Test number of atoms after mutation.

tests/test_mutate.py

@@ -6,6 +6,9 @@ import tempfile
 def test_mutate_1():
 def test_mutate_1():
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer.applyMutations(["ALA-57-GLY"], "A")
     fixer.applyMutations(["ALA-57-GLY"], "A")
+    fixer.findMissingResidues()     
+    fixer.findMissingAtoms()
+    fixer.addMissingAtoms()        
     fixer.addMissingHydrogens(7.0)
     fixer.addMissingHydrogens(7.0)
     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)
@@ -15,11 +18,20 @@ def test_mutate_1():
 
 
 def test_mutate_2():
 def test_mutate_2():
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
-    fixer.applyMutations(["ALA-57-GLY", "SER-56-ALA"], "A")
+    fixer.applyMutations(["ALA-57-LEU", "SER-56-ALA"], "A")
+    fixer.findMissingResidues()     
+    fixer.findMissingAtoms()
+    fixer.addMissingAtoms()        
     fixer.addMissingHydrogens(7.0)
     fixer.addMissingHydrogens(7.0)
     temp_pdb = tempfile.NamedTemporaryFile()
     temp_pdb = tempfile.NamedTemporaryFile()
-    assert list(fixer.topology.residues())[16].name == "GLY", "Name of mutated residue did not change correctly!"
-    assert list(fixer.topology.residues())[15].name == "ALA", "Name of mutated residue did not change correctly!"
+    new_residue57 = list(fixer.topology.residues())[16]
+    new_residue56 = list(fixer.topology.residues())[15]
+    assert new_residue57.name == "LEU", "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_residue57.atoms())) == 19, "Should have 19 atoms in ALA 56"
+
 
 
 @raises(ValueError)
 @raises(ValueError)
 def test_mutate_3_fails():
 def test_mutate_3_fails():
@@ -36,3 +48,4 @@ def test_mutate_4_fails():
 def test_mutate_5_fails():
 def test_mutate_5_fails():
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer.applyMutations(["ALA-1000-GLY", "SER-56-ALA"], "A")
     fixer.applyMutations(["ALA-1000-GLY", "SER-56-ALA"], "A")
+