Merge pull request #168 from peastman/single

Fixed error when a file contains only one residue

pdbfixer/pdbfixer.py

@@ -928,6 +928,7 @@ class PDBFixer(object):
             context.setPositions(newPositions)
             context.setPositions(newPositions)
             mm.LocalEnergyMinimizer.minimize(context)
             mm.LocalEnergyMinimizer.minimize(context)
             state = context.getState(getPositions=True)
             state = context.getState(getPositions=True)
+            if newTopology.getNumResidues() > 1:
                 nearest = self._findNearestDistance(context, newTopology, newAtoms)
                 nearest = self._findNearestDistance(context, newTopology, newAtoms)
                 if nearest < 0.13:
                 if nearest < 0.13:
 
 

pdbfixer/tests/test_mutate.py

@@ -10,8 +10,9 @@ def test_mutate_1():
     fixer.findMissingAtoms()
     fixer.findMissingAtoms()
     fixer.addMissingAtoms()        
     fixer.addMissingAtoms()        
     fixer.addMissingHydrogens(7.0)
     fixer.addMissingHydrogens(7.0)
-    temp_pdb = tempfile.NamedTemporaryFile(mode='w+')
+    with tempfile.NamedTemporaryFile(mode='w+') as temp_pdb:
         app.PDBFile.writeFile(fixer.topology, fixer.positions, temp_pdb)
         app.PDBFile.writeFile(fixer.topology, fixer.positions, temp_pdb)
+        temp_pdb.flush()
         pdb = app.PDBFile(temp_pdb.name)
         pdb = app.PDBFile(temp_pdb.name)
     
     
     new_residue57 = list(fixer.topology.residues())[16]
     new_residue57 = list(fixer.topology.residues())[16]