Try to use new LLM phi3 #memo #LLM

As name of LLM means that to use these kinds of models, we need enough GPU memory and it’s not so cost effective for personal use ;) To overcome the limitation, there are lots of technologies are developt and still be developping. LLAMA-cpp is one of the them. Today I would like to share new

Generate new molecules from fragments with Diffusion model #cheminformatics #rdkit #difflinker #memo

Designing linked molecule from fragments is one of the important task for drug desing such as FBDD, Scaffold hopping (e.g. replace core) and PROTAC molecule design. As readers know there are lots of solutions to do it, for examoke BROOD is one of the famous commercial package for fragment replacement. I can’t use commercial package

Try to use new version of REINVENT #cheminformatics #memo #rdkit

As many cheminformaticians know that (I expected…) REINVENT which is developed by AZ team is one of the useful and famous AI based compound generator in cheminformatics field. New version of REINVENT 4 is still active and recently it is version apped and added some useful code on the repositly. The DL framework is moved

Edit atom indices of RDKit Mol object #memo #cheminformatics

Atom indecies are unique number of each atom. And RDKit adds the index when mol object is generated. RDKit makes mol object from SMILES, Inchi, molblock and lots of formats. To make canonical representation of molecules, the atom indices are asigned allways same roules in automatically. The indices are asigned regardless of scaffold. So if