* Add molecules names into ScaffoldNetwork
- added parameter to ScaffoldNetwork Params to include molecule names in the
ScaffoldNetwork nodes corresponding to input molecules
* Document _Name assumption
- fixed a binary and instead of a boolean and
* Forgot has prop check before access
* Misunderstood semantics of CHECK vs. REQUIRE
* fixes
* do not leak MolCatalogParams
* do not leak points on align failures
* give python ownership of pointers returned in getFingerprintsHelper
* clean up ScaffoldNetwork ptr if createNetworkHelper fails
* manage FF ptrs during construction
* wire in ownsBondInvGenerator in getMorganGenerator
* manage weights in rdMolAlign CalcRMS
* fix ownership of matches list/tuple in generateRmsdTransMatchPyTuple
* manage stream in createForwardSupplier during construction
* drop redundant Point3D allocations in GetUSRDistributionsFromPoints
* fix signed comparison mismatch
* - 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>
* remove some more deprecated numpy stuff
* workaround for changes to random.shuffle in python 3.11
* fix pickling of rdkit mols in python 3.11
* add py311 build to CI
* update py311 CI
* remove qt for py311 for the moment
* only use the new code with pyversion >=3.11
* use the new logic for all pickle_suites
* need to work with older py too
* stop using CIP codes in the atomic canonicalization
this will change results in some cases, so lots of tests need to be updated.
* stop breaking string literals... ARGH
* tests now pass
* update double bond canonicalization
* update a python test
* some cleanup
* update expected results for cartridge
* fix a crashing bug in SubstructLibrary
* fix a bunch of other potential seg faults
These are all places where the result from pyObjectToVect(),
which can legitimately return a nullptr, is not checked before
being dereferenced.
* document behavior
clear the result vector for the other pythonObjectToVect() overload
* change error message
in response to review
* backup
* simple first pass, passes all tests
* cleanup a bunch of existing uses
* ensure that we can safely add atoms/bonds while in edit mode
* add context manager on python side
* handle exceptions properly in those
* changes in response to review
* 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
* Fixes#3153
Added logic to handle cases where there is C+ aromatic atom by adding an explicit hydrogen to it
* Improved tests by adding checks if the scaffold network is created correctly
* Replaced implemented linear search by pre-implemented STL find function
* change minimal cmake version to a consistent 3.5
* progress towards a cleanup
* get the basic python deps working
* two more libs
* another round of changes
all tests pass at this point
* next round of changes
all tests pass at this point
* close to done
all tests pass
* very close
* almost done
* shift the RDBoost dependencies around a bit
* remove an extraneous python linkage
this is trying to get the mac builds working again
* Only link to python if it was built shared (#3091)
* change in response to review
Co-Authored-By: Ric <ricrogz@users.noreply.github.com>
* move that suppression of the maybe-uninitialized warning to BoostStartInclude.h
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* backup
* rearrange the network to make it cleaner
- GenericBond scaffolds are now directly connected to the corresponding Generic scaffold
- Attachment points are no longer removed from Generic (or GenericBond) scaffolds
* remove dead code
* backup
* backup
* backup
* getting close to v0.1
* switch to using node indices
* add pruning and flattening
* support multiple mols
* example notebook
* backup
* initial commit
Just includes the basic API and flatten
* add the pruning step
* add removeAttachmentPoints()
* add makeScaffoldGeneric()
* improve compilation speed by adding catch_main.cpp
* add getMolFragments()
* doc cleanup
* actually add the network building code
* first pass at python wrapper
* allow edges to be nicely converted to strings
* get node counts working
* backup python notebook
* switch example notebook to use wrapped C++ code
* add BRICS fragmentation option
* fix a bug with removing attachment points to aromatic heteroatoms
* add provisional attachment point merger to notebook
* fix a bug with includeScaffoldsWithAttachments=false
* backup of efforts to get this working on windows
* backup of efforts to get this working on windows
* does not work. backup
* Fix a substructure crash on Windows
* re-enable tests
* adjust to the new BRICS form
* in-code documentation
* more doc updates
* reformat
* change the string output format for edges
* remove old python implementation
* remove obsolete test
* include a generic scaffold for the pruned structure too
* default to keepOnlyFirstFragment=false with BRICS params
* bug in removal of attachment points from generic scaffolds
* more testing
* support working from std::shared_ptr as well as boost::shared_ptr
* more testing
* disable debug printing
* use memo-ization in getMolFragments() to avoid duplicate work
* add SWIG wrapper and basic testing
* add define for RDK_USE_BOOST_SERIALIZATION
* add serialization at the C++ level
* add a string ctor for a scaffold networks
* add pickle support on the python side
* formatting
* remove old notebook
* move the fantastically useful iterable_convertor to RDBoost/Wrap.h
* expose parameter constructor with std::vector<std::string>
* add scaffoldnetwork to documentation
