[Rdkit-discuss] Fwd: sending warnings to stderr/stdout to files

Hi Rdkit forum,   Easy question, perhaps difficult to answer…    I’ve been reading a lot of support messages, many a very old about how to get warnings (only visible at the cmd line) to be send to files. I can get error messages sent, but not warnings.   The type I’m trying to capture ar

[Rdkit-discuss] Fwd: errors with stereoisomers

Hello RDKit gurus,   I've found an interesting issue with V2000 SDF files which have a carbon marked as "Either or unmarked stereocentre", a 3 in the atom-block.   The enclosed molecule throws these errors – note also that the word “begining" is spelt wrong in the stderr.   Is there a way

Re: [Rdkit-discuss] Fwd: sending warnings to stderr/stdout to files

Hi. Yes this works for me as per the RDKit docs.  But I need to pipe it to a file, any suggestions? Thanks. Mike Get Outlook for Android On Tue, Sep 24, 2019 at 10:28 PM +0100, "Lukas Pravda" wrote: Hi Mike,   The following code works for me:   import sys from i

Re: [Rdkit-discuss] how to handle metallocenes?

Hi Michal/Greg, Many thanks for your thoughts.  Compounds are from PubChem's Substances. I'm of the opinion to filter out these types of molecules, but this may be hard to do with billions of compounds...? What would be an efficient way to check parse drug like compounds, and reject organome

[Rdkit-discuss] Inchi which flavour??

Dear RdKit users,I was reading the inchi module docs and I couldn't find methods to call the InChI API.  Are these exposed in RDKit?  It says the default is the standard Inchi.  What happens when this conversion fails? Thanks,Mike___ Rdkit-discuss maili