Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

Hi Greg, I tried to investigate this further with github rdkit but I am as yet unable to configure/cmake it yet on this Mac (something related to boost python has changed) :-/ :-) - will keep poking at it and/or abstracting it... Thanks, Paul. On 19/02/2016 09:19, Greg Landrum wrote: > > >

Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

Hi Paul, That is indeed very strange behavior and I can't think of what would cause it. I'm not able to reproduce it with either the current github master, the 2015_09_2, or the 2015_03_1 release. Can you please send me a small test program that reproduces the problem? -greg On Wed, Feb 17,

Re: [Rdkit-discuss] Suppress stdout and stderr in rdkit

Hi Paolo, Thanks a lot for your prompt reply. I ended up coding this: from rdkit import Chem from rdkit import RDLogger smart = '[#6]1(:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2)-[#8,#6]' mol = Chem.MolFromSmarts(smart) lg = RDLogger.logger() lg.setLevel(RDLogger.CRITICAL) try:

Re: [Rdkit-discuss] Suppress stdout and stderr in rdkit

Dear Gaetano, you may try the following: from rdkit import rdBase rdBase.DisableLog('rdApp.error') You may check the logging levels you wish to disable/enable in rdkit/RDLogger.py, or use a wildcard such as 'rdApp.*' to affect all levels at once. Best, Paolo On 17/02/2016 23:54, Gaetano