I converted the attached mol file into a cml file using
MDLReader.read and CMLWriter.write.
Then I produced the SMILES String for the mol file using
Afterwards, I generated the SMILES String from the CML
file using the same method. It should have been the
same string as the one generated above, since both
files describe the same molecule. But they weren't,
although they were both correct.
I got the following strings:
mol -> SMILES:
mol-> cml-> SMILES:
I read the following:
"In order to use the canonical SMILES generator you
need to properly
configure the atoms in the molecule for which you want
to generate the
SMILES. The SmilesGenerator needs to know the
correct atomic mass in
order to generate the correct SMILES notation and it
also needs to know
the implicite hydrogen count in order to generate the
canonical order of
So maybe this is the problem?
Thanks for helping out!