* Allow the same core to match more than once in a molecule.
* Update annotation.
* Changes after review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Adds missing options docstring
* Always be cleaning
* Fix typos in RGroupDecomposition module
* Update documentation on configuring doxygen
* Was a step that I couldn't find reference to besides in the Makefile
* Undo american spelling of labelling
* British spelling appears more consistent
* Fix style of RGroupDecompositionParameters parameter
* Also fixes a typo
* Remove unintentional use of docstring
* Was assigning documentation about the parameters to the
RGroupDecomposition
* Remove empty string
* Apply suggestions from code review
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.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>
* - added gen_rdkit_stubs Python module to generate rdkit-stubs
- added patch_rdkit_docstrings Python module to patch existing C++ sources to fix docstrings missing self parameter and add named parameters taken from C++ signatures where possible
- added rdkit-stubs/CMakeLists.txt to build rdkit-stubs as part of the RDKit build
- added an option to CMakeLists.txt to enable building rdkit-stubs as part of the RDKit build (defaults to OFF)
* fixed CMakeLists.txt, rdkit-stubs/CMakeLists.txt and a doctest
* - added missing cmp_func parameter
- fixed case with overloads with optional parameters
- do not trim params if expected_param_count == -1
- add dummy parameter names if we could not find any
- keep into account member functions when making up parameter names
- address __init__ and make_constructor __init__ functions
- fix incorrectly assigned staticmethods
* patched sources
* address residual few remarks
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - added a convenience function to relabel R-groups in a chemist-friendly fashion
- exposed functionality to MinimalLib through a JSON option at molecule creation time
- added relevant unit tests
* changes in response to review
* added missing library
* fixed Python test
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - extracted the core matching logic into a separate function
- added relevant C++ and Python tests
* Update Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Support tautomer queries in RGD
* Continuing RGD and tautomer development
* Python and C# tests
* Python and C# tests
* C# test
* Typo fix
* For cire tautomer query update properties instead of full sanitization
* Added query comment
* Code review change
* Support Enumeration of input cores
* Mol enumeration test
* Remove useNormalMatch from RGroupDecomp
* Added comments for handling tautomeric core
* Added comments for handling tautomeric core
* 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.
* 1) fixed residual kekulization issues when R-labels are removed from aromatic atoms on the core
2) added removeAllHydrogenRGroupsAndLabels flag, which defaults to True. If set to False,
unused user-defined labels on the core will be retained. If also removeAllHydrogenRGroups
is set to False, all-hydrogen user-defined R-groups will be included in the output.
Under no circumstance dynamically-added R-groups (when onlyMatchAtRGroups=false)
that are all-hydrogen will be included in the output, as that's not useful (change
compared to previous behavior)
3) added tests for (1), (2) and for removeAllHydrogenRGroups, that had no tests so far
4) fixed a few documentation typos in the Python code and added some documentation
to the C++ sources
* added missing test files
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* 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>
* - 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>
* stop returning local memory in exceptions
* remove a couple unnecessary copies in loops
* fix a bug in the way the default MMFF aromatic parameters are constructed
* remove a bunch of loop-variable warnings
* remove a bunch of clang warnings
* disable clang warnings in python wrappers
* remove some warnings when building the python wrappers
* refactor RGroupDecompositionParameters to directly initialize data members
add params getter for the RGroupDecomposition object
* initial implementation of timeout
* refactor the timeout check
We could move the function that checks and throws the exception somewhere else
* re-enable the tests I stupidly left disabled
* Fixes#3224
add option to skip symmetrization entirely
* test #3224
* stupid mistake
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* Adds RGroupDecomp free function and python wrapper
* Fixes subtle bug, adds new RGroupDecomp API
* Updates results for the subtle bug fix. Verified results were correct.
* Removes smilesCaching.
* Changes RGroupDecompose ordering, adds docstrings and more tests
* Fixes#1550
* might as well update properties on the r groups too
* add option to remove Hs from sidechains;
expose a few more parameters to python;
expose ctor with parameter object to python
