* First try at using DistViolationContribs
only the most basic of testing has been done
also add ForceField::distance2 to allow some optimizations
* allow testing using old approach
* optimization
At this point testUFFForceFieldHelpers fails since the check for std::max_element
in the e_contribs vector at Embedder.cpp:513 is now doing something totally different
(instead of a bunch of small distance violation contribs, we have one big one).
We'll need to come up with something for this.
With the benchmarking set that I'm using - 500 DG conformers for ~465 COD molecules
using 10 threads - this runs in almost 10% less time than master.
* backup;
builds, tests do not pass
* all tests pass except the old failure
* more constification
* backup/debugging
* add fourthdim contribs the same way
* tests now pass
* deprecations
* remove unused vars and code
* changes in response to review
* 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
- fixes energies and gradients for dihedral and angle constraints in both MMFF and UFF
- adds butane scan tests for MMFF and UFF
- reduce huge angle/dihedral restraint force constants that cause the minimizer to struggle in tests
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* 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>
* 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
* - fixed UFF/MMFF torsion constraints when the dihedral is set to 0.0
- removed some code duplication
- added relevant test and fixed existing ones
* - fix Windows exports
* - added PRECONDITION for RDGeom::Point3D pointers
- removed inline keywords
* Fixes atom documentation
* Fixes#1461
This is a complicated one. Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0. The standard operations is
to check
URANGE(num, size-1)
Which (for unsigned integers) obviously rolls over.
This fixes all usage cases to be
URANGE(num+1, size)
And fixes the bugs found. (addBond and the mmff tests)
* Fixes#1461 - Updates URANGE_CHECK to be 0<=x<hi
* add a test (currently fails, of course)
* backup, not really working
* Fixes#1240
* a bit more parameter tweaking to get some more structures to embed
* passes all tests, but is still not 100 percent there
* generalize _centerInVolume for possible future use
* better testing of tetrahedral centers
update tests
* only test ring atoms
* handle 4-coordinate n too
* add a volume check; not all tests pass
* turn off debug printing
* rearrange the order of tests.
if this is not done, we get a seg fault when the github55 test runs.
the whole thing needs to be run under valgrind to track this down
* clear up a memory leak
* a bit more documentation
add a constant for one of the threshold values
* get more permissive on the energy tests.
Only do the extra tetrahedral tests for atoms in at least two rings.
* add a DEBUG_EMBEDDING option to make tracking down failures easier
* enable better debugging when the flag is set
* remove a FIX
* remove some debug printing from the tests
This covers at least the specific instances from the bug report.
Still need to figure out a general way to identify these automatically
to make sure all are fixed.
