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, frag_atoms);
to
CanonicalLabels(&mol, symmetry_classes, canonical_order, frag_atoms, 60);
will increase the timeout. If you compiled OpenBabel from source code this
is easy to do.
A better solution would be to have this as an option to the SMILES format...
Kind regards,
Tim
On Mon, Feb 20, 2017 at 2:02 PM, Jan-Joris Devogelaer <
janjoris.devogel...@gmail.com> wrote:
> 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...
> ==============================
>
> Empirically, I figured out that for a smaller test set no errors would
> occur
> and that only very large molecules will result in this error.
>
> Is there any way of dealing with this error?
>
> Thank you,
>
> Jan-Joris
>
>
>
> --
> View this message in context: http://forums.openbabel.org/
> Maximum-time-exceeded-tp4659742.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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