodes
the relative configuration of stereocenters, allowing
representation of racemic mixtures and compounds with
unknown absolute stereochemistry.
It does not include:
* Python wrapping
* invalidation of the enhanced stereochemistry
* use of enhanced stereochemistry in search
* depiction of enhanced stereochemistry.
* Update to reflect changes from #1971
* change names of enum elements to allow compilation in VS2017
I think it's also clearer to do things this way
* Addressed most review comments.
* Run missed test "testEnhancedStereoChemistry"
* In tests, added size checks to group equality checks
* Updated copyright statements
* Deleted mol created for a test
* Use perfect forwarding in RWMol::setStereoGroups()
* use references for stereo groups that are checked in write and pickle
* Updated stereogroup.h in hopes of fixing compilation on Windows.
* clang-format
* try allowing a switch to boost regex and requiring it for g++-4.8
* do a better job of that
* typo
* Code review comments. Updated Copyright notice.
* When an atom is deleted, delete stereo groups containing it.
Also updates StereoGroup toUse accessors instead of
constant member attributes. This allows move of StereoGroups.
* RDKit style guide
* Add header required on Windows.
* get the SWIG wrappers to build
* Fixes#1929
* add a tests to make sure bogus template directories work
* add a combined atomic number + aromaticity query operation to speed up SMARTS matches
Still needs to be recognized by the SMARTS writer, serialization, and no doubt a few other places.
* add a combined query for the single/aromatic bond query that shows up in SMARTS
* Stop using a dead pointer in the when parsing Marvin SMARTS in a CTAB
* At this point all tests pass on windows
* debugging info back in
* update the bison output
* 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
