Add hydrogens afterward in examples and tests.

pdbfixer/pdbfixer.py

@@ -579,6 +579,7 @@ class PDBFixer(object):
 
         >>> fixer = PDBFixer(pdbid='1VII')
         >>> fixer.applyMutations(["ALA-16-GLY"])
+        >>> fixer.addMissingHydrogens(7.0)
 
         """
         

tests/test_mutate.py

@@ -6,18 +6,21 @@ import tempfile
 def test_mutate_1():
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer.applyMutations(["ALA-16-GLY"])
+    fixer.addMissingHydrogens(7.0)
     app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())
 
 
 def test_mutate_2():
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer.applyMutations(["ALA-16-GLY", "SER-15-ALA"])
+    fixer.addMissingHydrogens(7.0)
     app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())
 
 @raises(ValueError)
 def test_mutate_3_fails():
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer.applyMutations(["ALA-15-GLY", "SER-15-ALA"])
+    fixer.addMissingHydrogens(7.0)
     app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())
 
 
@@ -25,4 +28,5 @@ def test_mutate_3_fails():
 def test_mutate_4_fails():
     fixer = pdbfixer.PDBFixer(pdbid='1VII')
     fixer.applyMutations(["ALA-16-WTF", "SER-15-ALA"])
+    fixer.addMissingHydrogens(7.0)
     app.PDBFile.writeFile(fixer.topology, fixer.positions, tempfile.TemporaryFile())