[Rdkit-discuss] PDBe-KB ligand centric pages survey

2019-04-04 Thread Lukas Pravda
Dear All, We are in the process of redesigning the ligand pages of PDBe and and RDKIT is playing a major role in it. We would be grateful if you could fill out a short survey to help us understand what information about small molecules / ligands you would find useful. The survey is

[Rdkit-discuss] FreeSASA proberadius

2019-04-04 Thread Illimar Hugo Rekand
Hello, RDKitters! I have an oddly specific question for you today. I am using RDKit's implemented FreeSASA feature for some contact surface area calculations. So far it's worked fine, but I'm missing a feature for setting the probe-radius for the SASA-calculations. I see that this radius is

Re: [Rdkit-discuss] Dihedral Restraints

2019-04-04 Thread Greg Landrum
Hi, On Tue, Apr 2, 2019 at 1:49 AM Phuong Chau wrote: > > Thank you RDKIT. I found this is a very helpful instruction about how to > get all the dihedral restraints of a molecule ( > https://sourceforge.net/p/rdkit/mailman/message/34554502/ ). From the > code provided, I have some questions: >

Re: [Rdkit-discuss] reaction SMARTS and double bonds

2019-04-04 Thread Jean-Marc Nuzillard
Problem solved. Many Thanks, Jean-Marc Le 04/04/2019 à 06:54, Greg Landrum a écrit : On Wed, Apr 3, 2019 at 8:26 PM Jean-Marc Nuzillard mailto:jm.nuzill...@univ-reims.fr>> wrote: Dear Greg, In [10] and Out[10] of your answer below (thanks!) incited me to believe that the