* - moved SMILES and RGroupDecomp JSON parsers to their own translation units
- added missing DLL export decorators that had been previously forgotten
- changed the signatures of MolToCXSmiles and updateCXSmilesFieldsFromJSON
to replace enum parameters with the underlying types
- updated ReleaseNotes.md
* make sure cxSmilesFields is only updated if the JSON string contains keys
belonging to the CXSmilesFields enum
* added missing copyright notices
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Code/GraphMol/Depictor/RDDepictor.h
- fixed typo in docstring
Code/GraphMol/RGroupDecomposition/RGroupCore.cpp
- added a missing const; formatting changes
Code/GraphMol/RGroupDecomposition/RGroupData.cpp, Code/GraphMol/RGroupDecomposition/RGroupData.h
- moved the code which merges disconnected R groups sharing the same attachment point into a single combined molecule to a private method, RGroupData::mergeIntoCombinedMol(). The method also includes logic to merge atom and bond highlights, if present.
- modernized a for loop
- isMolHydrogen is now a static function since it does not actually require any instance data
- implemented three static function to return the R group, Core and Mol labels, respectively
Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp, Code/GraphMol/RGroupDecomposition/RGroupDecomp.h
- implemented two private methods, RGroupDecomposition::labelAtomBondIndices() and RGroupDecomposition::setTargetAtomBondIndices(). The first method tags all atoms and bonds in the target molecule such that they can be tracked following core removal by RDKit::replaceCore(). The second method sets common_properties::_rgroupTargetAtoms and common_properties::_rgroupTargetBonds properties on core and R groups. These are vectors of atom and bond indices in the target molecule corresponding to core and R group atom/bonds, respectively, and can be used for color-coding the target molecule according to the R group decomposition it was subjected to, similarly to https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html
Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp
- formatting changes and for loop modernization
Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp, Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h
- implemented updateRGroupDecompositionParametersFromJSON()
- added includeTargetMolInResults boolean parameter
Code/GraphMol/RGroupDecomposition/RGroupMatch.h
- implemented RGroupMatch::setTargetMoleculeForHighlights() and RGroupMatch::getTargetMoleculeForHighlights() methods to, respectively set and get the target molecule where R group decomposition can be color-coded with highlights. This molecule includes the explicit H atoms corresponding to extracted R groups, if any.
Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp
- use a std::unique_ptr to store the pointer to the C++ RGroupDecomposition instance
- fixed typos in docstrings
Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py
- added test for the new includeTargetMolInResults parameter
Code/GraphMol/RGroupDecomposition/catch_rgd.cpp
- added test for the new includeTargetMolInResults parameter
Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
- formatting changes
Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp
- do not use deprecated constant
Code/MinimalLib/CMakeLists.txt
- added RDK_BUILD_MINIMAL_LIB_RGROUPDECOMP CMake flag to optionally expose R group decomposition functionality into MinimalLib
Code/MinimalLib/common.h
- added makeDummiesQueries flag to mol_from_input() (defaults to false)
- implemented parse_highlight_multi_colors() function to parse multi-color atom and bond highlights
- enable multi-color atom and bond highlighting
Code/MinimalLib/demo/rgd_demo.html
- added HTML page showcasing the multi-color highlights similarly to https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html
Code/MinimalLib/jswrapper.cpp
- removed checks for non-nullness of d_mol as d_mol cannot be directly accessed anymore
- replaced all instances of d_mol with get()
- implemented support for multi-color atom and bond highlights
- implemented optional support for R group decomposition
- added JSMol::copy() convenience method with same functionality as get_mol_copy() to duplicate a molecule
Code/MinimalLib/minilib.cpp, Code/MinimalLib/minilib.h
- replaced all occurrences of d_mol with get(), as d_mol is now private
- removed all occurrences of assert(d_mol) as non-nullness is checked at construction time and whenever get() is called
- JSMol is now split into two subbclasses, JSMolUnique and JSMolShared, which both inherit from the JSMol base class. JSMolUnique can be constructed from a RWMol* (as the old JSMol), while JSMolShared can be constructed from a ROMOL_SPTR. This avoids unnecessary copies when wrapping a ROMOL_SPTR (e.g., from subtructure library, JSMolList or R group decomposition) into a JSMol to pass it to JS. This also avoids that modifications done in the JS layer on a molecule stored in a MolList (e.g., adding a property) are not persisted because they are carried out on a volatile copy of the molecule rather than on the actual molecule.
