* 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
* 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>
with cmake --build . --target stubs (also make stubs on *NIX)
- improved the patching script to do a better assignment of
overloaded constructor parameters, whcih results in a number
of docstring fixes
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - added gen_rdkit_stubs Python module to generate rdkit-stubs
- added patch_rdkit_docstrings Python module to patch existing C++ sources to fix docstrings missing self parameter and add named parameters taken from C++ signatures where possible
- added rdkit-stubs/CMakeLists.txt to build rdkit-stubs as part of the RDKit build
- added an option to CMakeLists.txt to enable building rdkit-stubs as part of the RDKit build (defaults to OFF)
* fixed CMakeLists.txt, rdkit-stubs/CMakeLists.txt and a doctest
* - added missing cmp_func parameter
- fixed case with overloads with optional parameters
- do not trim params if expected_param_count == -1
- add dummy parameter names if we could not find any
- keep into account member functions when making up parameter names
- address __init__ and make_constructor __init__ functions
- fix incorrectly assigned staticmethods
* patched sources
* address residual few remarks
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* make sure that we can build without boost iostreams or seralization
adds some "private" variables on the python side to check for these compilation flags
* get out minimal cmake version correct
* get minimallib js building
installs an up-to-date cmake
also updates the version of boost being used for the minimallib
adds extra argument to allow the repo to be specified
* add RDKIT_CFFI_STATIC option
minimallib cmake cleanup
* clean up a lot of boost::iostreams nonsense
* find_package(boost cleanup
* update the swig wrappers
* updates to psql
* get the Qt demo working again
* fix? coordgen
* only use std::regex in moldraw2d test
this is consistent with the other tests
* cleanup the serialization stuff too
* support generalized substructure search in the SubstructLibrary
* simplify namespaces
* support the new functionality in the swig wrappers
* update mac swig version in CI
* ensure swig4
* switch mac_java ci builds to conda-forge
* change in response to review
* add copy ctor to extendedquerymol
* Back to the way it was
* un/signed comparisons in molops
* reference in loop in EmbeddedFrag.cpp
* un/signed comparison in filtercatalogtest.cpp
* un/signed comparison in Descriptors/catch_tests.cpp
* un/signed comparisons in DetermineBonds.cpp
* drop unused 'params' arg from static functions in MolInterchange/Writer.cpp
* un/signed comparisons in MolDraw2D/catch_tests.cpp
* unused var in SubgraphUtils.cpp
* 'move' preventing copy ellision in CDXMLParser.cpp
* fix infinite recursive call in SubstructLibraryWrap.cpp
* remove some more deprecated numpy stuff
* workaround for changes to random.shuffle in python 3.11
* fix pickling of rdkit mols in python 3.11
* add py311 build to CI
* update py311 CI
* remove qt for py311 for the moment
* only use the new code with pyversion >=3.11
* use the new logic for all pickle_suites
* need to work with older py too
The example for KeyFromPropHolder in the documentation here:
https://www.rdkit.org/docs/source/rdkit.Chem.rdSubstructLibrary.html
doesn't render the example correctly. I don't know if the extra new line fixes it, but it looks like that is the only difference to the previous code blocks.
* 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
* add boost::serialization support to ROMol
* add RWMol test
* get the windows DLL builds working
* switch FilterCatalog and SubstructLibrary to serialize ROMols
* an actual solution to the windows dll problem
* the FilterMatchers stuff was not working
* Support for logging via Python's logging module.
* Avoid the Python 3.9+ PyObject_CallOneArg function.
* Move logging functions to RDBase; Python logger by default; clean up tests.
* See if removing NOGIL fixes the Windows stall.
* get tests running on windows
* Reset to using C++ logging; whiespace tweaks.
* Longer timestamp grace period; try tempfile vs Windows logging stall.
* Clean up commented code; get details for log count bug.
* SubstructLibrary: Fix c++ threads calling into python
* FilterCatalog: Fix c++ threads calling into python
* Release notes; make sure Jupyter still logs to sys.stderr.
* Always use thread-local log buffers.
* de-verbosify a test
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* fix a crashing bug in SubstructLibrary
* fix a bunch of other potential seg faults
These are all places where the result from pyObjectToVect(),
which can legitimately return a nullptr, is not checked before
being dereferenced.
* document behavior
clear the result vector for the other pythonObjectToVect() overload
* change error message
in response to review
* Adds KeyFromPropHolder to hold user defined indices
* Add missing file
* I hate swig. Had to move keyholder classes into main header file, yuck.
But I added tests, so yay?
* Remove removed dependency
* Fix borked test
* Make consistent getKeys function, fix constness
* Fix overloaded call
* Remove GetKey/s from SubstructLibrary
* support MolBundles in the SubstructLibrary
* support SubstructMatchParameters in SubstructLibrary
* expose those methods to the python wrapper
* fix non-threadsafe build problem
* be explicit about sorting
* add the option to set the search order
* add example functions for setting the search order
* MolFragmenter: fix a leak when exceptions are thrown
* DistGeomHelpers: fix leaks when exceptions are thrown
* SubstructLibrary: fix usage of invalid memory
* clear up leaks found during ASAN testing
* 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>
* cleanup a bunch of g++ warnings
* make it work with clang
* remove some additional warnings based on CI builds
* fix that version number
* stop being verbose when building
* 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>
* - added some missing const keywords
- added an addFingerprint overload to allow passing pointers
- added a test
* changes in response to review
* removed print
* added missing shared_ptr declaration
* added PatternNumBitsHolder serialization
* - merged with upstream changes and resolved conflicts
- got rid of PatternNumBitsHolder and leveraged the serialization version to get the PatternHolder to be backwards-compatible
* built substructLibV1.pkl with an older version of boost
* reverted serialization version to 1
only write numBits if != 2048 and only read numBits if it exists in the archive
* bogus commit just to trigger a rebuild
* - 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>
* 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>
* 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>
* 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
* 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
* Exposes the stream interface for the substruct library
* Update SubstructLibraryWrap.cpp
* Adds docs
* Fix doctests
* Fixes another doc test
* More doc test fixes
