Maciej Wójcikowski

We are still missing docking phase (Vina) during generation of initial descriptors. RF-Score v4 needs docked conformers. We need to add additional `transformer` functionality to a `scorer` method. Eventually we...

Utilize Python Nodes [released recently](https://www.knime.com/blog/setting-up-the-knime-python-extension-revisited-for-python-30-and-20) in Knime 3.4 to support ODDT operations. Review 3D-e-Chem nodes on [github](https://github.com/3D-e-Chem) for inspitarion. You may want to use [NodeWizzard](https://www.knime.com/developer/documentation/wizard). Node types: * docking *...

- http://www.nyu.edu/projects/yzhang/DeltaVina/ - http://onlinelibrary.wiley.com/doi/10.1002/jcc.24667/abstract

Implement SMARTS filters mentioned in https://github.com/rdkit/rdkit/pull/536 and already in RDKit using pipeline module.

CXSmiles bond cfg not matching SMILES directions

3

There is a discrepancy between the bond directions and bonds cfg fields in CXSmiles output which is included by default in 2023.03.3 ```python Chem.SetUseLegacyStereoPerception(False) Chem.MolToCXSmiles(Chem.MolFromSmiles('C1\C(C)=C/CCCOC1')) ``` Returns `C/C1=C/CCCOCC1 |c:1|` Marvin...

[WIP] OpenMP support for compiled trees

1

What's new: - new argument was introduced `n_jobs` for better performance `model.predict(X, n_jobs=32)` - `n_jobs` has similar behavior to `joblib`, i.e. `n_jobs=-1` takes all CPUs, `n_jobs=-2` leaves one core idle,...

PostgreSQL GiST index is broken for negative SFP (diff fingerprints)

3

Indexing a column of `sfp` type results in empty results when using GIST index. The simplest example is to look for identical reaction using tanimoto similarity search. Similarity searches for...