Initial Work on Reading Crystal and Creation Gaussian Input

tests/shared/system/test_molecule.py

@@ -0,0 +1,87 @@
+from crystalpol.shared.system.molecule import Molecule
+from crystalpol.shared.system.atom import Atom
+
+import io
+
+import unittest
+
+
+class TestMolecule(unittest.TestCase):
+    def test_class_instantiation(self):
+        molecule = Molecule("TEST")
+
+        self.assertEqual(molecule.mol_name, "TEST")
+        self.assertIsInstance(molecule, Molecule)
+
+    def test_add_atom(self):
+        molecule = Molecule("TEST")
+
+        atom = Atom(
+            na=1,
+            rx=0,
+            ry=0,
+            rz=0,
+        )
+
+        molecule.add_atom(atom)
+
+        self.assertEqual(len(molecule.atoms), 1)
+        self.assertEqual(molecule.atoms[0], atom)
+
+    def test_update_charges(self):
+        molecule = Molecule("TEST")
+
+        atom = Atom(
+            na=1,
+            rx=0,
+            ry=0,
+            rz=0,
+        )
+
+        molecule.add_atom(atom)
+
+        molecule.update_charges([1])
+
+        self.assertEqual(molecule.atoms[-1].chg, 1)
+
+    def test_update_charges_raises_exception(self):
+        molecule = Molecule("TEST")
+
+        atom = Atom(
+            na=1,
+            rx=0,
+            ry=0,
+            rz=0,
+        )
+
+        molecule.add_atom(atom)
+
+        with self.assertRaises(ValueError):
+            molecule.update_charges([1, 1])
+
+    def test_print_mol_info(self):
+        molecule = Molecule("TEST")
+
+        atom = Atom(
+            na=1,
+            rx=0,
+            ry=0,
+            rz=0,
+        )
+
+        molecule.add_atom(atom)
+
+        with io.StringIO() as file:
+            molecule.print_mol_info(file)
+
+            file.seek(0)
+            info_string = file.read()
+
+        self.assertIsNotNone(info_string)
+        self.assertTrue(len(info_string) > 0)
+        self.assertTrue("Molecule Name: TEST" in info_string)
+        self.assertTrue("H    r: [0, 0, 0]    charge: None" in info_string)
+
+
+if __name__ == '__main__':
+    unittest.main()