* 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>
* 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
* 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
* 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>
* 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
* - 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
* Force thread safe initialization of default MMFF parameters
* Add a test that currently crashes for multithreaded initialization
* Don't optimize the same mol at the same time
* Remove extra copying
* Fix dereference
* Make all Collection Classes const compatible, remove old singletons
* Remove pre-thread intialization of MMFF params
* do not use new on loggers
* del pointers in testDistGeom
* Update Dict hasNonPOD status on bulk update
* delete new Dicts in memtest1.cpp
* fixes in MolSuppliers and testFMCS
* PeriodicTable singleton as unique_ptr
* fix EEM_arrays leak
* fix leaks in testPBF
* fix ParamCollection leak in test UFF
* fix leaks in MMFF
* clear prop dict before read in in pickler
* fix leaks in testFreeSASA
* fix leaks in test3D
* modernize Dict.h & SmilesParse.cpp
* fix leaks in testQuery
* fix leaks in testCrystalFF
* fix leaks in cxsmilesTest
* fix leaks in Catalog & mol cat test
* fix leaks in ShapeUtils & tests
* fix leaks in testSubgraphs1
* fix leaks testFingerprintGenerators
* fix leaks in Catalog/FilterCatalog
* fix leaks in graphmolqueryTest
* these changes reduce bison parse leaks
* fixed leaks in testChirality.cpp
* fix leaks + 2 tests in testMolWriter
* fix 4m leaks in substructLibraryTest
* small improvements to molTautomerTest; still leaks
* fix leaks in testRGroupDecomp
* fix leaks in test; parser still leaks
* fix leaks in itertest
* fix 4m leaks in testDepictor
* fixes in smatest; still leaking due to parser
* fixes in testSLNParse; still leaking due to parser
* flex/bison: always add atoms with ownership; smarts error cleanup
* fix leaks in testReaction
* fix leaks in testSubstructMatch
* fix leaks in resMolSupplierTest
* fix leaks in testChemTransforms + bug in ChemTransforms
* fix leaks in testPickler
* fix leaks in testMolTransform
* fix leaks in testFragCatalog
* fix leak in testSLNParse. Still leaks due to Smiles
* fixed most leaks in testMolSupplier
* pre bison fix
* fix some atom & bond parse problems; others still fail
* bison smiles & smarts, atoms & bonds more or less fixed
* fix leaks in molopstest.cpp
* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp
* fix leaks in moldraw2Dtest1
* fix leaks in testDescriptors
* fix leaks in testInchi
* fix leaks in testUFFForceFieldHelpers
* fix leaks in hanoiTest & new_canon.h
* fix leaks in testMMFFForceField
* fix leaks in graphmolTest1
* fix leaks in testMMFFForceFieldHelpers
* fix leaks in testDistGeomHelpers
* fix leaks in testMolAlign
* initialize occupancy & temp facto with default values
* fix leak in TautomerTransform
* updated suppressions
* fix testStructChecker
* fix logging & py tests
* fix TautomerTransform class/struct issue
* remove misplaced delete in testSLNParse
* deinit in testAvalonLib1
* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp
* fix random testMolWriter/Supplier fails
- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.
* use reset in FFs Params.cpp
* comments on testMMFFForceField
* unrequired 'if's added to mol suppliers
* correct cast in FilterCatalog.h
* use unique_ptr in MACCS Patterns
* remove unrequred if in new_canon
* update & move suppressions
* first pass, does not yet actually work
* pass2, same problems
* pass2, same problems
* another test
* new tests; bugfix
* move the code out to a header
* add a double bond example
* enable auto-downloads of the code
* move the function to its own namespace
* first pass at a basic python wrapper
* change coordgen commit used
* try supporting bond stereo; does not currently work
* cis/trans seems to now work.
* first pass at templates; needs testing
* use the fixed flag too
* need mol align
* expand test
* initial pass at python wrapper for template
* simplify tests
* add an option to directly use a substructure match for alignment
* scaling
* add #define
* Define a cache setting for RDK_COORDGEN_LIBS to allow these to be used in other packages
* return the conformer id from addCoords
* Make CoordGen the default when it’s available.
This is a backup commit… the tests don’t even come close to passing.
* add some debugging options for a bit
* add alignment step to testing when using non-fixed coords
* Add global to allow use of CoordGen to be disabled
get the basic depictor tests working
* make coordgen the default when it is available
* make sure things continue to work when coordgen is disabled
* get windows builds working
* mods to get this building on windows.
something is screwy with the fileParsersTest1
* no need to generate coords for the 1K C string
* fix java wrappers
* works on linux
* update the (stupid) way dependencies were handled on windows.
this allows a lot of cleanup of cmake files (still more to do)
the linux build is unlikely to work due to the way _statics aren't handled
* docs
* extend forceRDKit applicability
* switch coordgen version
* try using templates
* try to get the template dir finding reasonably robust w.r.t. conda install
* continuing to iterate on the way the template file is installed
* fix a problem caused by the merge
* remove test that should never have been checked in
* update expected results for cartridge tests
* switch back to using the RDKit as the default coordinate generator
* 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
* - optimization to UFF and MMFF forcefields
* - further optimizations (memset, factoring unnecessary in-loop
initialization out of the loop, replacing if clause with pre-increment)
* - fixed a couple of stylistic glitches
* - the torsionSmarts parameter in addTorsions() is now a const std::string&
* - implemented the DefaultTorsionBondSmarts singleton using boost::call_once()
