4 Commits

Author	SHA1	Message	Date
Paolo Tosco	786393beb1	Enable RGD highlights as in blog post (#7322) ... * 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>	2024-09-16 16:14:13 +02:00
Paolo Tosco	6c966b4fe5	RGD code cleanup (#7186) ... * RGD code cleanup - made an effort to give more meaningful names to variables (e.g., renamed most instances of attachment (point) to avoid ambiguity as attachment may be interpreted as either the R-group atom or its neighbor atom on the core, which are two different things) - replaced the old school removeAtom() method with begin/commitBatchEdit() - added std::move and std::make_move_iterator where relevant to avoid potential unintended copying - replaced instances of container.size() == 0 and !container.size() with container.empty() for better clarity - replaced std::map::find() with std::map::at() where the key was not needed - replaced expensive std::find_if with more efficient alternative - added some missing const keywords and added references to avoid copying where appropriate - replaced for loops with modern implicit looping alternatives where convenient - avoid calling MolToSmiles when VERBOSE is not defined as the result is anyway not used - removed "oops, exponential is a pain" code snippet as I believe 1. it is never executed 2. it is not tested 3. I do not think it is correct - removed check for data->matches.size() > 1 as I do not believe it is correct - Use std::unique_ptr::reset instead of defining a new std::unique_ptr and moving it to the original one * changes in response to review * change in response to review * replaced std::set with boost::dynamic_bitset to save time on std::set::insert and std::set::find * make sure we do not go out of bounds --------- Co-authored-by: ptosco <paolo.tosco@novartis.com>	2024-03-03 05:34:13 +01:00
Ric	58d135a874	Reformat C/C++ code ahead of 2023.03 release (#6295) ... * format files * format template files too	2023-04-28 04:42:35 +02:00
Gareth Jones	a383b9e1dd	Refactor RGD moving function implementations from header to source files (#5958) ... * Create implementations for functions defined in header files * Fix testRGroupInternals.cpp include * Add windows dll export to RGroupData * Fix swig wrappers * Remove unused RGroupData constructor * Fix RGD CMakeLists.txt	2023-01-20 15:01:45 +01:00