* Added fingerprints to GeneralizedSubstruct search
* Small change to fire tests
* Edits from code review
* Updated swig - newobject not required for GeneralizedSubstruct fingerprint methods
* GeneralizedSubstruct only supports unique_ptr in SWIG4.1
* - 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
* 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
* enable Werror on Mac and Linux
* do not fail on boost multiprecision pessimizing move
* fix eigen array_bounds warning
* Fix unused arg in Rascal MCS
* fix range-loop-construct warning in Rascal MCES
* fix sign mismatched comparison
* drop unused lambda capture
* allow FMCS timeout test more time under Debug (not a warning!)
* fix fwd declaration of struct RascalClusterOptions
* fix deallocator mismatch
* fix two minor leaks
* fix a real leak
* more minor leaks
* fix another real leak, plus some potential ones
* fix std::move preventing copy ellision
* allow longer run time for debug builds
* make maxBondMatchPairs and getLargestFragSize unsigned int
* make snake case camel case
* update to current master, fix new warnings
* update again and more fixes
* add #include <optional>
* fix char array deallocation
* update and fixes in Marvin writer
* unsigned int
* more copy ellision fixes
* more copy ellision fixes, and typos
* and some more
* framework for extended query.
serialization works
to/from text doesn't work
* first pass at getting substructure search working
basic tests
improved error handling (try not to take down the server thread!)
* add serialization to MolBundle
* we really need to pickle mol properties
* basic support for molbundle
including substructure search
* tautomer and molbundle queries to JSON
* remove debug msg
* cleanup debug
initial index steps (not tested)
* remove indexing stuff since it wasn't working
will try to come back to that
* add xqm to update script
* add c++ testing for molbundle serialization
* add serialization of molbundles to python interface
* support expanding molbundles to arrays of tautomer queries
* edge cases
Signed-off-by: greg landrum <greg.landrum@gmail.com>
* change in response to review
* a bunch of updates
* make sure the mol props needed for XQMs are being serialized
* update update script
* fix binary string output from ExtendedQueryMols in python
* tautomer queries should serialize properties
* more testing never hurts
* combo of generic groups and generalized queries works
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Fix weird quotes?
---------
Signed-off-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* fixes a copy constructor issue:
In copy constructor ‘boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]’,
inlined from ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14:
/usr/include/boost/smart_ptr/shared_ptr.hpp:416:66: warning: ‘*(const boost::shared_ptr<RDKit::ROMol>*)((char*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)).boost::shared_ptr<RDKit::ROMol>::px’ may be used uninitialized [-Wmaybe-uninitialized]
416 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn )
| ~~^~
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’:
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: ‘<anonymous>’ declared here
129 | ROMOL_SPTR react = python::extract<ROMOL_SPTR>(reactant);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:17:
In copy constructor ‘boost::detail::shared_count::shared_count(const boost::detail::shared_count&)’,
inlined from ‘boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]’ at /usr/include/boost/smart_ptr/shared_ptr.hpp:416:72,
inlined from ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14:
/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: ‘((const boost::detail::shared_count*)((char*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)))[1].boost::detail::shared_count::pi_’ may be used uninitialized [-Wmaybe-uninitialized]
438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_)
| ~~^~~
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’:
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: ‘<anonymous>’ declared here
129 | ROMOL_SPTR react = python::extract<ROMOL_SPTR>(reactant);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Fixes a (weird) allocation warning in GCC 12
In file included from /usr/include/c++/12/bits/alloc_traits.h:33,
from /usr/include/c++/12/ext/alloc_traits.h:34,
from /usr/include/c++/12/bits/basic_string.h:39,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/streambuf:41,
from /usr/include/c++/12/bits/streambuf_iterator.h:35,
from /usr/include/c++/12/iterator:66,
from /usr/include/boost/iterator/iterator_traits.hpp:10,
from /usr/include/boost/range/iterator_range_core.hpp:26,
from /usr/include/boost/range/iterator_range.hpp:13,
from /usr/include/boost/iostreams/traits.hpp:38,
from /usr/include/boost/iostreams/detail/call_traits.hpp:15,
from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22,
from /usr/include/boost/iostreams/tee.hpp:18,
from /tmp/rdkit_builder/rdkit/Code/RDGeneral/RDLog.h:17,
from /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:11:
In function ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = pair<int, int>; _Args = {const pair<int, int>&}]’,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const pair<int, int>*; _ForwardIterator = pair<int, int>*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const std::pair<int, int>*; _ForwardIterator = std::pair<int, int>*; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const pair<int, int>*; _ForwardIterator = pair<int, int>*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = const pair<int, int>*; _ForwardIterator = pair<int, int>*; _Tp = pair<int, int>]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const std::pair<int, int>*; _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/vector.tcc:808:38,
inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1409:17,
inlined from ‘void testReplaceCoreMatchVectMultipleMappingToCore()’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:974:17:
/usr/include/c++/12/bits/stl_construct.h:119:7: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 56 bytes into a region of size 48 overflows the destination [-Wstringop-overflow=]
119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/c++/12/bits/c++allocator.h:33,
from /usr/include/c++/12/bits/allocator.h:46,
from /usr/include/c++/12/string:41:
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = std::pair<int, int>]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_CharT> >::allocate(allocator_type&, size_type) [with _Tp = std::pair<int, int>]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:378:33,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const std::pair<int, int>*; _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/vector.tcc:799:40,
inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1409:17,
inlined from ‘void testReplaceCoreMatchVectMultipleMappingToCore()’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:974:17:
/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset [8, 56] into destination object of size 56 allocated by ‘operator new’
137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
* finalForce maybe uninitialized in inlined copy constructor
* failure is being used uninitialized
* MaeWriter::write overrides a method of the base class without being marked 'override'
This one is annoying because it happens in an exported header, so it propagates
to any code using the header!
* otq is never used
* fix implicitly declared assignment operator warning
* variables in catch statements that are never used
* fix type (sign) mismatch warning
* drop duplicate export macro
* bring over XQMol.h
* bring XQMol over for a separate PR
* backup... need to move these files
* refactor
* substruct
* oops
* testing basics
* basic tests
* more test
* more testing
* add empty() method to MolBundle
* easy creation of ExtendedQueryMols
* SRU test
* reorg
* the MolEnumerator should clear out residual reaction properties
* support to/from JSON
* cleanup
* first past at python wrappers
put the new code in a namespace
* less stupid names
more tests
* undo some unnecessary changes
* remove compiler warning
* release GIL during hasSubstructMatch too
* support adjustQueryProperties
* support toggling which operations apply
Fix the tautomer tests to include a molecule which actually requires the tautomer matching
