In this year I moved from MedChem team to CompChem team. And now I need to learn SBDD. Today I struggled mol object that has 3D information.
I would like to replace hydrogen which attached aromatic carbon to some atoms. I thought it is easy if I use rdChemReactions method. But I found that it was not good approach. Because RunReactants method generates products but the method can not keep 3D information of reacted atoms.
It is very interesting and good information for me. Let see example code.
Following code is very simple example.
At first, I tried to replace atom with rdChemReactions method. It worked well but the position of fluorine atom was 0, 0, 0. It indicates that the method can not keep 3D information. I think it is reasonable because some chemical reaction dramatically changes molecular conformation.
The second example used Editable mol.
This approach could keep 3D information, it means that the method do just replace atom!
Of course bond length of C-H and C-F is different but the approach is more suitable for atom scanning I think.
I always surprised that RDKit has many useful function for drug design.