Merge pull request #1210 from jchodera/top

Added getNumAtoms, getNumResidues, getNumChains to simtk.openmm.app.Topology

wrappers/python/simtk/openmm/app/topology.py

@@ -62,12 +62,30 @@ class Topology(object):
 
     def __repr__(self):
         nchains = len(self._chains)
-        nres = sum(1 for r in self.residues())
-        natom = sum(1 for a in self.atoms())
+        nres = self._numResidues
+        natom = self._numAtoms
         nbond = len(self._bonds)
         return '<%s; %d chains, %d residues, %d atoms, %d bonds>' % (
                 type(self).__name__, nchains, nres, natom, nbond)
 
+    def getNumAtoms(self):
+        """Return the number of atoms in the Topology.
+        """
+        natom = self._numAtoms
+        return natom
+
+    def getNumResidues(self):
+        """Return the number of residues in the Topology.
+        """
+        nres = self._numResidues
+        return nres
+
+    def getNumChains(self):
+        """Return the number of chains in the Topology.
+        """
+        nchain = len(self._chains)
+        return nchain
+
     def addChain(self, id=None):
         """Create a new Chain and add it to the Topology.
 

wrappers/python/tests/TestTopology.py

+import sys
+import unittest
+from simtk.openmm.app import *
+from simtk.openmm import *
+from simtk.unit import *
+import simtk.openmm.app.element as elem
+if sys.version_info >= (3, 0):
+    from io import StringIO
+else:
+    from cStringIO import StringIO
+
+
+class TestTopology(unittest.TestCase):
+    """Test the Topology object"""
+
+
+    def check_pdbfile(self, pdbfilename, natoms, nres, nchains):
+        """Check that a PDB file has the specified number of atoms, residues, and chains."""
+        pdb = PDBFile(pdbfilename)
+        top = pdb.topology
+        self.assertEqual(pdb.topology.getNumAtoms(), natoms)
+        self.assertEqual(pdb.topology.getNumResidues(), nres)
+        self.assertEqual(pdb.topology.getNumChains(), nchains)
+
+    def test_getters(self):
+        """Test getters for number of atoms, residues, chains."""
+        self.check_pdbfile('systems/1T2Y.pdb', 271, 25, 1)
+
+if __name__ == '__main__':
+    unittest.main()