Paolo Tosco

RGD with tetrazole core yields to core that cannot be kekulized

6

**To Reproduce** ```python from rdkit import Chem from rdkit.Chem import rdRGroupDecomposition core = Chem.MolFromSmiles("n1nn[nH]c1Cc1ccccc1") core ```  ```python mol = Chem.MolFromSmiles("n1nnn(C)c1Cc1ccccc1") mol ```  ```python rgd = rdRGroupDecomposition.RGroupDecomposition(core) rgd.Add(mol) 0...

**Describe the bug** Originally reported by James Davidson in #5504. Simple reproducible: ```python import rdkit rdkit.__version__ '2022.09.1pre' from rdkit import Chem from rdkit.Chem import rdFMCS smis = ["C", "O", "N",...

Distorted depiction

9

I found a combination of ring systems that yields a distorted depiction: ``` from rdkit import Chem from rdkit.Chem import rdDepictor rdDepictor.SetPreferCoordGen(True) Chem.MolFromSmiles("CC1C2CCC1CC(c1cccc3cc(-c4ccc5cccc(S)c5c4)sc13)C2") ```  Interestingly, removing either the methyl...

**IMPORTANT NOTICE** @greglandrum In the interest of preserving the functionality of your coronary arteries, I wish to give you a heads up about a couple of interesting macros for `enum`...

Clashes in 2D layout with bridged systems

9

@rachelnwalker @cdvonbargen Following conversations we had during the 2023 RDKit UGM, here's a report of a case where the RDKit generates a layout with many clashes, while CoordGen does a...

This PR cleans up valences in `atomic_data.cpp`. In addiition to a few missing `-1` valences for some alkali metals (Rb, Cs, Fr), which I believe should be added in analogy...

RGD highlights as in blog post

8

This PR contributes a convenient way to visualize multi-colored R-group highlights on the molecule which undergo R-group decomposition, as showcased in this [blog post](https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html), but requiring only a handful of...

The structure with a single positive charge yields the expected 2 resonance structures: ``` from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole, MolsToGridImage IPythonConsole.drawOptions.addAtomIndices = True mol = Chem.MolFromSmiles("O[NH+]=[C-]NC") mol...

Get pytest to run without incurring in a circular import when RDKit Python modules are installed out-of-tree

3

Since we moved to `pytest` I was not able to run `pythonSourceTests` in my out-of-tree installation because of this error: ``` $ ctest -I 284,284 -V [...] test 284 Start...

In `CMakeLists.txt` we define `BOOST_NO_CXX98_FUNCTION_BASE` for `clang` versions >= 15: ``` if (CMAKE_COMPILER_IS_CLANG OR CMAKE_COMPILER_IS_EMCC) if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 15) target_compile_definitions(rdkit_base INTERFACE -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_NO_CXX98_FUNCTION_BASE -D_HAS_AUTO_PTR_ETC=0) target_compile_options(rdkit_base INTERFACE -Wno-deprecated-builtins -Wno-deprecated-non-prototype -Wno-unused-parameter) endif()...