Hi all, I'm having a dozen of compounds, where some of them have a charged atom (see the attached SMILES file).
When I parse the file I get sanitization errors on the compounds with the
charged atoms.
But when I view them with MarvinView 6.2.0 all goes fine.
I'm using an RDKit build from github, version "2014.03.1pre".
In order to see what sanitization error occurs in each case I did the
following:
1. To parse all compounds without sanitization
suppl = Chem.SmilesMolSupplier('data/SurfactantTestCompounds.smi',
titleLine=True, sanitize=False)
molsList = [x for x in suppl if x is not None]
print len(molsList)
2. Sanitize the compounds and catch specific errors
for m in molsList:
error = Chem.SanitizeMol(m, catchErrors=True)
if error:
print m.GetProp("_Name"), Chem.MolToSmiles(m), error
2.1 the output is as follows
NaLAS CCCCCCCC(CCCC)c1ccc(S(=O)(=O)O[Na+])cc1 SANITIZE_PROPERTIES
NaOLAS CCCCCCCC(CCCC)C1=CC=CC=C1S(=O)(=O)O[Na+] SANITIZE_PROPERTIES
SLES3EO CCCCCCCCCCCCOCCOCCOCCOS(=O)(=O)O[Na+] SANITIZE_PROPERTIES
SLES2EO CCCCCCCCCCCCOCCOCCOS(=O)(=O)O[Na+] SANITIZE_PROPERTIES
SLES1EO CCCCCCCCCCCCOCCOS(=O)(=O)O[Na+] SANITIZE_PROPERTIES
SDS CCCCCCCCCCCCOS(=O)(=O)O[Na+] SANITIZE_PROPERTIES
DTAC CCCCCCCCCCCC[N+](C)(C)(C)[Cl-] SANITIZE_PROPERTIES
Sdoc CCCCCCCCCCCC(=O)O[Na+] SANITIZE_PROPERTIES
3. Visualize compounds
Draw.MolsToGridImage(molsList, molsPerRow=5, legends=[x.GetProp('_Name')
for x in molsList], kekulize=True)
For visualized output check
http://nbviewer.ipython.org/gist/anonymous/11248962/Sanitization_Errors.ipynb
Is this an expected behaviour?
Is there something I can do as a fix?
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
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SurfactantTestCompounds.smi
Description: application/smil
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