Any chance of a test case (an example SDF or SMILES that causes the problem)?
- Noel On 20 February 2017 at 22:38, Tim Vandermeersch <tim.vandermeer...@gmail.com> wrote: > 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. >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
