* 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>
* - exposed reaction drawing in MinimalLib
- fixed a typo in the error message "JSON doesn't contain 'atoms' field, or it is not an array"
- replaced RapidJson HasMember() with FindMember() to avoid a duplicate lookup in case the member exists and can be accessed
- some cosmetic style changes (avoid multiple variable declarations on a single line, use curly bracket also for one-liner if clauses, use auto where possible)
- capitalized "greg Landrum" to "Greg Landrum" (well deserved)
- exposed other FPs in addition to Morgan and Pattern FPs in MinimalLib
- added relevant tests
* - update CXSMARTS test in MinimalLib
* Changes in response to review:
- exposed reaction drawing functionality to CFFI and added relevant tests
- refactored fingerprint code to use JSON details and deprecated the Morgan/pattern fingerprint functions that used multiple parameters
- all fingerprints are now exposed to both JS and CFFI with no code duplication
- fixed a potential crash bug in the CFFI library where calling get_morgan_fp(), get_rdkit_fp() or get_pattern_fp with a NULL mol_pkl would result in dereferencing a nullptr
* removed debugging printouts committed accidentally
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* Npm publishing files - v1 in progress
* refactor .gitignore and package.json
* 2021.3.1-beta.0
* edit readme
* 2021.3.1-beta.1
* first version of read me and small tweak to docker build
* rdkit spelling uniform in readme
* 2021.3.1-beta.2
* update TOC
* add file to .gitignore
* 2021.3.1-beta.3
* add additional comment
* add back real readme
* add release tag example
* edit comment in git ignore
* add a link to unpkg.com
* 2021.3.1-beta.4
* final tweak to readme
* 2021.3.1-beta.5
* fix typo
* 2021.3.1-beta.6
* additional edits to README.md
* 2021.3.1-beta.7
* last minor readme edit
* 2021.3.1-beta.8
* add badges
* 2021.3.1-beta.9
* point homepage to minimallib readme
* 2021.3.1-beta.10
* 2021.3.1-beta.11
* make the js file the entry point
* 2021.3.1-beta.12
* fix release without dist
* 2021.3.1-beta.13
* add license badge to readme
* 2021.3.1-beta.14
* apply all reviews
getting started html file is now official demo
use npm version with --no-git-tag-version
use placeholder for version in npm package
add new line in all files
edit description and authors in package.json
* update live demo to be the getting started page
* add logging of version in readme example
* apply new set of review
fix author field for good
add back demo.html
edit readme accordingly
edit dockerfile to include GettingStarted.html in dist
* include proper getting started file in build
* edit publish process based on new PLACEHOLDER version
* update version in readme
* update toc
* add back placeholder
* remove ugly readme warning
* backup, does not work
* backup
* baby steps
* basics are now working
* more progress
* add substructure highlighting
* get the FT stuff working too
* get the FT stuff working too
* empirical corrections to dashed bonds
* enable coordgen support
* change min font size
* support dashed lines
* some cleanup
* support all MolDraw2D options when parsing from JSON
* parse MolDraw2D options from JSON
* show stereogroup labels when they are present
* switch to using the new CIP labels in minilib
* update demo to show controlling options
* move all the JS code into jswrapper.cpp
pass the canvas itself instead of the id to the JS functions
introduce offset
* remove extra emscripten load
* cleanup debugging stuff
* update freetype tests
* update non-freetype tests
* changes in response to review
* not really working from cmake, but can be compiled by hand
* now a cmake build works
* add a bunch of new stuff
* lots of changes
* demo
* substructure highlighting (crude) and descriptors
* include amw
* update
* cleanup
* add first fingerprint
* add tests
* add fp
* make the new stuff optional
* add Dockerfile
* add a readme
* switch to using JSON for complex return values
