* fix aliasing bug in MultithreadedSDMolSupplier
* update GeneralFileReader to v2 API
* add backwards incompatibility note
* v1 of this
* The helper function needs to be inline
* forgot the tests
* allow non-threadsafe builds
* MultithreadedMolSuppliers can now be destroyed without being used.
This was previously not possible
* add callbacks to the multithreaded readers
* document the new functions
* switch to storing the queues in unique_ptrs
* does not work
* only do those tests when in MT mode
* more generalfilereader cleanup
* tests pass
* passes tests
* extremely basic python wrapper
* better wrapper
* does not work
* tests pass
* test data
* fix failing test on ARM macs
we need to followup on why the wedging is different here
* move some stuff to the cpp file
the idea is to have the windows DLL builds not break
* fix(?) win64 linkage problems
* remove a warning in non-multi-threaded builds
* fix non-multi-threaded work
* well, at least local windows builds work
* remove duplicated code
* refactoring
simplification?
* simplify mutext handling
* review suggestions
* 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
* Fixes#3797
* [WIP] Add tautomer queries to the substruct library
* Add TautomerQuery to CMake
* Add missing TautomerQuery functions, python wrapper and tests
* Add python wrappers for Substruct Library Tautomer Queries
* Explictly label non-const pattern function now that we have both
* Use boost::shared_ptr not std::shared_ptr
* Fix java builds
* One more try to fix java builds
* Fix Java Tests
* Run clang format
* Reenable tests
* Fix annoyingly stupid bug and annoying commit of debug code
* Fix documentation
* reenable ifdef threadsafe check
* Throw warning and perform tautomer search instead of bailing with incorrect fingerprints
* Simplfy api with templates
* Fix SubstructLibrary java issues
* minor API cleanup
* simplify the SWIG wrappers
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* - enable SubstructLibrary to build without threading support
- enforce consistency across single- and multi-threaded runs
- improve performance on single-threaded runs avoiding overhead of spawning threads
- consolidate internalCountMatches and internalGetMatches into one function to reduce code duplication
- fix a bug in Python CountMatches whjich would run on 1000 threads
* reverted Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp as it is now in its own PR (#3558)
* - added missing cast
- removed unnecessary std::make_move_iterator
- added Brian's test
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add threaded pattern generator to help speed up library creation
* Add size to FPHolderBase
* Add more complete python wrapper, fix leak in doctest
* Add basic usage test for addPatterns, fix I/O leak
* Add basic test for trusted smiles
* Actually add the new code
* Export addPatterns on windows
* Try fixing the cartridge build
* Change pattern_factory to PatternFactory
* Change boost::ref to std::ref
