* move mol weight and formula calculators to MolOps and refactor them a bit.
The descriptors are still there and should remain.
* remove other unnecessary dependencies on Descriptors
* Update adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
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Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.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>
* add RDKIT_CFFI_STATIC option
minimallib cmake cleanup
* clean up a lot of boost::iostreams nonsense
* find_package(boost cleanup
* update the swig wrappers
* updates to psql
* get the Qt demo working again
* fix? coordgen
* only use std::regex in moldraw2d test
this is consistent with the other tests
* cleanup the serialization stuff too
* disable the info and debug logs by default
* adjust tests to the newly disabled logs
* add LogStateSetter
* namespace reorg
* add some tests
* remove vestigial code
* switch to using std::vector
* minor preparatory refactor
* add test
* add reaction literals
* tests for the new literals
* add runReactant
first steps to making things work
* remove works
* backup
* all current tests passing except bond-order changes
some atom-property copying fixed
* bond changes now work
* handle atomic stereo
* some cleanup and more tests
* docs
* not-working
* add KekulizeIfPossible()
* return a value from KekulizeIfPossible
* Revert "not-working"
This reverts commit 2ebd8a5519.
* add in-place reactions to python wrapper
* simplify deprotection wrapper code
* support in-place deprotection
* changes in response to review
* forgotten change
* test getIdOfEntryWithBitId()
* remove unused functions
* improve bv tests in python wrapper
* more UniformGrid tests
* improve deprotect coverage
* improve abbreviations coverage
* add operator!= to DeprotectData
* more testing for adjustQueryProperties
* fix a copy-paste bug
* copy-paste bug
* more testing
* more testing
* more testing
* fix an edge case bug in getValenceContrib
* more bond tests
* add operator!= to StereoInfo
tests StereoInfo::operator==
* make some internal functions testable
* more testing
* minor code cleanup
* fix some bad caching behavior in getDistanceMat() and get3DDistanceMat()
testing
* test FixeMolSizeMolBundle() copy ctor
* deprecate BalabanJ
* more testing
* testing
* mods to get things working for windows DLL builds
(don't bother running some of the tests there)
* fix a typo
* Add deprotection library
* Add copyrights
* Add dll exports
* Fix doc strings, use std::shared_ptr
* Changes for Review
* clang-format
* Fix seg fault and compile issues
* Fix namespace issue
* Add examples to datastructure and use them for testing
* Make the test actually compile and run
* Remove greek character
