Biopython 1.55 causes unit test problems

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To reproduce this problem:

1. Run a full set of unit tests with the latest install of Biopython (version 
1.55):

>>>import MDAnalysis.tests
>>>MDAnalysis.tests.test(verbose=3, label='full') 

While the expected output would be a successful unit test without major 
warnings, there are several log reports of problems with a specific component 
of the new version of Biopython.

There are two main 'error reports' in the unit test output, one for 
TestPDBReader and the other for TestPDBReaderBig (each repeated several times 
for different atoms):

a) test_coordinates (MDAnalysis.tests.test_coordinates.TestPDBReader) ... 
/sansom/sc2/bioc1009/.local/lib/python2.6/site-packages/biopython-1.55-py2.6-lin
ux-i686.egg/Bio/PDB/Atom.py:71: PDBConstructionWarning: Atom object (name=N) 
without element
  PDBConstructionWarning)

b) test_coordinates (MDAnalysis.tests.test_coordinates.TestPDBReaderBig) ... 
/sansom/sc2/bioc1009/.local/lib/python2.6/site-packages/biopython-1.55-py2.6-lin
ux-i686.egg/Bio/PDB/Atom.py:71: PDBConstructionWarning: Atom object (name=H1) 
without element
  PDBConstructionWarning)

There is also a large amount of output looking like this:
N --> ?
HT1 --> ?
HT2 --> ?
HT3 --> ?
CA --> ?
HA --> ?

(See the attached logfile for the merged and complete stdout and stderr streams 
resulting from the unit test)

Original issue reported on code.google.com by tyler.je.reddy@gmail.com on 29 Sep 2010 at 9:44

Attachments:

• Tyler_MDA_log.txt

[GoogleCodeExporter]

Bio.PDB reader also misses atoms when two atoms have the same name in a 
residue. This is bad so I am changing the MDAnalysis default to use the 
PrimitivePDBReader (see ReleaseNotes070 and r530).

Original comment by orbeckst on 2 Nov 2010 at 12:32

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I don't think we can do anything about this except getting rid of the Bio.PDB 
reader. I am closing this as won't fix.

Original comment by orbeckst on 13 Sep 2011 at 3:24

• Changed state: WontFix
• Added labels: Priority-Low
• Removed labels: Priority-Medium