* move molzip to its own file
* basics working
* more testing
* another test
* minor
* fix doxygen comment format
* fix alignment with co-directional exit vectors;
some modernization
* JSON parsing
python wrapper
* response to review
* response to review
* explicitly test that the first frag does not move
---------
Co-authored-by: = <=>
* Mostly working.
* Clear out debugging writes.
* Avoid a mol copy.
* Left some debugging in.
* Move the fix into fragmentOnBonds.
* Add test.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Fixes#8379
* check in some working tests
* test passes
* test passes
* test passes
* test passes
* test passes
* ensure that the invariants flush the streams on failure
* tests pass
* test passes
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* Fixes#8391
* tests pass
* fix a test with legacy
not clear why this was not causing problems before
* make a test work
* Fixes#8396
* gcc builds work
* fingerprint tests pass
* mention backwards incompatible change
* fix a problem with FindMolChiralCenters
* more testing details
* enable the test status output
* Fixes#8432
fix a bug in double-bond stereo handling for template matching
* all depictor tests pass
* use the new-stereo chiral ranks in the depiction code
* always assign new-stereo chiral ranks
* make _ChiralAtomRank a computed property
This is analogous to _CIPRank
* tweak to the way the atom ordering is computed for 2D coordinate generation
* update two expected results
* backup
* response to review
* tests pass
* tests pass
---------
Co-authored-by: = <=>
* Test on at least enough dummyLabels.
* Use std::uint rather than boost::uint.
* Modern bond traversal.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* remove no-op macros and dead code (pt 2)
* test failures due to whitespace changes?
* actually run the testFeatures tests
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* 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>
* 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
* 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
* Test routine working
* Fix python molzip signature clash
* Update SWIG bindings
* Add C++ and Python documentation
* Add C++ and Python documentation
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Initial development and test
* Sort of working tests
* Copy corodinates to new core
* Clear stereochemistry on core atoms with unlabelled rgroups
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Continuing development
* Updated development
* Fixed Chirality Issues
* All tests working
* Remove some unused code
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Working tests
* Tidy test code
* Adjust catch_rgd for stereochemistry in output cores
* Build ring info in output cores
* Fix Mac OS bug
* Fix for MCS and onlyMatchAtRGroups
* Brian's optimization suggestion
* Fix core group coordinate bug
* Test for replaceCore and multiple core bonds to chiral atom
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Changes in response to Greg's code review
* R group stereo bond attachment fix
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* MolZip now saves the bonddir when zipping
* Add test for saving bonddir in MolZip
* Save either the first or second bond dir, fix the test to actually test
* Add more comprehensive bonddir checking and atom reordering
* Fix the atom swaps after the consistency check
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* Fix for RGD dummy atom bug
* Also fix labelling issues in the R group containing input dummy atom
* minor tweaks to the proposed fix
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* add ROMol::atomBonds() and ROMol::atomNeighbors() methods
* remove some warnings
* start using the new code
* add default for those template params
* some more applications
* get the SWIG builds working
* get rid of extraneous ref
* remove extraneous comments
* collection of doxygen fixes
* more files with fixed doxygen comments
* more doxygen fixes
* more doxygen fixes
* last set of doxygen comment fixes
Co-authored-by: Jason Biggs <jasonb@wolfram.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
* 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
* Make sure that added R-groups have non-zero coordinates
* - renamed setHydrogenCoords to setTerminalAtomCoords (and parameters accordingly)
- switched from ROMol* to RoMol& to remove a PRECONDITION
- documented the newly exposed C++ function
- added a Python wrapper
- added C++ and Python tests
* fixed conflicts and added a test
* Update Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolOps.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Wrap/MolOps.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* changes in response to review
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* backup
* simple first pass, passes all tests
* cleanup a bunch of existing uses
* ensure that we can safely add atoms/bonds while in edit mode
* add context manager on python side
* handle exceptions properly in those
* changes in response to review
* RGD modifications for any atom and index labels
* Continued development
* All tests working
* Added comment
* CR changes suggested by PTosco
* Fix catch_rgd for autocrlf
* Core dummy matches on output. RGroups on heavy atom. Dummy atoms User rgroups only when they are degree 1.
* Start work on test fixes
* testRGroupDecomp test working
* CPP and Python tests working
* Removed options for matching core query atoms on sidechains
* Windows build fix
* R groups off ring. User group matches single heavy substituent. Remove extraneous hydrogens
* Updated fingerprint variance score and tie selection
* Refactor fingerprint variance score functions to class
* Removed fingerprint distance score
* Boost::trim fix
* Updated RGD test notebook
* Fixed AddHs.cpp
* - fixes the kekulization issue
- avoids that empty R-group labels are included in cores
- makes sure that SMILES cores are always canonical
- adds a few missing const declarations and avoids unintentional copying
* Support for allowNonTerminalRGroups parameter. Remove R groups that contain H or Nothing. Ignore R group labels on non-dummy atoms
* Fixed tests for Paolo's changes. Rebuilt test notebook. Increased weighting of rgroup penalty in fingerprint variance score
* remove some debug output
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
