* update AvalonTools to version 2.0.1
* Improvements to 2D depiction and alignment/RMSD calculation
- Refactored the straightenDepiction code which is now much simpler and more readable and supports a minimizeRotation parameter
- added C++, Python and JS tests for the new minimizeRotation parameter
- refactored tests to use CalcRMS rather than an internal implementation to compute RMS deviations
- Removed duplicated code in CalcRMS() and getBestRMS() and made their APIs consistent with respect to supported parameters
IMPORTANT NOTE: for backwards compatibility I set the CalcRMS() default for the new symmetrizeConjugatedTerminalGroups
to false as this parameter was not originally supported. @greg: I would be very much in favor of setting this to true instead
if you agree, even though it might change results for existing scripts, as I think it is a much more sensible default.
- Improved documentation to clarify the difference between CalcRMS() and getBestRMS()
- Added unit tests for CalcRMS() as there was none previously
- Added tests for the additional CalcRMS() and getBestRMS() parameters
- Added a new getBestAlignmentTransform() function
- The CFFI function set_2d_coords_aligned() now returns the matching atoms similarly to the C++, Python and JS counterparts
IMPORTANT NOTE: this required an API change for the additional char ** parameter used to return the match.
Existing code using set_2d_coords_aligned() will fail to compile and will require a last NULL parameter to be added to compile again
- Removed duplicated code between CFFI set_2d_coords_aligned() and JS generate_aligned_coords()
- Added has_2d_coords() to the CFFI library
- generate_aligned_coords() now supports JSON parameters and the previous versions are deprecated
- set_2d_coords_aligned() and generate_aligned_coords() both support an alignOnly parameter (which defaults to false).
If set to true, rather than re-generating a fresh 2D layout around templateMol, the existing coordinates (if any) are simply aligned
to the provided templateMol. If the molecule has no coordinates, a set of 2D coordinates is generated independently of templateMol
and then aligned to the provided templateMol
- avoid that when acceptFailure is false set_2d_coords_aligned() and generate_aligned_coords() overwrite existing coordinates
* - explicitly link testDepictor to MolAlign library
* - add MolAlign dependency to testDepictor (rather than to the catch test as in the previous commit)
- add a couple of tweaks
* suppress compiler warnings (1st pass)
* warnings: 2nd pass
* warnings: 3rd pass
* - alignOnly mode should also support allowRGroups
* - fixed C++ build
- added tests for allowRGroups+alignOnly combination
* changes in response to review
* added an entry to backward incompatible changes regarding set_2d_coords_aligned()
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.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
* Remove out_1 and out_2, only need for directed graphs.
* Variable renaming, no other changes.
* Fix a couple things that were forgotten during the rename
* Only one of these counts is updated now.
* Add ifdef to enable/disable VF2Pruning
* Add degree bound check, could be pushed down to the generic VertexCheck predicate.
* The stack knows at each point what was added, by passing these into the Backtrack call the clone allocation can be removed.
* Indent and rename added_node1 to node1.
* Now the clone is removed we can add a member function to handle the recursion cleanly.
* Also make for MatchAll a member function.
* Set lim=0 to mean infinity.
* VF2Plus optimisation, when candidate is in the terminal set select from a mapped neighbours adjacency list.
* Optimisation hint.
* Use a struct for the Pair removing the need for double pointer and heap alloc/delete of the iterators.
* disable pruning by default (it's a bit quicker to not do this)
* update expected test results
The updated VF2 code can return symmetric results in a different order
than we were getting previously. The results are still correct, but they
change some of the downstream things that don't do symmetrization
* update expected java results
This removes some redundancy from some of the test code in order to bring
the runtime down. This does not affect test coverage and shouldn't do
anything bad to the overall test quality.
* 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
* boost::thread mostly gone... still need to get rid of once
everything compiles
* replace boost::call_once
* remove link-time dependency on boost::thread
* first pass at using async
* switch to using async everywhere
Code/ForceField/MMFF/Params.h, Code/ForceField/UFF/Params.h,
Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp
and Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h (I realized
their uselessness thanks to a warning issued by Intel C++ compiler)
- refactored O3A code
- added the possibility to set weighted constraints on selected
atom pairs
- added an option to carry out local-only optimization
data races in the multithreaded test
- Removed a spurious #include in Code/ForceField/Wrap/ForceField.cpp
- Restored caching in Code/GraphMol/Descriptors/Crippen.cpp
and scoring functions
- Added cost, weight and scoring functions using atom-based
Crippen logP contributions
- Added relevant tests for the new functionality
Important points:
-----------------
- The constructors now accept optional pointers to
MolHistogram objects instead of pointers to arrays of
double. I think it is better for performance, since
rebuilding the histogram involves running through two
nested loops over all atoms, even though the
3DDistanceMat is provided to the O3A constructor.
This change breaks binary compatibility with previous
C++ programs linking to RDKit MolAlign library; I do not
think this is big issue, and while I was there I made
other changes which cause binary incompatibility.
If needed, we may preserve binary compatibility
reverting the MolHistogram change and the other ones.
- From Python, nothing changed in the interface to previous
MMFFO3A functionality. It MIGHT be more appropriate to
change the "GetO3A()" function into "GetMMFFO3A()", but
I have not done that to avoid breaking existing scripts;
the choice is yours
- As of now, the code contains a number of conditional
compilation directives checking for the
USE_O3A_CONSTRUCTOR macro; if USE_O3A_CONSTRUCTOR is
defined, then the code is built with an alternative O3A
constructor which allows choosing whether one wishes
to use MMFF or Crippen descriptors. Otherwise, no
alternative constructor is built, but rather two
functions which return a pointer to an O3A object.
I prefer by far the first solution (namely, with
USE_O3A_CONSTRUCTOR defined), but again, the choice is
yours. The code is tested and works in both cases.
- Custom cost, weight and scoring functions can easily
be defined in external programs without need to rebuild
the RDKit, allowing flexibility. The new custom
functionality can be accessed by calling the "bigger"
O3A constructor.
computed in the usual way, while previously the value computed
by MolAlign::AlignMol(), which incorporates weights, was returned
- the C++ and Python test results were updated accordingly
