* make sure that loggers can be enabled, disabled, captured and tee'd from MinimalLib without issues
* changes in response to review
* change in response to review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - Fix#8029
- avoid unnecessary rounding errors in the JSON writer
- remove a warning when compiling MinimalLib without SubstructLIbrary support
* changes in response to review
* changes in response to review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - moved SMILES and RGroupDecomp JSON parsers to their own translation units
- added missing DLL export decorators that had been previously forgotten
- changed the signatures of MolToCXSmiles and updateCXSmilesFieldsFromJSON
to replace enum parameters with the underlying types
- updated ReleaseNotes.md
* make sure cxSmilesFields is only updated if the JSON string contains keys
belonging to the CXSmilesFields enum
* added missing copyright notices
---------
Co-authored-by: ptosco <paolo.tosco@novartis.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>
* - renamed getParamsFromJSON() to updateSmilesWriteParamsFromJSON() and moved it from the anonymous namespace to the RDKit namespace such that it is publicly available
- implemented updateCXSmilesFieldsAndRestoreBondDirOptionFromJSON()
- added CFFI and JS tests
- get_smiles(), get_smarts(), get_cxsmiles() and get_cxsmarts() are now available in MinimalLib in both CFFI and JS layers and they can be passed JSON parameters
- CFFI get_qmol() now returns NULL if it fails to generate a RWMol rather than returning the "Error!" const char[] string, for consistency with what get_mol() and get_rxn() do. This was documented in release notes
* suggestions
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* MMPA functions exposure
* Minilib exposure: mmp
* minilib: mmpa - test added
* minilib: mmpa - failing test added
* - MolList should return null when the corresponding ROMOL_SPTR is a nullptr
- changed first into cores
- changed second into sidechains
- renamed some functions and constants
* - made JSMolList::at() and JSMolList::pop() robust against attempting to dereference null ROMOL_SPTR
- added tests for the above
* Update Code/MinimalLib/minilib.h
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* changes after review
* Update Code/MinimalLib/minilib.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* - added StoreAll to parseMCSParametersJSON()
- added get_mcs() to MinimalLib which returns results as JSON
- added tests for get_mcs()
* added test
* changes in response to review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
1. tee: the log is captured in a buffer but also sent to the native output channel
2. capture: the log is captured in a buffer without being sent to the native output channel
- removed duplicate logging_needs_init and needs_init atomic bool variables from cffiwrapper.cpp and consolidated them into a static LoggingFlag d_loggingNeedsInit class variable
- added relevant C and JS tests
Co-authored-by: ptosco <paolo.tosco@novartis.com>
- setAromaticity (defaults to true)
- fastFindRings (defaults to true; only used when sanitize=false)
- assignStereo (defaults to true)
These options avoid doing unnecessary work when the molecule is only used for specific purposes (e.g., computing FPs or doing substructure searches)
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - deprecate JSMol::is_valid() and JSReaction::is_valid()
- methods returning JSMol and JSReaction objects now return nullptr upon failure rather than an invalid object
* changes in response to review
* unexposed JSReaction::is_valid given it was not exposed before this PR
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* reverted all changes that did not really belong to this PR
* I had forgotten ChemReactions_static
* changes in response to review
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - enable using JSSubstructLibrary with no fp by passing num_bits 0
- get rid of dynamic_cast which never looks great
- add unit tests for no-fingerprint JSSubstructLibrary
* change in response to review
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - implemented in-place aromatisation/kekulisation
- avoid that attempting to aromatise a query mol throws an exception due calcImplicitValence() not having been called
- add unit tests for the above
* change in response to review
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* Fixes some issues in the SubstructLibrary JS implementation
- FastFindRings() was not being called
- a count_matches() overload was missing
- count_matches() was ignoring the numThreads parameter
- adding a PatternFingerprintMol created with a certain number of bits to the PatternHolder will *not* work: one needs to create the PatternHolder with the desired number of bits, and then call makeFingerprint
- improved tests to make sure the library actually behaves as expected
* added functionality to serialize/deserialize a JSSubstructLibrary and get matches as UInt32Array
* I had forgotten to run clang-format
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - expose [sg]etUseLegacyStereo()
