[Rdkit-discuss] Optimize the ligand in the protein pocket with rdkit

to make such optimization with MMFFoptimizer or UFFoptimizer directly? If we can only optimize the ligand, can I add some virtual point to mimic the protein pocket environment so that the ligand wouldn't overlap with protein atoms after minimization? Many Thanks. Best, Changge Changge Ji

[Rdkit-discuss] Sanitize Error

such error? Many thanks for your help. Best, Changge Changge Ji -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link

[Rdkit-discuss] Delete several Atoms

Dear all, Is there an easy way to delete several atoms in a molecule according to an index list ? RWMol RemoveAtom() can only delete one atom each time. And after that, the index changed. Many Thanks. Best, Changge Changge Ji

[Rdkit-discuss] About Explict [H] in Smarts.

Dear All, I'm a new to rdkit. I fount that the molecule 'c1c1' don't fit to the smarts 'c1cc([#1,F,Cl,I])ccc1' --- mol = Chem.MolFromSmiles('c1c1') fap = FragmentMatcher.FragmentMatcher() smarts = 'c1cc([#1,F,Cl,I])ccc1'