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  1. Jalview
  2. JAL-1998

PDBfile parser fails with 'ArithmeticException' for some PDB entries

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.8.2b1, 2.9, 2.9.0b2
    • Fix Version/s: 2.10.0
    • Component/s: None
    • Labels:
      None

      Description

      While executing the SIFTS N2NScan, I discovered that the PDBfile parser throws an Arithmetic exception caused by division by zero.

      To reproduce, try fetching one of the following entries using the PDB sequence fetcher: 1a08; 1a09; 1a07; 1a1a; 1a1b; 1a1b; 1a1e.
          
      Stack trace:

      java.lang.ArithmeticException: / by zero
      at MCview.PDBChain.makeCaBondList(PDBChain.java:255)
      at MCview.PDBfile.makeCaBondList(PDBfile.java:518)
      at MCview.PDBfile.parse(PDBfile.java:200)
      at jalview.io.AlignFile.doParse(AlignFile.java:169)
      at MCview.PDBfile.<init>(PDBfile.java:85)
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:281)
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
      at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
      at java.lang.Thread.run(Thread.java:745)
      Failed to read alignment using the 'PDB' reader.
      java.lang.ArithmeticException: / by zero
      INFO : jalview.bin.Jalview - Error retrieving 1a08 from PDB
      java.io.IOException: Formats currently supported are
      BLC, CLUSTAL, FASTA, MSF, PileUp, PIR, PFAM, STH, PDB, JnetFile, RNAML, PHYLIP, JSON, GFF v2 or v3, and HTML.
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:350)
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
      at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
      at java.lang.Thread.run(Thread.java:745)
      INFO - Error retrieving 1a08 from PDB
      java.io.IOException: Formats currently supported are
      BLC, CLUSTAL, FASTA, MSF, PileUp, PIR, PFAM, STH, PDB, JnetFile, RNAML, PHYLIP, JSON, GFF v2 or v3, and HTML.
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:350)
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
      at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
      at java.lang.Thread.run(Thread.java:745)

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              Assignee:
              tcnofoegbu Tochukwu Charles N Ofoegbu
              Reporter:
              tcnofoegbu Tochukwu Charles N Ofoegbu
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                Created:
                Updated:
                Resolved: