* progress, passes tests, needs more optimization
* passes tests
* minor
* cleanup
set diagonal elements of matrix
* replace numeric consts with enum
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* does not work
* basically works
(at least it seems to)
needs more tesing and verification
* optimization and improved tests
passes local tests
* response to review
* Condense MMFF electrostatics and contrib instances.
Previously, a separate contrib had been added for each common term.
Each of these required a separate allocation, and a separate dynamic dispatch
on call. This change moves to an SOA style, making data access contiguous and
drastically reducing the number of calls.
* Make suggested copyright fixes and svn artifact removals
* throw if close to zero
* fix moldraw2DTestCatch
* Fix testRGroupDecomp
* fix one test in distGeomHelpersCatch
* fix tests in distGeomHelpersCatch
* retry finding a dir vector when adding Hs
* push UFF fixes to calculateCosY
* fix the setTerminalAtomCoords deg 4 patch
* add a test
* reduce zero tolerance
* fixes
* do not leak MolCatalogParams
* do not leak points on align failures
* give python ownership of pointers returned in getFingerprintsHelper
* clean up ScaffoldNetwork ptr if createNetworkHelper fails
* manage FF ptrs during construction
* wire in ownsBondInvGenerator in getMorganGenerator
* manage weights in rdMolAlign CalcRMS
* fix ownership of matches list/tuple in generateRmsdTransMatchPyTuple
* manage stream in createForwardSupplier during construction
* drop redundant Point3D allocations in GetUSRDistributionsFromPoints
* fix signed comparison mismatch
* move distance constraint to forcefield
* move position and torsion constraint to force field, also remove some unused includes
* sorting includes
* add missing files
* add angles and distances
* add Inversions
* add torsiona angle contribs
* use new contribs in test
* use new inversion and torsion contribs in dg
* use new distance contribs in dg
* use new angle constraints in dg
* use new constraints in FF tests
* update docstrings
* remove unused import
* include new contribs
* cleanup includes
* make changes requested by @greglandrum
* use std::move instead of release
* 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
* fix unsigned int to int comparison
* revert previous mistake
* declaration & init together, sinthetaSq in [0, 1]
* range based for-loops
* switch-statements
* declaration position changed
* declaration position changed
* declaration position changed
* declaration position changed, switch statements
* declaration position changed
* declaration position changed
* change in if statement
* now with const iterators
* declaration at initialization
* convert to static casts
* use switch when possible, no breaks
* Update Code/Geometry/point.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* change from review
remove redundant PRECONDITION
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* fix unsigned int to int comparison
* revert previous mistake
* declaration & init together, sinthetaSq in [0, 1]
* using std::swap
* use that sinThetaSq in [0,1]
* declare & init at same time
* use knowledge about target range
* use std::clamp
* use std::max
* numerically more stable trigonometrics
* numerically more stable trigonometrics
* numerically more stable trigonometrics
* range based for-loop
* actually do the assignement
* Update Code/ForceField/MMFF/Params.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* implemented suggested changes
* Revert "implemented suggested changes"
This reverts commit f56e8f0ab2.
* auto typing
* remove old comment
* revert to numerically more stable expression
* now correctly formatted
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.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>
* 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
* 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>
* Remove accidentally tracked files and unset x flag
* Ignore ComicNeue
* Unify test tag to `reader`
* Trivial destructors
* Bump CMAKE_CXX_STANDARD to 14 (#4165)
- 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>
* stop returning local memory in exceptions
* remove a couple unnecessary copies in loops
* fix a bug in the way the default MMFF aromatic parameters are constructed
* remove a bunch of loop-variable warnings
* remove a bunch of clang warnings
* disable clang warnings in python wrappers
* remove some warnings when building the python wrappers
* 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>
* 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
* a round of cleanups courtesy of PVS studio
* add a test to make sure that a warning is a false alarm
* bug fix
* Fix a UFF bug
* more PVS studio cleanups
* next round of PVS studio cleanups
* completely remove the chances for that bug
* changes in response to review
* add an additional test
+ a bit of reformatting that snuck in
