* disable the info and debug logs by default
* adjust tests to the newly disabled logs
* add LogStateSetter
* namespace reorg
* add some tests
* remove vestigial code
* switch to using std::vector
* [WIP-ENH]: Support greater use of `findAtomEnvironmentOfRadiusN()`
This PR is the feature support for PR 4262. I am not so confident when coding the C++ as it is my first time hands-on experience
There are still many thing that should be done but I still need several support
* Update MolOps.cpp
* Fix build error
Fix according to this? https://www.boost.org/doc/libs/1_42_0/libs/python/doc/v2/object.html#object-spec-ctors
* Fix build error
* Fix test2.cpp
* Fix `include` issue
* Fixed as requested
* Update Subgraphs.cpp
* Update Subgraphs.cpp
* Update Subgraphs.cpp
* Fix reported error, correct doc
* Update MolOps.cpp
* Update test and fix error
* Fix default argument
* Fix duplication
* Update Subgraphs.cpp
* Fix test bug
* Updated a test and fix reported error
* Update Subgraphs.cpp
* Fix reported error
* Update test2.cpp
* Fix reported error of memleak and introduce new function
* Fix incorrect variable
* Update test2.cpp
* Update test2.cpp
* Update MolOps.cpp
* Update MolOps.cpp
* Fix algorithm & Add test docs
* Update test2.cpp
* Update Subgraphs.cpp
* New argument `bondDist` - Optimize the `FindAtomEnvFromMToN`
Documentation is syncronized the meaning between C++ and Python
- New argument `bondDist`
- `findAtomEnvironmentOfRadiusMToN()` now called once instead of twice due to the introduction of `bondDist`
* Update Subgraphs.cpp
* Update test2.cpp
* Fix casting
* Correct the test
* Update Subgraphs.cpp
* Remove buggy function and replace argument position
* Update Subgraphs.h
* Fix build failed
* Optimization
Reduce graph expansion if it is the last radius
* Adjust codebase based on review
- Update Copyright
- Add doc to prove optimization
* suggested changes
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Nonchiral atoms should be removed from StereoGroups
This fixes a bug where atoms which have no chirality were left in StereoGroups
In order to make this work, ROMol::setStereoGroups() needed to be made public.
That shouldn't be a problem since it doesn't change connectivity.
* support CXSmiles extensions in the hashes
* initial tests for that
* some cleanup
* copyright header cleanup
* minor refactoring
* call out the changes in the release notes
* extension and more testing
* add python wrappers
* fix build
* recheck
* install DrawTextQt.h
* Some additional cleanup and merge to the current state of master (#8)
* silence warnings in MSVC compliatons (#5044)
* enable the multithreaded LeaderPicker on linux (#5043)
* enable the multithreaded leaderpicker on linux
* response to review
* AtomSymbol needs to have a virtual destructor (#5045)
* AtomSymbol needs to have a virtual destructor
* additional cleanup of virtual functions
* typo fix
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Expose MolzipParams::atomSymbols to python (#5054)
* [WIP] Clean up the warning landscape (#5048)
* suppress a bunch of warnings from third-party code
get rid of one warning in RDKit code
* corrections
* fix the maeparser flags
* remove some more inchi warnings with clang
* Further cleanup of the public interface.
Get all the DrawText bits out of the header files used by client code.
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* suppress a bunch of warnings from third-party code
get rid of one warning in RDKit code
* corrections
* fix the maeparser flags
* remove some more inchi warnings with clang
* MolDraw2D refactoring
- rename setupMoleculeDraw->initMoleculeDraw
- track whether or not initDrawing() has been called
- centralize calls to initDrawing() and clearDrawing() into initMoleculeDraw()
- update svg hashes in tests
* update some expected test results
* support changing font scale and default scale
add reaction test
* does not work... this is hard
* all tests pass
* do something about legends
* docs
* more tests
* more docs
* cleanup
* going around in circles...
hopefully converging
* cleanup
* Single bond skeleton works.
* Simple bond drawing seems to be working.
* Initial addition of atom symbols.
* Stash of not-quite-working atom symbols prior to major surgery.
