def test_can_get_rmsd(self, mock_pair):
structure = AtomStructure(self.atom1, self.atom2, self.atom3)
other = Mock(AtomStructure)
other_atoms = [Mock(), Mock(), Mock()]
self.atom1.distance_to.return_value = 5
self.atom2.distance_to.return_value = 1
self.atom3.distance_to.return_value = -1
mock_pair.return_value = {
self.atom1: other_atoms[0],
self.atom2: other_atoms[1],
self.atom3: other_atoms[2]
}
rmsd = structure.rmsd_with(other)
mock_pair.assert_called_with(other)
self.atom1.distance_to.assert_called_with(other_atoms[0])
self.atom2.distance_to.assert_called_with(other_atoms[1])
self.atom3.distance_to.assert_called_with(other_atoms[2])
self.assertEqual(rmsd, 3)
def test_can_get_rmsd_after_superposition(self, mock_onto, mock_pair):
structure = AtomStructure(self.atom1, self.atom2, self.atom3)
other = Mock(AtomStructure)
other_atoms = [Mock(), Mock(), Mock()]
self.atom1.distance_to.return_value = 5
self.atom2.distance_to.return_value = 1
self.atom3.distance_to.return_value = -1
self.atom1.location = (1, 2, 3)
self.atom2.location = (4, 5, 6)
self.atom3.location = (7, 8, 9)
mock_pair.return_value = {
self.atom1: other_atoms[0],
self.atom2: other_atoms[1],
self.atom3: other_atoms[2]
}
rmsd = structure.rmsd_with(other, superimpose=True)
mock_onto.assert_called_with(other)
self.atom1.move_to.assert_called_with(1, 2, 3)
self.atom2.move_to.assert_called_with(4, 5, 6)
self.atom3.move_to.assert_called_with(7, 8, 9)