- In MolToSmiles() doIsomericSmiles should default to true as in C++ and Python
- added missing parameters to MolToSmiles() and MolToMolBlock()
- added SmilesWriteParams MolToSmiles() overload
- added and updated Java tests
* - changes in response to review
- exposed the same functionality also in MinimalLib and CFFI and added tests
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - fix indentation
- fix regex check (which currently always fails)
* wip
* - added clearMolBlockWedgingInfo()
- added invertMolBlockWedgingInfo()
- MinimalLib::generate_aligned_coords() now inverts stereochemistry if a rigid-body alignment transformation caused chiality inversion
- MinimalLib::generate_aligned_coords() now clears stereochemistry if coordinates changed
- added JSMol::clear_prop() to the already existing JSMol::get_prop() and JSMol::set_prop()
- renamed commonchem to rdkitjson in JS unit test
- added relevant unit tests
* fixed mistake in logic
* - added add_hs_in_place() and remove_hs_in_place() to the JS MinmalLib
- added relevant tests
* - removed check for existence of a property ahead of clearing it as it is not necessary; updated the clearProp docstring to reflect this
- updated the MolFileStereochem.h docstrings based on review comments and fixed a typo
- fixed two (legitimate) compiler warnings as get_molblock() and get_v3kmolblock() should return nullptr and not a pointer to an empty string; added tests for this as there was none
- in MinimalLib/common.h, moved the check of whether a molecule has undergone a flip around the Z axis to a function in the anonymous namespace
- in MinimalLib/common.h, added logic to preserve original wedging (and eventually invert it) also when alignOnly is set to false, in case the wedging is all within the constrained scaffold
- added thourough testing of the wedging logic on both CFFI and JS sides
* - added equality operator to CXXAtomIter and CXXBondIter classes such that they can used with implicit loop STL algorithms
- added relevant unit tests
* fix Windows build
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - added add_hs_in_place() and remove_hs_in_place() to the JS MinmalLib
- added relevant tests
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - enable get_molblock(details_json) from MinimalLib as it is already enabled in CFFI
- enable useMolBlockWedging on get_molblock() in both CFFI and JS MinimalLib
- add tests
* - expose also addChiralHs
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - extend prepareAndDrawMolecule() with missing optional parameters already supported by prepareMolForDrawing()
- enable useMolBlockWedging, wedgeBonds, addChiralHs, forceCoords, wavyBonds in CFFI/MinimalLib
- add relevant CFFI and JS unit tests
* Replace AllProps with a smaller subset
* make sure we pickle properties Python-side
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
- removed details from get_maccs_fp calls since there are no adjustable parameters
- exposed get_maccs_fp to JS
- added tests and adjusted existing ones since some deprecated functions were removed and do not need testing anymore
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* update AvalonTools to version 2.0.1
* Improvements to 2D depiction and alignment/RMSD calculation
- Refactored the straightenDepiction code which is now much simpler and more readable and supports a minimizeRotation parameter
- added C++, Python and JS tests for the new minimizeRotation parameter
- refactored tests to use CalcRMS rather than an internal implementation to compute RMS deviations
- Removed duplicated code in CalcRMS() and getBestRMS() and made their APIs consistent with respect to supported parameters
IMPORTANT NOTE: for backwards compatibility I set the CalcRMS() default for the new symmetrizeConjugatedTerminalGroups
to false as this parameter was not originally supported. @greg: I would be very much in favor of setting this to true instead
if you agree, even though it might change results for existing scripts, as I think it is a much more sensible default.
- Improved documentation to clarify the difference between CalcRMS() and getBestRMS()
- Added unit tests for CalcRMS() as there was none previously
- Added tests for the additional CalcRMS() and getBestRMS() parameters
- Added a new getBestAlignmentTransform() function
- The CFFI function set_2d_coords_aligned() now returns the matching atoms similarly to the C++, Python and JS counterparts
IMPORTANT NOTE: this required an API change for the additional char ** parameter used to return the match.
Existing code using set_2d_coords_aligned() will fail to compile and will require a last NULL parameter to be added to compile again
- Removed duplicated code between CFFI set_2d_coords_aligned() and JS generate_aligned_coords()
- Added has_2d_coords() to the CFFI library
- generate_aligned_coords() now supports JSON parameters and the previous versions are deprecated
- set_2d_coords_aligned() and generate_aligned_coords() both support an alignOnly parameter (which defaults to false).