* Atom symbols seem to be working. Major surgery not required, just inverted Y coords at the outset.
* Add classes to atom labels.
* Renamed AtomLabel AtomSymbol.
* Add highlights.
* Fix bug from PR4839.
* Molecule note.
* Added atom notes.
* Added bond notes.
* Extract radicals.
* Annotation via new DrawAnnotation class.
* Add brackets.
* Add linknodes.
* Add close contacts.
* Add attachment points. Fix wavy lines.
* Draw molecules in grid.
* Tidy.
* Fix radicals when font has hit maxFontSize.
Make getDrawCoords work.
* Draw primitives take atom or draw coords.
* Fix legends.
* More fixing for tests. DrawMol::setScale now takes font scale as well.
* tidy debug writes
* Variable fraction of panel for legend.
* Better legend positioning.
* Fix sub- and super-script spacing.
Added spaces to Freetype strings.
* Basic reaction drawing.
* Reaction highlighting.
* Minor tweak to reacctions.
* Tweaked reaction DrawMol widths.
* Fix atomTags.
* Fix catch tests except contours.
* Contouring working in catch_tests.cpp.
* Fix catch tests.
* AtomSymbol and DrawAnnotation into MolDraw2D_detail.
* DrawMol and DrawShape into MolDraw2D_detail.
* DrawText inot MolDraw2D_detail.
* Machete out.
* DrawText goes private.
* Move some stuff about, such as StringRect to its own header.
* Python wrapper compiles (but crashes when Draw imported).
* More tidying. Python DrawArrow failing.
* Linux changes.
* Fixed error in DrawShapeArrow spotted by valgrind.
Fixed some warnings from gcc.
* Maybe fixed DrawArrow.
* Added basic argparse interface.
* Added newlines.
* Changes in response to review.
Non-const args in move constructors and operator=.
Added missing classes to MolDraw2D_detail.
Deleted move operator= where it had been forgotten.
Fixed copyright dates.
* Deleted all default c'tors in derived classes.
* Changes in response to review:
Wedge widths now a proportion of mean bond length in draw coords..
Add padding below legend when positioning it.
* Fix tests.
* Fix the private/protected mess of the new classes.
* Moved doesLineIntersect etc.
* Reinstate original alignString for non-FT drawings.
* More faffing about with reaction layouts.
* Fix font sizes in testGitHub3391.
* Fix atom notes fitting inside fat wedges.
* Fix molecule annotation font size.
* More fixes of rectangle/triangle collision detection.
* Test for highlight linewidth multiplier.
* Use push_back not emplace_back.
* Attempt at better Freetype char spacing.
* Option to turn off TEST_ASSERT. Currently off.
* Fixed embarrassing maths to do with wedge fatness.
* More tidying post-review.
* Document highlight_linewidth_multipliers.
* Expose baseFontSize to Python.
* Changes in response to review.
* Allow DrawMolecules molecules to be drawn to different scales.
* Fix bond sneaking between C:8 in, for example, reactions.
* Fix bad re-factoring.
* Fix globbing.
* Changes in response to review.
* Add invariant check.
* Add draw option to fix font size.
* suggested changes
* Update catch test results.
* Fix expected freetype results.
* Fix non-freetype drawers.
* Fin non-freetype test results.
* get the Qt drawer working too
* Fix disappearing reaction highlights.
* Changes as result of review.
* Fixed non-FreeType hash codes for reaction SVGs. Extra comment in catch_tests.
* reactant highlighting was clearning properties
* Fix for failing contour python test.
* fix a non-freetype problem
* swig wrappers working
* Bump timeouts in test.
Co-authored-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Fixes#4996
also switches to using the GraphMol version of catch_main.cpp so builds are faster
* Fixes#4998
we should probably discuss this one
* compare with previous results
* some initial work...
Still some real questions here about what should be done with dp_mol data members
* add some tests for move semantics of Dict and Props
remove extraneous clear()
* more in-depth testing of the molecule results
* test refactoring
* improve the molecule move test
* fix some leaks found by valgrind
the new tests are now all clean in valgrind
* additional classes
QueryAtom, QueryBond, RingInfo, Conformer
* get swig working again.
