* 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>
* support read-only access to cstates from python
* expose GetBrackets
* expose getAttachPoints too
remove vestigial SubstanceGroupCState_VECT
* backup
* backup
* basics working
* backup
* add label_mol_abbreviations
* fix a bug in the chirality handling
* add linkers, needs more testing
* add another peptide test
* sanitize results by default
* just need rings
* getting started with the C++ form of abbreviations
* a bit of error handling
* add findApplicableMatches
* actually apply the abbreviations
* make the getDefault functions more efficient
* add labeling (creating s groups)
* docs
* basic python wrappers (maybe this is enough?)
* add _displayLabel and _displayLabelW support to MolDraw2D
update the docs for that
* use displayLabel props
* add more default abbrevs
* change default linker defns
add parseLinkers convenience function
* make sure attachment point atoms aren't aromatic
* change the color of dummies to be darker gray
* remove python implementation
* support abbreviations in the java wrappers
* add abbreviations to the csharp wrappers
* add abbreviations to the js wrappers
* add molParity to the list of atom props not written to CXSMILES
* support condensing SUP substance groups
* add that to the python wrappers
* Update testAbbreviations.py
* clear ring info if we added it
* document that the molecules with abbreviations removed have not been sanitized
* 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
