Hi,
Unfortunatly this is not possible out-of-the-box.
The SMILES format uses the default timeout (5 seconds) for calculating the
canonical code (specified in include/openbabel/canon.h). Changing the call
in src/formats/smilesformat.cpp from
CanonicalLabels(&mol, symmetry_classes, canonical_order
Dear,
When converting every entry of a multimolecule .sd file to the .can smiles
format in Python 3.5, I get the following error approximately 30 times for
23000 entries:
*** Open Babel Error in OpenBabel::CanonicalLabelsImpl::CalcCanonicalLabels
maximum time exceeded...
==
