Test atom numbers

pdbfixer/pdbfixer.py

@@ -575,6 +575,7 @@ class PDBFixer(object):
 
 
         >>> fixer = PDBFixer(pdbid='1VII')
         >>> fixer = PDBFixer(pdbid='1VII')
         >>> fixer.applyMutations(["ALA-57-GLY"])
         >>> fixer.applyMutations(["ALA-57-GLY"])
+        >>> fixer.findMissingResidues()     
         >>> fixer.findMissingAtoms()
         >>> fixer.findMissingAtoms()
         >>> fixer.addMissingAtoms()        
         >>> fixer.addMissingAtoms()        
         >>> fixer.addMissingHydrogens(7.0)
         >>> fixer.addMissingHydrogens(7.0)

tests/test_mutate.py

@@ -13,7 +13,10 @@ def test_mutate_1():
     temp_pdb = tempfile.NamedTemporaryFile()
     temp_pdb = tempfile.NamedTemporaryFile()
     app.PDBFile.writeFile(fixer.topology, fixer.positions, temp_pdb)
     app.PDBFile.writeFile(fixer.topology, fixer.positions, temp_pdb)
     pdb = app.PDBFile(temp_pdb.name)
     pdb = app.PDBFile(temp_pdb.name)
-    assert list(pdb.topology.residues())[16].name == "GLY", "Name of mutated residue did not change correctly!"
+    
+    new_residue57 = list(fixer.topology.residues())[16]
+    assert new_residue57.name == "GLY", "Name of mutated residue did not change correctly!"
+    assert len(list(new_residue57.atoms())) == 7, "Should have 7 atoms in GLY 56"    
 
 
 
 
 def test_mutate_2():
 def test_mutate_2():
@@ -30,7 +33,7 @@ def test_mutate_2():
     assert new_residue56.name == "ALA", "Name of mutated residue did not change correctly!"
     assert new_residue56.name == "ALA", "Name of mutated residue did not change correctly!"
     
     
     assert len(list(new_residue56.atoms())) == 10, "Should have 10 atoms in ALA 56"
     assert len(list(new_residue56.atoms())) == 10, "Should have 10 atoms in ALA 56"
-    assert len(list(new_residue57.atoms())) == 19, "Should have 19 atoms in ALA 56"
+    assert len(list(new_residue57.atoms())) == 19, "Should have 19 atoms in LEU 57"
 
 
 
 
 @raises(ValueError)
 @raises(ValueError)