Pavel

I analyzed the attached files and found issues in ProLIF rules. Hope this will simplify analysis and fixing. **case 1**: ```python import prolif as plf from rdkit import Chem protein_fname...

Thanks for the example! It might be reasonable to open a discussion on pharmacophore patterns or transfer this issue to discussions. I'm still not completely sure how hydrophobic pattern should...

I suggest to make other changes related to ionic features, both positive and negative, and include them in this PR. The issue - not recognized delocalization of charges that miss...

This pattern `!$(*(~a)~a)` designates an atom not connected to two aromatic atoms, the atom itself may be not aromatic, e.g. Ph-O-Ph. Diphenylethers are very weak acceptors, Therefore, we may exclude...

I agree with current patterns. Yes, we can use [C] in guanidine pattern. I have no further suggestions.

Thank you as well. Great work! We use this tool regularly.

Hi Andrea, I installed guacamol 0.5.4 to test and everything works as expected. It might be that crem itself was installed incorrectly. You may install crem from pip or github...

You are welcome! Currently there is only this tutorial to demonstrate basic abilities. If you have some questions even general ones ask them here. Later I would be able to...

I expected that there is enough information in README to make an own fragment database. 1. There is a script which makes everything. It takes input SMILES and returns a...

Forgot to mention. I added a simple tutorial how to use CReM in combination with machine learning models.The tutorial is in example dir.