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
Sent: Friday, June 12, 2020 7:06 AM
To: Bennion, Brian
Cc: rdkit-discuss
Subject: Re: [Rdkit-discuss] trying to figure out what an rdkit warning means
On Thu, Jun 11, 2020 at 4:04 PM Bennion, Brian
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
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