Re: [Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial

... sounds like a good explanation. If this is indeed the case, it would be reasonable to force flush to get guaranteed non-random behavior. Thanks! Best, Dmitri > On Jul 5, 2016, at 7:39 AM, Brian Kelley wrote: > > After some digging, it looks like the underlying C++

Re: [Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial

After some digging, it looks like the underlying C++ streams aren't flushing. This means that python might not actually have all the information when you print them out. We may have to enable a "flush" function for these streams for better error reporting on the python side, I'll need to

Re: [Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial

Dmitri, Could you send me the notebook that displays these issues? I can't reproduce them. Thanks, Brian On Tue, Jun 28, 2016 at 6:25 PM, Brian Kelley wrote: > It looks like there may be an issue calling WrapLogs twice. If you see > the error messages in the

Re: [Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial

Hi Brian, First off, now I can capture the warnings, so for practical purposes my question has been addressed, thank you for helping me get to this point. Cool trick with StringIO. I can even just do: Python 3.5.1 :: Anaconda 2.4.0 (x86_64), OSX 10.11.5, jupyter 4.1.0, Firefox ``` import io

Re: [Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial

Hi Greg - Thank you very much for the clear and detailed explanation! (and, now that I have a chance to say this, thank you for putting the project together; being able to work with chemistry in the python notebook is great, and having hooks into pandas is really cool) In this case I was

Re: [Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial

Hi Dmitri, The results that come back from the MCS in that examples really describe queries, not necessarily stable molecules or things that can be accurately translated into SMILES. I'll describe below what's going on to cause the error, but the more important question is: what are you trying

[Rdkit-discuss] SMILES string from SureChEMBL iPython Notebook Tutorial

Dear RDKitters, I would appreciate any comments on the following: I am looking at the 'SureChEMBL iPython Notebook Tutorial' http://nbviewer.jupyter.org/github/rdkit/UGM_2014/blob/master/Notebooks/Vardenafil.ipynb following along with rdkit '2016.03.1' on OSX In Cell 142, there is this