Not sure why this is necessary, but SWIG is a mysterious beast
* fixes in response to review
* updates in response to review
* first pass at writing v3K rxns
* python wrapper
* test other C++ call
* cleanup
* Fixes Windows DLL build issue
* changes in response to review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Nonchiral atoms should be removed from StereoGroups
This fixes a bug where atoms which have no chirality were left in StereoGroups
In order to make this work, ROMol::setStereoGroups() needed to be made public.
That shouldn't be a problem since it doesn't change connectivity.
* fix some broken old tests
* update cartridge tests
* RWMol: replace atom in stereo groups
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=36998, a
use-after-free in initFromOther.
* Fix out-of-bounds write in iterateCIPRanks
If the rank has not changed in the current iteration, the cipEntries
vectors might not have increased in size. Accessing `numIts + 1`
resulted in an out-of-bounds write. This commit skip the cipEntries
update when the rank is unchanged.
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=28660
* Fix use of uninitialized values in MolSGroupParsing
`stream >> count` may silently fail without an exception. In that case,
`count` was uninitialized but used. This commit initalizes `count` to 0,
as well as other variables that may be read without being initialized.
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=25220
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=25225
* Fix vector size cast in streamReadVec
In 32-bit systems, the implicit conversions from 64-bit to a 32-bit
size_t could lead to an underallocation of the vector. This would follow
by a out-of-bounds write while trying to populate the vector. Now, the
code throws an exception in case of a cast that would change the size.
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=28034
* RWMol: improve atom replacement in stereo groups
This code is cleaner and more efficient.
* Add test for replaceAtom and stereo groups
* Move isEarlyAtom to a table format to reduce lock contention in getPeriodicTable
* Fix He early atom status
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* fixes#4721
* - store in RingInfo the index of the ring(s) each atom and bond belongs to rather tham just their size
- expand the RingInfo API with a few useful methods
- identify rings that are certainly aliphatic upfront
- avoid unnecessary copying atomRings when RingInfo is already initialized
* - code modernization and cleanup
- better handling of dummies in aromatic rings
- exposed atomMembers() and bondMembers()
- added several tests
* - avoid order dependency on rings
- added test for the above
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* Later cores with more R-groups should only be chosen when they are structurally related, i.e. when they are superstructures of earlier cores
* 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>
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* start with some basic tests
these currently fail, of course
* prep work
* minor refactoring and prep work
* get better at handling spaces
* first pass, needs completion and testing
loads more testing required
coordinate bonds don't work at all yet
I'm suspicious about the SGroup hierarchy
* more progress
agents and products are now parsed
more testing added
way more testing needed
* correctly ignore names
test cleanup
* more sgroup improvements and testing
now I think most everything is there and the basics are tested
* all tests pass
* link nodes and variable attachment points
* more cleanup and testing
* changes in response to review
* Support for logging via Python's logging module.
* Avoid the Python 3.9+ PyObject_CallOneArg function.
* Move logging functions to RDBase; Python logger by default; clean up tests.
* See if removing NOGIL fixes the Windows stall.
* get tests running on windows
* Reset to using C++ logging; whiespace tweaks.
* Longer timestamp grace period; try tempfile vs Windows logging stall.
* Clean up commented code; get details for log count bug.
* SubstructLibrary: Fix c++ threads calling into python
* FilterCatalog: Fix c++ threads calling into python
* Release notes; make sure Jupyter still logs to sys.stderr.
* Always use thread-local log buffers.
* de-verbosify a test
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* resolves oss-fuzz #24399
* clean up some undefined behavior
* fix some UB in mergeQueryHs
* be more defensive
* defensive programming
* fix a _cxsmilesBondIdx bug
* more defensive programming
* Support wildcard in input structures
* Fix typos
* Handle R groups containing a single wildcard and wildcards with group numbers
* Reorder tests
* Use propety instead of isotope to mark input dummy
* fix the windows DLL builds
* Added constexpr for dummy input atom property
* Omitted to replace one instance of string 'INPUT_DUMMY'
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