Code/MinimalLib/tests/tests.js
- added a test for pesistence of modifications made to JSSharedMol
- added tests for RGD
- added test for JSMol::copy()
Code/RDGeneral/RDValue.h
- removed trailing comma from vector properties such that they can be deserialized as syntactically correct JSON
Code/RDGeneral/types.cpp, Code/RDGeneral/types.h
- added _rgroupTargetAtoms and _rgroupTargetBonds common_properties
* Code/GraphMol/Depictor/RDDepictor.h
- fixed typo in docstring
Code/GraphMol/RGroupDecomposition/RGroupCore.cpp
- added a missing const; formatting changes
Code/GraphMol/RGroupDecomposition/RGroupData.cpp, Code/GraphMol/RGroupDecomposition/RGroupData.h
- moved the code which merges disconnected R groups sharing the same attachment point into a single combined molecule to a private method, RGroupData::mergeIntoCombinedMol(). The method also includes logic to merge atom and bond highlights, if present.
- modernized a for loop
- isMolHydrogen is now a static function since it does not actually require any instance data
- implemented three static function to return the R group, Core and Mol labels, respectively
Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp, Code/GraphMol/RGroupDecomposition/RGroupDecomp.h
- implemented two private methods, RGroupDecomposition::labelAtomBondIndices() and RGroupDecomposition::setTargetAtomBondIndices(). The first method tags all atoms and bonds in the target molecule such that they can be tracked following core removal by RDKit::replaceCore(). The second method sets common_properties::_rgroupTargetAtoms and common_properties::_rgroupTargetBonds properties on core and R groups. These are vectors of atom and bond indices in the target molecule corresponding to core and R group atom/bonds, respectively, and can be used for color-coding the target molecule according to the R group decomposition it was subjected to, similarly to https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html
Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp
- formatting changes and for loop modernization
Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp, Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h
- implemented updateRGroupDecompositionParametersFromJSON()
- added includeTargetMolInResults boolean parameter
Code/GraphMol/RGroupDecomposition/RGroupMatch.h
- implemented RGroupMatch::setTargetMoleculeForHighlights() and RGroupMatch::getTargetMoleculeForHighlights() methods to, respectively set and get the target molecule where R group decomposition can be color-coded with highlights. This molecule includes the explicit H atoms corresponding to extracted R groups, if any.
Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp
- use a std::unique_ptr to store the pointer to the C++ RGroupDecomposition instance
- fixed typos in docstrings
Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py
- added test for the new includeTargetMolInResults parameter
Code/GraphMol/RGroupDecomposition/catch_rgd.cpp
- added test for the new includeTargetMolInResults parameter
Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
- formatting changes
Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp
- do not use deprecated constant
Code/MinimalLib/CMakeLists.txt
- added RDK_BUILD_MINIMAL_LIB_RGROUPDECOMP CMake flag to optionally expose R group decomposition functionality into MinimalLib
Code/MinimalLib/common.h
- added makeDummiesQueries flag to mol_from_input() (defaults to false)
- implemented parse_highlight_multi_colors() function to parse multi-color atom and bond highlights
- enable multi-color atom and bond highlighting
Code/MinimalLib/demo/rgd_demo.html
- added HTML page showcasing the multi-color highlights similarly to https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html
Code/MinimalLib/jswrapper.cpp
- removed checks for non-nullness of d_mol as d_mol cannot be directly accessed anymore
- replaced all instances of d_mol with get()
- implemented support for multi-color atom and bond highlights
- implemented optional support for R group decomposition
- JSMol is now split into two subbclasses, JSMol and JSMolShared, which both inherit from the JSMolBase class. While JSMol can be constructed from a RWMol* as usual, JSMolShared can be constructed from a ROMOL_SPTR. This avoids unnecessary copies when wrapping a ROMOL_SPTR (e.g., from subtructure library, JSMolList or R group decomposition) into a JSMol to pass it to JS. This also avoids that modifications done in the JS layer on a molecule stored in a MolList (e.g., adding a property) are not persisted because they are carried out on a volatile copy of the molecule rather than on the actual molecule.
