#62 concat PDBModels with and without biomol info fails

closed-fixed
5
2013-04-25
2013-04-25
Raik Gruenberg
No

PDBModel.concat fails if only one of the models has a biomol record. Related to previous bugfix. This also makes capACE and capNME fail in PDBCleaner.

ProfileError Traceback (most recent call last)
<ipython-input-30-59808851051b> in <module>()
7
8 clean = B.AmberParmBuilder( chromo )
----> 9 m1 = clean.capNME( chromo, 0 )
10 m2 = clean.capACE( chromo, 0 )
11 m3 = clean.capNME( m2, 0)
/usr/local/lib/python2.7/dist-packages/Biskit/AmberParmBuilder.pyc in capNME(self, model, chain)
326 """
327 cleaner = PDBCleaner( model, log=self.log )
--> 328 return cleaner.capNME( model, chain, breaks=True)
329
330

/usr/local/lib/python2.7/dist-packages/Biskit/PDBCleaner.pyc in capNME(self, model, chain, breaks)
457
458 ## concat cap on chain
--> 459 m_chain = m_chain.concat( cap, newChain=False )
460
461 ## should be obsolete now
/usr/local/lib/python2.7/dist-packages/Biskit/PDBModel.pyc in concat(self, *models, **kw) 2180 try: 2181 k = max(self.biounit.keys())+1 -> 2182 r.residues['biomol'][self.lenResidues():] += k 2183 r.biounit = self.biounit.append(m.biounit) 2184 r.biounit.model = r /usr/local/lib/python2.7/dist-packages/Biskit/ProfileCollection.pyc in __getitem__(self, k) 363 return self.__getslice__( k ) 364 --> 365 return self.get( k ) 366 367 /usr/local/lib/python2.7/dist-packages/Biskit/PDBModel.pyc in get(self, name, default, update, updateMissing) 104 r = None 105 else: --> 106 raise ProfileError, e 107 108 if r is None and (update or updateMissing):
ProfileError: No profile found with name biomol

Discussion

  • Raik Gruenberg
    Raik Gruenberg
    2013-04-25

    • status: open --> closed-fixed
     
  • Raik Gruenberg
    Raik Gruenberg
    2013-04-25

    Temporary bugfix: The biomol record is now deleted during PDBModel.concat