Allow truncated MODEL line in PDB files

[tanhevg]

See https://github.com/BioJulia/BioFmtSpecimens/pull/28 Once that is merged, tests should be updated in this PR. BioFmtSpecimens/PDB/1SSU_err.pdb is referenced from the tests, but it does not generate an error any longer, so should be replaced with a real file from SCOPe

[jgreener64]

Thanks for finding this error and providing a fix.

I think the important line should be changed to curr_model = parse(Int, line[11:min(14, end)]) though. The PDB specification states that the model serial is in columns 11-14: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL. It should not go beyond that, though you are correct that it should not error if it is e.g. 13 characters long.

The corollary is that the 1SSU_err file should still error, it is not valid PDB format.

Would you be able to change that line and remove changes to the 1SSU_err test? Then this can be merged once the new file is added to the specimens repo.

[codecov[bot]]

Codecov Report

Merging #12 into master will not change coverage. The diff coverage is 100%.

@@           Coverage Diff           @@
##           master      #12   +/-   ##
=======================================
  Coverage   91.07%   91.07%           
=======================================
  Files           5        5           
  Lines        1121     1121           
=======================================
  Hits         1021     1021           
  Misses        100      100

Impacted Files	Coverage Δ
src/pdb.jl	88.47% <100%> (ø)	:arrow_up:

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[tanhevg]

The tests have been updated with the new PDB file in BioFmtSpecimens. All tests pass; the Travis build fails because of ftp timeout.

[jgreener64]

Thanks a lot!