Give nicer error when index not found.

pdbfixer/pdbfixer.py

@@ -592,6 +592,9 @@ class PDBFixer(object):
             old_name, index, new_name = mut_str.split("-")
             index = int(index)
             
+            if index not in index_to_old_name:
+                raise(KeyError("Cannot find index %d in system!" % index))
+            
             if index_to_old_name[index] != old_name:
                 raise(ValueError("You asked to mutate %s %d, but that residue is actually %s!" % (old_name, index, index_to_old_name[index])))
             

tests/test_mutate.py

@@ -30,3 +30,11 @@ def test_mutate_4_fails():
     fixer.applyMutations(["ALA-16-WTF", "SER-15-ALA"])
     fixer.addMissingHydrogens(7.0)
     app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())
+
+
+@raises(KeyError)
+def test_mutate_5_fails():
+    fixer = pdbfixer.PDBFixer(pdbid='1VII')
+    fixer.applyMutations(["ALA-1000-GLY", "SER-15-ALA"])
+    fixer.addMissingHydrogens(7.0)
+    app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())