Details
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Type:
Bug
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Status: Open
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Priority:
Minor
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Resolution: Unresolved
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Affects Version/s: 2.11.0
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Fix Version/s: None
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Component/s: Datamodel, Structures, Test suite
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Labels:
Description
The method
public boolean isNonPositional()
{
return begin == 0 && end == 0;
}
in SequenceFeature is not sufficient and causes sequence features to be missed and, as a result, causes PDBSequenceFetcherTest to fail.
In the test for model 4im2, there is a residue with resno 0 -- SER0. PDBChain.makeResidueList attempts to add SER0 to the SequenceFeatureStore, but the store adds it to the nonpositional list rather than to its featureStore, since it has end=0 and start=0.
It's curious to me why this has not been caught before. Am I the first to run PDBSequenceFetcherTest?
public boolean isNonPositional()
{
return begin == 0 && end == 0;
}
in SequenceFeature is not sufficient and causes sequence features to be missed and, as a result, causes PDBSequenceFetcherTest to fail.
In the test for model 4im2, there is a residue with resno 0 -- SER0. PDBChain.makeResidueList attempts to add SER0 to the SequenceFeatureStore, but the store adds it to the nonpositional list rather than to its featureStore, since it has end=0 and start=0.
It's curious to me why this has not been caught before. Am I the first to run PDBSequenceFetcherTest?