* Make shape on subset of atoms in molecule.
Optional radius for dummy atoms.
* Re-factor.
Add ShapeInputOptions.
* Python wrapper for options.
* Add non-standard radii option.
Add function to align a shape on a shape.
Add function to align conformer based on shape-shape transformation.
* Python wrappers for AlignShapes and TransformConformer.
* Add the new thing for Python options.
* Add option for excluding atoms from color features.
No partial color features if using atomSubset.
* In AlignShapes, don't change the fit shape (apart from transforming it) in case it will be used again.
* Rename it AlignShape to be consistent with AlignMolecule.
* Response to review.
* Undo clang-format
* Fix botched merge.
* Typo.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* c++20 builds working
* get MolStandardize building with clang19
* get FMCS building with clang-19
* set cxx version to c++20
* remove a few more compiler warnings
* bump min boost version, CI cleanup
* boost 1.81 is not available from conda-forge
* remove unused constants
* bump linux version for CI
* remove another unused variable
* fix (hopefully) cartridge CI builds
* simplify cartridge environment
* try postgresql14 in CI
* start the postgresql service
* change the columns used in the pandastools nbtest
* remove missed merge conflict artifact
* get github4823 test to pass with numpy 2.2
* remove a compiler warning/error with g++13
* avoid a segfault in CoordGen when a double bond has stereo spec but no stereo atoms
* changes in response to review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* refactor the code to determine whether or not an atom is in brackets
* move the definition of isMetal to QueryOps
* atoms bound to metals in SMILES should always be in square brackets
Implementation and some test updates
needs confirmation that all of tests run
* basic tests pass
* java tests pass
* update js tests
* doc updates
* Update Code/GraphMol/catch_graphmol.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* Update Code/GraphMol/SmilesParse/test.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* finish fixing tests
* bump yaehmop version to allow compilation to work
---------
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* - Make sure that FreeSASA can be built as DLL on Windows (MSVC & MinGW
compilers)
- avoid an unnecessary code patch by using only a .def file for
exporting symbols
* get the Windows DLL build to work with either MSVC or MinGW compilers
* FindPython Development.Module instead of Development
`Development` grabs `Development.Embed` since CMake 3.18
which is too much, and doesn't work on a manylinux build context
* Set CMake minimum version to 3.18
* initial support for pubchem-align3d
* works, passes the tests
* bump commit we are using
* update readme
* disable pubchem shape for limited depedencies build
* comment from review
* get windows dll builds working
* stupid oversight
* changes in response to review
get rid of the "using namespace std"
test that the alignment is re-entrant
* cmake modernization
- get rid of some warnings
- switch to what I hope is the correct way of doing things
- bump min cmake version to 3.16
- bump min boost version to 1.70
This builds on linux
* remove some usages of PYTHON_EXECUTABLE
* remove old-school python usage from coverage tests
* remove unused CI file
* bump boost version for windows builds to 1.84
* still trying to get the ci builds working
* typo
* eventually the CI will work
* robustify some tests
* 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>
---------
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>
* make sure that we can build without boost iostreams or seralization
adds some "private" variables on the python side to check for these compilation flags
* get out minimal cmake version correct
* get minimallib js building
installs an up-to-date cmake
also updates the version of boost being used for the minimallib
adds extra argument to allow the repo to be specified
* 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
* ci updates
* forgotten update
* inch by inch
* remove unused variable
* try a gcc bump
* get rid of a bunch of unused-but-set errors in clang16
* be more selective
* disable a test in an obsolete module which is mysteriously failing
* misc adaptations/modernizations
plus a few changes to allow pytest discovery
* get the recap unittests running
* pytest config updates
* all tests pass
* integrate the pytest stuff into ctest
* integrate Projects dir
better cmake integration
* ci build env updates
* ignore more files
* remove six.py
* cleanup UnitTestPandasTools
* cleanup pytest
* remove obsolete use of rdkit.six from doctests
* update release notes
* mysterious CI fix
* add conftest to remove some tests
* remove the old python-based testing infrastructure
---------
Co-authored-by: Ric <ricrogz@gmail.com>
* - fixed a crash in Avalon occurring when an atom idx in the bond table is out of bounds
- removed 0-padding ahead of parsing bond line as it is unnecessary and potentially harmful
- forked Avalon so it can be patched more conveniently
* updated the Avalon pre-relase number and updated the checksum
* updated pre-release number and checksum
* moved the Avalon fork under RDKit organization
updated checksum and release
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
