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* 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>