* extra SSS match functions for atoms/bonds
initial implementation and testing
* add baseline to test
* add a functor for matching atom coords
* support the extra checks in python
* refactor the way the python callbacks are handled
* test tolerances
* expose the AtomCoordsMatcher to python
* allow the extra checks to override the default matching
---------
Co-authored-by: = <=>
- 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>
* - generateDepictionMatching2DStructure can be used with referencePattern smaller than reference
to only use part of a scaffold
- adds generateDepictionMatching2DStructure overload to pass a matchVect instead of doing a substructure match
- adds allowRGroups parameter to enable using a scaffold bearing R groups as reference
* changes in response to review
* added comments
* fixes failing doctest
* - reverted change committed accidentally
- fixed get_sss_json for the case where R groups are not included in the match
- added tests for the return value of generate_aligned_coords
* Documented the value returned by GenerateDepictionMatching2DStructure (Python)
* changes in response to review
* - changes in response to review
- fixed sortMatchesByDegreeOfCoreSubstitution that was not working
- added Python wrappers for sortMatchesByDegreeOfCoreSubstitution and getMostSubstitutedCoreMatch
- added C++ and Pyhon unit tests for the above
* added missing variable initialization
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* backup, does not work
* working on the C++ side
* backup
* fix the API
* document the new functionality
* improve that example
* final bit of cleanup
* switch to std::function
* unused vars in bison parser cleanup
* initialization order in TopologicalTorsionGenerator
* unused params in SLN bison
* sln flex unused params
* throwing destructor in TDTWriter
* signed comparison in substructmethods
* unused input param in smiles/smarts bison
* unused ms param in sln bison
* signed comparison in FingerprintGenerator
* store return of fscanf in StructCheckerOptions
* unreferenced var in catch
* uninitialized value in FileParserUtils
* avoid override overload warning in MolDraw2DSVG
* non-final overrides in Validate.h
* unused static var in Avalon
* unused vars in catch blocks
* make AvalonTools avalonSimilarityBits & avalonSSSBits const int
* assert fscanf result in StructCheckerOptions
* first pass at adding a SubstructMatchParameter struct
* start moving the rest of the backend to use the parameters
* backend at least mostly moved over
* add aromaticMatchesConjugated
add tests
* switch over the MolBundle too
Add templates to reduce duplicated code
* support older compilers
let's see if it works...
* add SubstructMatchParameters to Python wrapper
* remove some deprecations and warnings
* damn compilers
* parameter support for bundles in python wrapper
* add the parameters to the java wrappers
* response to review
