def test_adds_maps_to_force(self):
with mock.patch(
"meld.system.openmm_runner.cmap.np.loadtxt") as mock_loadtxt:
# this is a bit hacky and depends on what order the maps are loaded in
expected_gly = 3.0 * 0. + 7.0 * 1. + np.zeros((24, 24)).flatten()
expected_pro = 3.0 * 2. + 7.0 * 3. + np.zeros((24, 24)).flatten()
expected_ala = 3.0 * 4. + 7.0 * 5. + np.zeros((24, 24)).flatten()
expected_gen = 3.0 * 6. + 7.0 * 7. + np.zeros((24, 24)).flatten()
mock_loadtxt.side_effect = self.maps
adder = CMAPAdder(self.system.top_string,
alpha_bias=3.0,
beta_bias=7.0)
adder.add_to_openmm(self.mock_openmm_system)
self.assertEqual(self.MockCMAP.call_count, 1)
self.assertEqual(self.mock_cmap.addMap.call_count, 4)
# make sure all of the sizes are correct
add_map_args = self.mock_cmap.addMap.call_args_list
self.assertEqual(add_map_args[0][0][0], 24)
self.assertEqual(add_map_args[1][0][0], 24)
self.assertEqual(add_map_args[2][0][0], 24)
self.assertEqual(add_map_args[3][0][0], 24)
# make sure the maps are correct
np.testing.assert_almost_equal(add_map_args[0][0][1], expected_gly)
np.testing.assert_almost_equal(add_map_args[1][0][1], expected_pro)
np.testing.assert_almost_equal(add_map_args[2][0][1], expected_ala)
np.testing.assert_almost_equal(add_map_args[3][0][1], expected_gen)
def test_correct_torsions_should_be_added_to_force(self):
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
# map should be #2 for alanine
# all atom indices are zero-based in openmm
self.mock_cmap.addTorsion.assert_called_once_with(2, 10, 12, 14, 20, 12, 14, 20, 22)
def test_adds_maps_to_force(self):
with mock.patch('meld.system.openmm_runner.cmap.np.loadtxt') as mock_loadtxt:
# this is a bit hacky and depends on what order the maps are loaded in
expected_gly = 3.0 * 0. + 7.0 * 1. + np.zeros((24, 24)).flatten()
expected_pro = 3.0 * 2. + 7.0 * 3. + np.zeros((24, 24)).flatten()
expected_ala = 3.0 * 4. + 7.0 * 5. + np.zeros((24, 24)).flatten()
expected_gen = 3.0 * 6. + 7.0 * 7. + np.zeros((24, 24)).flatten()
mock_loadtxt.side_effect = self.maps
adder = CMAPAdder(self.system.top_string, alpha_bias=3.0, beta_bias=7.0)
adder.add_to_openmm(self.mock_openmm_system)
self.assertEqual(self.MockCMAP.call_count, 1)
self.assertEqual(self.mock_cmap.addMap.call_count, 4)
# make sure all of the sizes are correct
add_map_args = self.mock_cmap.addMap.call_args_list
self.assertEqual(add_map_args[0][0][0], 24)
self.assertEqual(add_map_args[1][0][0], 24)
self.assertEqual(add_map_args[2][0][0], 24)
self.assertEqual(add_map_args[3][0][0], 24)
# make sure the maps are correct
np.testing.assert_almost_equal(add_map_args[0][0][1], expected_gly)
np.testing.assert_almost_equal(add_map_args[1][0][1], expected_pro)
np.testing.assert_almost_equal(add_map_args[2][0][1], expected_ala)
np.testing.assert_almost_equal(add_map_args[3][0][1], expected_gen)
def test_correct_map_used_for_ALA(self):
self.make_system('ALA')
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
self.mock_cmap.addTorsion.assert_called_once_with(2, ANY, ANY, ANY, ANY, ANY, ANY, ANY, ANY)
def test_correct_torsions_should_be_added_to_force(self):
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
# map should be #2 for alanine
# all atom indices are zero-based in openmm
self.mock_cmap.addTorsion.assert_called_once_with(
