RGD highlights as in blog post #7322
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added 7 commits
March 25, 2024 19:34
- 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
- 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
…tosco/rdkit into rgd-highlights-as-in-blog-post
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This PR contributes a convenient way to visualize multi-colored R-group highlights on the molecule which undergo R-group decomposition, as showcased in this blog post, but requiring only a handful of Python commands and no need for substructure matches on top of what is already accomplished by the RGD algorithm itself. The highlighting functionality can also be accessed from JS, as exemplified in the
rgd_demo.htmlHTML page:A few other JSON settings were also exposed to JS and CFFI, namely to enable assigning chiral types based on mol parity and to convert dummy atoms into queries.