first test cases for convenient superposition method

modules/mol/alg/tests/CMakeLists.txt

 set(OST_MOL_ALG_UNIT_TESTS
   test_superposition.cc
   tests.cc
+  test_convenient_superpose.py
 )
 
 ost_unittest(mol_alg "${OST_MOL_ALG_UNIT_TESTS}")

modules/mol/alg/tests/test_convenient_superpose.py

+import unittest
+import os
+import random
+
+class TestConvenientSuperpose(unittest.TestCase):
+  
+  def setUp(self):
+    pass
+  
+  def runAtomOrdering(self, view1, view2):
+    # call atom ordering function here
+    return view1, view2
+  
+  def assertEqualAtomOrder(self, view1, view2):
+    self.assertEquals(len(view1.atoms),len(view2.atoms))
+    for a1, a2 in zip(view1.atoms, view2.atoms):
+      self.assertEquals(a1.element, a2.element)
+      self.assertTrue(geom.Equal(a1.pos, a2.pos))
+
+  def testAssertion(self):
+    ent1_ent = io.LoadEntity(os.path.join("testfiles","1aho.pdb"))
+    ent1_view = ent1_ent.Select("")
+    self.assertEqualAtomOrder(ent1_ent, ent1_ent)
+    self.assertEqualAtomOrder(ent1_ent, ent1_view)
+    self.assertEqualAtomOrder(ent1_view, ent1_ent)
+    self.assertEqualAtomOrder(ent1_view, ent1_view)
+    self.assertRaises(AssertionError, self.assertEqualAtomOrder, ent1_view.Select("ele!=H"), ent1_view)
+    
+  def testCorrectlyOrdered(self):
+    ent1_ent = io.LoadEntity(os.path.join("testfiles","1aho.pdb"))
+    ent1_view = ent1_ent.Select("")
+    view1, view2 = self.runAtomOrdering(ent1_ent, ent1_ent)
+    self.assertEqualAtomOrder(view1, view2)    
+    view1, view2 = self.runAtomOrdering(ent1_view, ent1_ent)
+    self.assertEqualAtomOrder(view1, view2)
+    view1, view2 = self.runAtomOrdering(ent1_ent, ent1_view)
+    self.assertEqualAtomOrder(view1, view2)
+    view1, view2 = self.runAtomOrdering(ent1_view, ent1_view)
+    self.assertEqualAtomOrder(view1, view2)
+    
+  def testMissingFirstAtom(self):
+    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
+    ent_view_missing = ent_view.Select("not (cname=A and rnum=1 and aname=N)")
+    view1, view2 = self.runAtomOrdering(ent_view, ent_view_missing)
+    self.assertEqualAtomOrder(view1, view2)
+    view1, view2 = self.runAtomOrdering(ent_view_missing, ent_view)
+    self.assertEqualAtomOrder(view1, view2)
+    
+  def testMissingManyAtoms(self):
+    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
+    ent_view_missing = ent_view.Select("not (cname=A and rnum=3,19,32 and aname=CB,CA,CD)")
+    view1, view2 = self.runAtomOrdering(ent_view, ent_view_missing)
+    self.assertEqualAtomOrder(view1, view2)
+    view1, view2 = self.runAtomOrdering(ent_view_missing, ent_view)
+    self.assertEqualAtomOrder(view1, view2)
+    
+  def testMissingFirstResidue(self):
+    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
+    ent_view_missing = ent_view.Select("not (cname=A and rnum=1)")
+    view1, view2 = self.runAtomOrdering(ent_view, ent_view_missing)
+    self.assertEqualAtomOrder(view1, view2)
+    view1, view2 = self.runAtomOrdering(ent_view_missing, ent_view)
+    self.assertEqualAtomOrder(view1, view2)
+  
+  def testMissingHydrogens(self):
+    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
+    ent_view_missing = ent_view.Select("ele!=H")
+    view1, view2 = self.runAtomOrdering(ent_view, ent_view_missing)
+    self.assertEqualAtomOrder(view1, view2)
+    view1, view2 = self.runAtomOrdering(ent_view_missing, ent_view)
+    self.assertEqualAtomOrder(view1, view2)
+  
+  def testWrongAtomOrder(self):
+    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
+    ent_view_wrong = ent_view.CreateEmptyView()
+    for c in ent_view.chains:
+      ent_view_wrong.AddChain(c)
+      for r in c.residues:
+        ent_view_wrong.AddResidue(r)
+        atoms = r.atoms
+        random.shuffle(atoms)
+        for a in atoms:
+          ent_view_wrong.AddAtom(a)
+    view1, view2 = self.runAtomOrdering(ent_view, ent_view_wrong)
+    self.assertEqualAtomOrder(view1, view2)
+    view1, view2 = self.runAtomOrdering(ent_view_wrong, ent_view)
+    self.assertEqualAtomOrder(view1, view2)
+  
+  def testWrongResidueOrder(self):
+    '''
+    there is a bug in ost (BZDNG-260) that gives weird atom counts here, thus
+    this test is skipped for the moment
+    
+    
+    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
+    ent_view_wrong = ent_view.CreateEmptyView()
+    for c in ent_view.chains:
+      ent_view_wrong.AddChain(c)
+      residues = c.residues
+      random.shuffle(residues)
+      for r in residues:
+        ent_view_wrong.AddResidue(r)
+        for a in r.atoms:
+          av=ent_view_wrong.AddAtom(a)
+    view1, view2 = self.runAtomOrdering(ent_view, ent_view_wrong)
+    self.assertEqualAtomOrder(view1, view2)
+    view1, view2 = self.runAtomOrdering(ent_view_wrong, ent_view)
+    self.assertEqualAtomOrder(view1, view2)
+    '''
+    pass
+    
+if __name__ == "__main__":
+  unittest.main()
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