tests

wrappers/python/tests/TestPdbFile.py

@@ -70,7 +70,6 @@ class TestPdbFile(unittest.TestCase):
         pdb = PDBFile(open('systems/triclinic.pdb', 'rb'))
         self.assertEqual(len(pdb.positions), 8)
 
-
     def assertVecAlmostEqual(self, p1, p2, tol=1e-7):
         unit = p1.unit
         p1 = p1.value_in_unit(unit)
@@ -79,7 +78,21 @@ class TestPdbFile(unittest.TestCase):
         for i in range(3):
             diff = abs(p1[i]-p2[i])/scale
             self.assertTrue(diff < tol)
-
+            
+    def test_ExtraParticles(self):
+        """Test reading, and writing and re-reading of a file containing extra particle atoms."""
+        pdb = PDBFile('systems/tip5p.pdb')  
+        for atom in pdb.topology.atoms():
+            if atom.index > 2:
+                self.assertEqual(None, atom.element)
+        output = StringIO()
+        PDBFile.writeFile(pdb.topology, pdb.positions, output)
+        input = StringIO(output.getvalue())
+        pdb = PDBFile(input, extraParticleIdentifier = '')
+        for atom in pdb.topology.atoms():
+            if atom.index > 2:
+                self.assertEqual(None, atom.element)    
+                      
 
 if __name__ == '__main__':
     unittest.main()

wrappers/python/tests/systems/tip5p.pdb

+CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1           1 
+ATOM      1  O   HOH A   1      20.612  20.351  16.218  1.00  0.00          O
+ATOM      2  H1  HOH A   1      20.565  20.405  15.264  1.00  0.00          H
+ATOM      3  H2  HOH A   1      21.273  19.679  16.387  1.00  0.00          H
+ATOM      4  D1  HOH A   1      20.808  20.964  16.492  1.00  0.00          EP
+ATOM      5  D2  HOH A   1      19.994  20.162  16.486  1.00  0.00          EP 
+TER       6      HOH A   1
+END