When I was looking for Inchi options on the rdkit docs. this is what I found.
rdkit.Chem.inchi.MolToInchi(mol, options='', logLevel=None, treatWarningAsError=False) Returns the standard InChI string for a molecule Keyword arguments: logLevel – the log level used for logging logs and messages from InChI API. set to None to diable the logging completely treatWarningAsError – set to True to raise an exception in case of a molecule that generates warning in calling InChI API. The resultant InChI string and AuxInfo string as well as the error message are encoded in the exception. Returns: the standard InChI string returned by InChI API for the input molecule As far as viewing the smiles strings to 2D structure, i have been using an web service openmolecule.org. So that engine might be translating the smiles string and doing similar things as the sanitize function in rdkit is doing, if its not just using rdkit as well. Brian ________________________________ From: Greg Landrum <greg.land...@gmail.com> Sent: Friday, June 12, 2020 7:06 AM To: Bennion, Brian <benni...@llnl.gov> Cc: rdkit-discuss <rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] trying to figure out what an rdkit warning means On Thu, Jun 11, 2020 at 4:04 PM Bennion, Brian <benni...@llnl.gov<mailto:benni...@llnl.gov>> wrote: Thank you for the explanation Greg. When the smiles strings are viewed I see the E designation for them two trans double bonds. What other double bond is missing ? How do you view the SMILES strings? The way you are currently constructing the molecule (without sanitization) means that the RDKit doesn't see the stereochemistry information that's present in them. Also, is it possible within RDKit to activate the fixedH layer in the inchi creation? Sure, all of the InChI options can be provided just like you would on the command line to the InChI executable: In [54]: m1 = Chem.MolFromSmiles('CC1=CNC=N1') In [55]: m2 = Chem.MolFromSmiles('CC1=CN=CN1') In [58]: Chem.MolToInchi(m1,options='/FixedH') Out[58]: 'InChI=1/C4H6N2/c1-4-2-5-3-6-4/h2-3H,1H3,(H,5,6)/f/h5H' In [59]: Chem.MolToInchi(m2,options='/FixedH') Out[59]: 'InChI=1/C4H6N2/c1-4-2-5-3-6-4/h2-3H,1H3,(H,5,6)/f/h6H' In [60]: Chem.MolToInchi(m1)==Chem.MolToInchi(m2) Out[60]: True Best, -greg
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
