def test_adds_maps_to_force(self):
with mock.patch("meld.runner.transform.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 * 0.0 + 7.0 * 1.0 + np.zeros((24, 24)).flatten()
expected_pro = 3.0 * 2.0 + 7.0 * 3.0 + np.zeros((24, 24)).flatten()
expected_ala = 3.0 * 4.0 + 7.0 * 5.0 + np.zeros((24, 24)).flatten()
expected_gen = 3.0 * 6.0 + 7.0 * 7.0 + np.zeros((24, 24)).flatten()
mock_loadtxt.side_effect = self.maps
opt = options.RunOptions()
opt.use_amap = True
opt.amap_alpha_bias = 3.0
opt.amap_beta_bias = 7.0
adder = cmap.CMAPTransformer(opt, self.system.top_string)
adder.add_interactions(mock.Mock(), self.mock_openmm_system, mock.Mock())
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_force_should_be_added_to_system(self):
opt = options.RunOptions()
opt.use_amap = True
adder = cmap.CMAPTransformer(opt, self.system.top_string)
adder.add_interactions(mock.Mock(), self.mock_openmm_system, mock.Mock())
self.mock_openmm_system.addForce.assert_called_once_with(self.mock_cmap)
def test_correct_torsions_should_be_added_to_force(self):
opt = options.RunOptions()
opt.use_amap = True
adder = cmap.CMAPTransformer(opt, self.system.top_string)
adder.add_interactions(mock.Mock(), self.mock_openmm_system, mock.Mock())
# 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")
opt = options.RunOptions()
opt.use_amap = True
adder = cmap.CMAPTransformer(opt, self.system.top_string)
adder.add_interactions(mock.Mock(), self.mock_openmm_system, mock.Mock)
self.mock_cmap.addTorsion.assert_called_once_with(
2, 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)
opt = options.RunOptions()
opt.use_amap = True
adder = cmap.CMAPTransformer(opt, self.system.top_string)
adder.add_interactions(mock.Mock(), self.mock_openmm_system, mock.Mock())
self.mock_cmap.addTorsion.assert_called_once_with(
3, ANY, ANY, ANY, ANY, ANY, ANY, ANY, ANY
)