2, 10, 12, 14, 20, 12, 14, 20, 22)
def test_correct_map_used_for_ALA(self):
self.make_system("ALA")
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
self.mock_cmap.addTorsion.assert_called_once_with(
2, ANY, ANY, ANY, ANY, ANY, ANY, ANY, ANY)
def test_correct_torsions_should_be_added_to_force(self):
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
# map should be #2 for alanine
# all atom indices are zero-based in openmm
expected_calls = [
mock.call(2, 10, 12, 14, 20, 12, 14, 20, 22),
mock.call(2, 43, 45, 47, 53, 45, 47, 53, 55),
]
self.mock_cmap.addTorsion.assert_has_calls(expected_calls)
def test_correct_torsions_should_be_added_to_force(self):
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
# map should be #2 for alanine
# all atom indices are zero-based in openmm
expected_calls = [
mock.call(2, 10, 12, 14, 20, 12, 14, 20, 22),
mock.call(2, 43, 45, 47, 53, 45, 47, 53, 55)
]
self.mock_cmap.addTorsion.assert_has_calls(expected_calls)
def test_correct_map_used_for_general_case(self):
res_names = ['CYS', 'CYX', 'ASP', 'ASH', 'GLU', 'GLH', 'PHE', 'HIS', 'HID', 'HIE', 'HIP',
'LYS', 'LYN', 'MET', 'SER', 'TRP', 'TYR', 'ILE', 'ASN', 'GLN', 'THR', 'TRP',
'LEU', 'ARG']
for res in res_names:
self.mock_cmap.reset_mock()
self.make_system(res)
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
self.mock_cmap.addTorsion.assert_called_once_with(3, ANY, ANY, ANY, ANY, ANY, ANY, ANY, ANY)
def test_correct_map_used_for_general_case(self):
res_names = [
'CYS', 'CYX', 'ASP', 'ASH', 'GLU', 'GLH', 'PHE', 'HIS', 'HID',
'HIE', 'HIP', 'LYS', 'LYN', 'MET', 'SER', 'TRP', 'TYR', 'ILE',
'ASN', 'GLN', 'THR', 'TRP', 'LEU', 'ARG'
]
for res in res_names:
self.mock_cmap.reset_mock()
self.make_system(res)
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
self.mock_cmap.addTorsion.assert_called_once_with(
3, ANY, ANY, ANY, ANY, ANY, ANY, ANY, ANY)
def test_correct_map_used_for_general_case(self):
res_names = [
"CYS",
"CYX",
"ASP",
"ASH",
"GLU",
"GLH",
"PHE",
"HIS",
"HID",
"HIE",
"HIP",
"LYS",
"LYN",
"MET",
"SER",
"TRP",
"TYR",
"ILE",
"ASN",
"GLN",
"THR",
"TRP",
"LEU",
"ARG",
]
for res in res_names:
self.mock_cmap.reset_mock()
self.make_system(res)
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
self.mock_cmap.addTorsion.assert_called_once_with(
3, ANY, ANY, ANY, ANY, ANY, ANY, ANY, ANY
)
def test_correct_map_used_for_general_case(self):
res_names = [
"CYS",
"CYX",
"ASP",
"ASH",
"GLU",
"GLH",
"PHE",
"HIS",
"HID",
"HIE",
"HIP",
"LYS",
"LYN",
"MET",
"SER",
"TRP",
"TYR",
"ILE",
"ASN",
"GLN",
"THR",
"TRP",
"LEU",
"ARG",
]
for res in res_names:
self.mock_cmap.reset_mock()
self.make_system(res)
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
self.mock_cmap.addTorsion.assert_called_once_with(
3, ANY, ANY, ANY, ANY, ANY, ANY, ANY, ANY)
def test_force_should_be_added_to_system(self):
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
self.mock_openmm_system.addForce.assert_called_once_with(
self.mock_cmap)
def test_force_should_be_added_to_system(self):
adder = CMAPAdder(self.system.top_string)
adder.add_to_openmm(self.mock_openmm_system)
self.mock_openmm_system.addForce.assert_called_once_with(self.mock_cmap)