DSSP.py mask & compress fail, returing KeyError 4 and 5

[neb9]

With 1AM7:

Traceback (most recent call last):
  File "1.py", line 11, in <module>
    m = m.compress(m.maskProtein())
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2309, in compress
    return self.take( N0.nonzero( mask ), *initArgs, **initKw )
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2249, in take
    r.biounit = self.biounit.take(i)
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/BioUnit.py", line 107, in take
    r.biomol = dict([ (bm , self.biomol[bm]) for bm in remaining_biomols ])
KeyError: 4

With 1CA1:

  File "1.py", line 11, in <module>
    m = m.compress(m.maskProtein())
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2309, in compress
    return self.take( N0.nonzero( mask ), *initArgs, **initKw )
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2249, in take
    r.biounit = self.biounit.take(i)
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/BioUnit.py", line 107, in take
    r.biomol = dict([ (bm , self.biomol[bm]) for bm in remaining_biomols ])
KeyError: 5

[neb9]

I set m.biomol = None in the line before, by the way

[graik]

There is a radical / pragmatic solution here which is to delete the following lines in PDBModel.take:

    ## copy the biounit
    try:
        r.biounit = self.biounit.take(i)
        r.biounit.model = r
    except AttributeError:
        pass

This should pretty much solve all your problems with biounit.

When I have the time to look into it, I will probably end up doing exactly that anyway and restrict the BioUnit functionality to a separate module that is less integrated with PDBModel.

Greetings Raik

On Sat, Nov 19, 2016 at 8:41 PM, neb9 notifications@github.com wrote:

I set m.biomol = None in the line before, by the way

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Raik Grünberg http://www.raiks.de/contact.html

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[graik]

biomol take / compress / concat is now deactivated by default.