Apologies for repeated posting. Using RDKit 2011.12.1.
I can read an SDF file (attached: test.sdf) using ForwardSDMolSupplier (with sanitization explicitly turned on) - but I cannot write the molecule back to a second SD file using SDWriter. Interestingly, upon writing it fails with a sanitization error (ValueError: "Sanitization error: Can't kekulize mol"). Note that the molecule is not null and I am not doing anything with the molecule. My question is: how did the molecule pass the initial sanitization test (when it is read) but not the second (when it is written) ? Code attached for ease of reproducibility. - Jean-Paul Ebejer Early Stage Researcher
#!/usr/bin/env python
from rdkit import Chem
# let us make sure sanitization is explicitely on
suppl = Chem.ForwardSDMolSupplier('test.sdf', sanitize=True)
wr = Chem.SDWriter('out.sdf')
for m in suppl:
# we have a mol instance
print "Here is your read mol:", m
# but we cannot write it
wr.write(m)
wr.flush()
wr.close()
suppl.close()
test.sdf
Description: application/extension-sdf
------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2
_______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
