* Use distances on all valid paths rather than just shortest distance.
* Optimise BondPaths.
* Optimise BondPaths.
* Hash coded for the bond paths.
* Faster find all paths.
* Build in gcc working.
* Comment.
* Remove debugging code.
* Update GettingStartedInPython.rst.
* Now need to split the clique and keep the largest fragment.
Lots of warnings about how slow this is.
Split out long tests.
* Back out a lot of changes. Remove the distance check with singleLargestFrag when building modular product.
* Tidy code.
Update docstrings.
Add explanation to GettingStartedInPython.rst.
* Fix single fragment test.
* Response to review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Attempt at completeRingsOnly in mces
* changed option name and added a test
* code review
* check aromaticity and bond type matches before checking ring equivalencies
* update if statement
* typo
* Add option to specify minimum clique size directly.
* Make the minCliqueSize uint and default to 0.
* Brain-fade.
* Send timeout and 'too many bonds' message to BOOST_LOG rather than std::cout, std::cerr respectively.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* New option - exactAtomTypeMatch.
* Python wrapper.
* REQUIRE(res.size()) not CHECK. If it fails, you get seg fault on subsequent tests otherwise.
* Change option name.
* C++ implementation of equivalent atoms via SMARTS.
* Python wrapper.
* Tidy.
* Check for too many classes.
* Better handling of spaces in split.
* Pass string by reference. Doh.
* Add ignoreBondOrders option.
* - 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>
* Expose singleLargestFrag option to Python.
* Better documentation.
A couple more things exposed.
* Expose RascalClusterOptions.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