If set to true, rather than re-generating a fresh 2D layout around templateMol, the existing coordinates (if any) are simply aligned
to the provided templateMol. If the molecule has no coordinates, a set of 2D coordinates is generated independently of templateMol
and then aligned to the provided templateMol
- avoid that when acceptFailure is false set_2d_coords_aligned() and generate_aligned_coords() overwrite existing coordinates
* - explicitly link testDepictor to MolAlign library
* - add MolAlign dependency to testDepictor (rather than to the catch test as in the previous commit)
- add a couple of tweaks
* suppress compiler warnings (1st pass)
* warnings: 2nd pass
* warnings: 3rd pass
* - alignOnly mode should also support allowRGroups
* - fixed C++ build
- added tests for allowRGroups+alignOnly combination
* changes in response to review
* added an entry to backward incompatible changes regarding set_2d_coords_aligned()
Co-authored-by: Tosco, Paolo <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>
* Add JSMol::get_prop() and JSMol::set_prop()
* Remove trailing space in MinimalLib test code
* Add JSMol::has_prop()
* Add JSMol::get_prop_list()
* Add test_prop to MinimalLib test case
* add a global feature flag to control use of the new chirality code
* expose that flag to minimallib
* add getters for allowNontetrahedralChilrality and useLegacyStereoPerception
* switch to using environment variables to store the values
* document that
correct the documentation about nontetrahedral stereo
* yay visual c++
* in response to review
* - Abbreviations::applyMatches() sets the _abbreviationMapping molecule property to relate the atom indices in the molecule with abbreviations to the atom indices in the original molecule
* added support for bond index mappings
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - adds normalizeDepiction() and Python wrappers
- adds straightenDepiction() and Python wrappers
- adds an early check for R-labels to be in the accepted range to avoid throwing an exception later on
- adds a kekulize flag to process_details() to enable depicting molecules which fail to kekulize from JavaScript
- adds JavaScript functions to get fingerprints as Uint8Array
- adds JavaScript function to generate pickled molecule as Uint8Array
- adds JavaScript function to restore molecule from Uint8Array pickled
- adds has_coords() JavaScript function
- adds set_new_coords() to set JSMol coordinates in-place
- adds get_mol_copy() to obtain a JSMol copy
* fix build failures
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - expose SubstructureLibrary to MinimalLib
- expose acceptFailure flag to MinimalLib generate_aligned_coords
- expose merge_query_hs functionality to MinimalLib
- expose kekulize flag to MinimalLib get_mol
- add relevant JS tests
* integrates previous commit
* changes in response to review
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* set all source code files to have native line endings
* normalized all source code line endings
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* hello world works
* more
* more
minimallib needs to be tested
* parse substructure parameters from JSON
* add substruct search and parameters
* add descriptors
* register more descriptors
* fingerprints, first pass
* stop outputting tiny coord vals
* support generating 2d coords
* coordgen testing
* return nulls
* initial 3d support; add/removeHs; cleanup
* Embedding parameters from JSON
* update
* pattern fp, fps as bytes
* use json to configure MFP
* use json to configure rdkit and pattern fps
* aligned 2d coords
* parsing options
* options for writers
* rename remove_hs
* get this working on windows (kind of)
* silence some msvc warnings
* cmake updates
* update python tests
* add the CFFI code to CI builds
* cleanup line ending mess?
* a couple small fixes
* make this work with URF
* support coordMap in the 3D coordinate generation
* updates in response to review
* - generateDepictionMatching2DStructure can be used with referencePattern smaller than reference
to only use part of a scaffold
- adds generateDepictionMatching2DStructure overload to pass a matchVect instead of doing a substructure match
- adds allowRGroups parameter to enable using a scaffold bearing R groups as reference
* changes in response to review
* added comments
* fixes failing doctest
* - reverted change committed accidentally
- fixed get_sss_json for the case where R groups are not included in the match
- added tests for the return value of generate_aligned_coords
* Documented the value returned by GenerateDepictionMatching2DStructure (Python)
* changes in response to review
* - changes in response to review
- fixed sortMatchesByDegreeOfCoreSubstitution that was not working
- added Python wrappers for sortMatchesByDegreeOfCoreSubstitution and getMostSubstitutedCoreMatch
- added C++ and Pyhon unit tests for the above
* added missing variable initialization
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