- added JSMolBase::copy() convenience method with same functionality as get_mol_copy() to duplicate a molecule
Code/MinimalLib/minilib.cpp, Code/MinimalLib/minilib.h
- replaced all occurrences of d_mol with get(), as d_mol is now private
- removed all occurrences of assert(d_mol) as non-nullness is checked at construction time and whenever get() is called
Code/MinimalLib/tests/tests.js
- added a test for pesistence of modifications made to JSMolShared
- added tests for RGD
- added test for JSMolBase::copy()
Code/RDGeneral/RDValue.h
- removed trailing comma from vector properties such that they can be deserialized as syntactically correct JSON
Code/RDGeneral/types.cpp, Code/RDGeneral/types.h
- added _rgroupTargetAtoms and _rgroupTargetBonds common_properties
* added assignChiralTypesFromMolParity flag
* added test for makeDummiesQueries
* added CFFI tests
* reordered tests
* re-added piece of code that had gone accidentally lost while merging conflicts
* Removed CHECK_INVARIANT following code review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* ci updates
* forgotten update
* inch by inch
* remove unused variable
* try a gcc bump
* get rid of a bunch of unused-but-set errors in clang16
* be more selective
* disable a test in an obsolete module which is mysteriously failing
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Initial development and test
* Sort of working tests
* Copy corodinates to new core
* Clear stereochemistry on core atoms with unlabelled rgroups
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Continuing development
* Updated development
* Fixed Chirality Issues
* All tests working
* Remove some unused code
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Working tests
* Tidy test code
* Adjust catch_rgd for stereochemistry in output cores
* Build ring info in output cores
* Fix Mac OS bug
* Fix for MCS and onlyMatchAtRGroups
* Brian's optimization suggestion
* Fix core group coordinate bug
* Test for replaceCore and multiple core bonds to chiral atom
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Fixed typo in tests
* Undo change to master
* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Changes in response to Greg's code review
* R group stereo bond attachment fix
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* support substructure search parameters in RGD.
Still needs testing/verification of the enhanced stereo stuff
* test enhanced stereo
* add support to python wrapper
unfortunately some python reformatting got mixed in there.
* RGD modifications for any atom and index labels
* Continued development
* All tests working
* Added comment
* CR changes suggested by PTosco
* Fix catch_rgd for autocrlf
* Core dummy matches on output. RGroups on heavy atom. Dummy atoms User rgroups only when they are degree 1.
* Start work on test fixes
* testRGroupDecomp test working
* CPP and Python tests working
* Removed options for matching core query atoms on sidechains
* Windows build fix
* R groups off ring. User group matches single heavy substituent. Remove extraneous hydrogens
* Updated fingerprint variance score and tie selection
* Refactor fingerprint variance score functions to class
* Removed fingerprint distance score
* Boost::trim fix
* Updated RGD test notebook
* Fixed AddHs.cpp
* - fixes the kekulization issue
- avoids that empty R-group labels are included in cores
- makes sure that SMILES cores are always canonical
- adds a few missing const declarations and avoids unintentional copying
* Support for allowNonTerminalRGroups parameter. Remove R groups that contain H or Nothing. Ignore R group labels on non-dummy atoms
* Fixed tests for Paolo's changes. Rebuilt test notebook. Increased weighting of rgroup penalty in fingerprint variance score
* remove some debug output
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Exploration
* Initial work on GA fro Rgroup Symmetry
* GA for rgroup decomp and fingerprint rgroup symmetry scoring
* Continuing development
* Exploration
* Initial work on GA fro Rgroup Symmetry
* GA for rgroup decomp and fingerprint rgroup symmetry scoring
* Continuing development
* Further development
* Continued tweaks
* Function rename
* Continued tweaks
* Bug fix for variance calculation
* Copyright notices. Remove Eigen dependency. RdKit logging. Clock fix.
* Changes to fix build failures
* Fixes for Windows dynamic DLL build
* Included GA export.h file
* Fixed RGroupDecomp CMakeLists.txt
* Notebooks working, GGroup labelling bug fixed
* Fix windows build. More options for example GA program
* More bugs found and tests adjusted
* Fixed Python rgroup test
* Trivial change to trigger CI
* OSX java and windows build fixes
* Windows DLL fix
* Fix segmentation error
* proposed change
* Possible fix for segmentation fault
* CR fixes
* CR fixes
* CR fixes
* Recreates molecules from rgroups where possible
Co-authored-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* - replaced set with vector for SMILES-based R-group equivalence
- the first GreedyChunk is constituted by chunkSize+1 mols
- labeled R-groups may not be extracted when onlyMatchAtRGroups==false
- labeled geminal R-groups are incorrectly scored
- my attempt to introduce consistency in R-group labeling was buggy
- added a DEBUG pre-processor directive to the tests to make debugging easier
- added a unit test
- fixed unit test results which were inconsistent with the expected behavior
* changes in response to review
* - Fixes three bugs in the R-group decomposition code
* - delete iterator properly during loop so the Mac does not complain
* added more tests
Co-authored-by: user173873 <user173873@FF026.local>
