* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* fix for CI build
* attempt to fix java build in CI
* attempt to fix java build in CI #2
* New routine to remove non-explicit 3D-geneated chirality
* changed to use pair for atrop atoms and related bonds
* Changes as per PR reviews
* PR review respnses
* PR review reponse - more
* Fix merge from master
* fixing java ci after merge
* Updated the help doc for atripisomers
* update the atropisomer docs
* improve the images
* add the source CXSMILES
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
- Switched from dynamic to static allocation for an instance of `MCSParameters`
- Switched to using `auto` where possible
- Added a few `CHECK_INVARIANT` where appropriate before dereferencing pointers
- Moved some inline comments to the previous line to improve readability
- Added a early check for `CompleteRingsOnly` in `checkBondRingMatch()` to improve computational efficiency
- Removed `RingMatchTableSet` entirely as 1) it is unnecessary since its functionality is already provided by `RingInfo` 2) it abused the `userData` pointer. This allows cleaning up and simplifying the code, particularly the Python wrappers which had a significant amount of added complexity to support it
- Removed all the code that was deprecated several releases ago
- Reimplemented ringFusionCheck() from scratch to address several bug reports; also switched from std::set to boost::dynamic_bitset for better efficiency
- Replaced boost::tie with boost::make_iterator_range
- Modernized `for` loops where possible
- Removed entirely the QueryRings structure as its functionality is already available in RingInfo
- Removed entirely the _DFS() function since the same algorithm can be implemented in a simpler and more efficient way using RingInfo (from 2m28.441s to 2m9.859s for the same task)
- Replaced std::vector<bool> with boost::dynamic_bitset
- Replaced C-style casts with C++ casts
- Replaced some size_t with unsigned int
- Refactored checkIfRingsAreClosed() such that checkNoLoneRingAtoms() is not needed anymore
- Added a test for slow runtimes with CompleteRingsOnly
- Setting Timeout to 0 means no timeout, as it should be
- Removed unused `steps` variable from `MaximumCommonSubgraph::growSeeds`
- Storing both Atom and Bond pointers and their indices on Seed and MCS data structures is time-consuming and a potential source of incons
istencies; storing pointers is sufficient
- Promoted `MaximumCommonSubgraph::match` from `private` to `public`
- `NewBonds` was declared `mutable`, but `Seed::fillNewBonds()` was incorrectly declared as `non-const`, which caused the need for an ugly
(and unnecessary) `const_cast`.
I have now removed the `const_cast` and correctly declared functions that alter `NewBonds` as `const`, since `NewBonds` is explicitly `mut
able`
- Removed some useless random scoping that was peppering the MCS code
- Removed a significant amount of duplicate code from the Python wrappers by inheriting from a base `PyMCSWrapper` class
- Fixed#6082
- Fixed#5510
- Fixed#5457
- Fixed#5440
- Fixed#5411
- Fixed#3965
- Fixed#6578
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* 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
* 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>
* 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>
* - MatchFusedRings does not imply CompleteRingsOnly anymore
* - use a more specific query molecule rather than an ambiguous SMARTS string in MCSResult
* - changes in response to review
* add the ring decomposer lib (temporarily?)
* simplify makefile
* very basics work
* backup
* basics working
* builds and basic tests pass
* get this building again
* expose the ring families
* add tests on the python side
* make the pywrapper for this optional
* remove some extra bits
* cleanup
* switch to using RDL as an external project
* make sure this still works if we do not use the URF code
* remove BUILD_ALWAYS
* fix linkage of Java wrapper and cartridge (hopefully)
* fix cmake for wrappers (hopefully)
* forgot a semicolon
* try to force URF lib to build first
* improve memory management and interface
* fix dependency specifier
* make pointer initialization explicit
This may not be necessary, but it feels safer.
* not pleasing and needs to be cleaned up
but it builds
* not pleasing and needs to be cleaned up
but it builds
* cleanup in preparation for merging
* cleanup in preparation for merging
* switch to rareylab repo
* fix updated copyright date
* Fix updated copyright date
* switch to a specific library tag
Co-Authored-By: Florian Flachsenberg <flachsenberg@zbh.uni-hamburg.de>
* change in response to review
