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GLYCAM-Web / gmml

Glycam Molecular Modeling Library
GNU Lesser General Public License v3.0
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Sequences with dUA cause segfaults #137

Closed gitoliver closed 1 year ago

gitoliver commented 2 years ago

Running test 013 with a dUA sequence: dUA1-4DGalpNAcb1-OME dUA-4DGalpNAcb1-OME Both cause segfaults, the latter is what's generated by the website, that might be a separate bug. Here is the gmml level log info from just before the segfault: Fri Apr 29 05:41:41 2022 >>> /programs/gems/gmml/src/MolecularMetadata/GLYCAM/glycam06ResidueNameGenerator.cc:28 >>> [INFO]: Inputs: linkages: Terminal isomer: inputResName: dUA ringType: residueModifier: configuration: Fri Apr 29 05:41:41 2022 >>> /programs/gems/gmml/src/MolecularMetadata/GLYCAM/glycam06ResidueNameGenerator.cc:96 >>> [INFO]: Returning: 045

Fri Apr 29 05:41:41 2022 >>> /programs/gems/gmml/src/InputSet/CondensedSequence/assemblyBuilder.cpp:89 >>> [INFO]: Found prep entry: 045 for dUA

Fri Apr 29 05:41:41 2022 >>> /programs/gems/gmml/src/MolecularModeling/Residue/residuebuilder.cc:41 >>> [INFO]: Building residue from prep residue ...

gitoliver commented 2 years ago

Fix is available in the gmml-test branch, however the nomenclature is now the more specific: dUAa1-4 The others should give to the user error explaining the sequence is incorrect. Close this issue once websites versioned after vexed-vala make their way to glycam.org