Add unit tests for measure_distances, measure_angles, measure_dihedrals

src/molecule.py

@@ -3554,7 +3554,8 @@ def read_pdb(self, fnm, **kwargs):
                     conect_B_list.append(int(line_rest[:5]) - 1)
                     line_rest = line_rest[5:]
                 for conect_B in conect_B_list:
-                    bonds.append([conect_A, conect_B])
+                    bond = (min((conect_A, conect_B)), max((conect_A, conect_B)))
+                    bonds.append(bond)
 
         Answer={"xyzs":XYZList, "chain":list(ChainID), "altloc":list(AltLoc), "icode":list(ICode),
                 "atomname":[str(i) for i in AtomNames], "resid":list(ResidueID), "resname":list(ResidueNames),

test/test_molecule.py

@@ -40,6 +40,30 @@ def test_xyz_conversion(self):
         msg = "\nConversion from pdb to xyz yields different xyz coordinates\npdb:\n%s\n\ngro:\n%s\n" %\
         (str(self.molecule.Data['xyzs'][0]), str(molecule1.Data['xyzs'][0])))
 
+    def test_measure_distances(self):
+        """Check measure distance functions"""
+        result = np.array(self.molecule.measure_distances(1701, 1706))
+        EXPECTED_DISTANCE_RESULTS = np.array([1.80])
+        self.assertNdArrayEqual(EXPECTED_DISTANCE_RESULTS,result,delta=0.01,
+                                msg="\nMeasured distance has changed from previously calculated values.\n"
+                                "If this seems reasonable, update EXPECTED_DISTANCE_RESULTS in test_molecule.py with these values")
+
+    def test_measure_angles(self):
+        """Check measure angle functions"""
+        result = np.array(self.molecule.measure_angles(1771, 1769, 1772))
+        EXPECTED_ANGLE_RESULTS = np.array([114.11])
+        self.assertNdArrayEqual(EXPECTED_ANGLE_RESULTS,result,delta=0.01,
+                                msg="\nMeasured angle has changed from previously calculated values.\n"
+                                "If this seems reasonable, update EXPECTED_ANGLE_RESULTS in test_molecule.py with these values")
+
+    def test_measure_dihedrals(self):
+        """Check measure dihedral functions"""
+        result = np.array(self.molecule.measure_dihedrals(1709, 1706, 1701, 1702))
+        EXPECTED_DIHEDRAL_RESULTS = np.array([176.54])
+        self.assertNdArrayEqual(EXPECTED_DIHEDRAL_RESULTS,result,delta=0.01,
+                                msg="\nMeasured dihedral angle has changed from previously calculated values.\n"
+                                "If this seems reasonable, update EXPECTED_DIHEDRAL_RESULTS in test_molecule.py with these values")
+
     def test_gro_conversion(self):
         """Check molecule conversion from pdb to gro format"""
         self.logger.debug("\nCreating gro file from pdb... ")
@@ -106,6 +130,14 @@ def setUp(self):
             self.skipTest("Input pdb file test/files/%s doesn't exist" % self.source)
         except:
             self.fail("\nUnable to open gro file")
+
+    def test_measure_dihedrals(self):
+        """Check measure dihedral functions"""
+        result = np.array(self.molecule.measure_dihedrals(1131, 1112, 1113, 1114))
+        EXPECTED_DIHEDRAL_RESULTS = np.array([-157.223])
+        self.assertNdArrayEqual(EXPECTED_DIHEDRAL_RESULTS,result,delta=0.001,
+                                msg="\nMeasured dihedral angle has changed from previously calculated values.\n"
+                                "If this seems reasonable, update EXPECTED_DIHEDRAL_RESULTS in test_molecule.py with these values")
 
     def test_lipid_molecules(self):
         """Check for the correct number of molecules in a rectangular cell with broken molecules"""