def test_select_one_atom(self):
traj_handler = TrajectoryHandlerStub([("one atom",[[[1,2,3]]]),
("another atom", [[[4,5,6]]]),
("two atoms", [[[4,5,6],[7,8,9]]]),
("no atoms", [[]])])
self.assertItemsEqual([1,2,3], RMSDMatrixBuilder.select_one_atom(traj_handler, "one atom"))
with self.assertRaises(SystemExit):
RMSDMatrixBuilder.select_one_atom(traj_handler, "two atoms")
with self.assertRaises(SystemExit):
RMSDMatrixBuilder.select_one_atom(traj_handler, "no atoms")
def test_select_one_atom(self):
traj_handler = TrajectoryHandlerStub([("one atom", [[[1, 2, 3]]]),
("another atom", [[[4, 5, 6]]]),
("two atoms", [[[4, 5, 6],
[7, 8, 9]]]),
("no atoms", [[]])])
self.assertItemsEqual([1, 2, 3],
RMSDMatrixBuilder.select_one_atom(
traj_handler, "one atom"))
with self.assertRaises(SystemExit):
RMSDMatrixBuilder.select_one_atom(traj_handler, "two atoms")
with self.assertRaises(SystemExit):
RMSDMatrixBuilder.select_one_atom(traj_handler, "no atoms")
def test_process_group(self):
matrix_parameters = {
"symmetries": {
"first_equivalence": {
"common": "my common text",
"equivalences": [["one atom", "another atom"], ["yet another atom", "final atom"]],
},
"second_equivalence": {"common": "my common text", "equivalences": [["one atom", "yet another atom"]]},
}
}
traj_handler = TrajectoryHandlerStub(
[
("my common text and one atom", numpy.array([[[1, 2, 3]]])),
("my common text and another atom", numpy.array([[[4, 5, 6]]])),
("my common text and yet another atom", numpy.array([[[7, 8, 9]]])),
("my common text and final atom", numpy.array([[[10, 11, 12]]])),
]
)
calc_selection_coordsets = numpy.array(
[
[
[0, 0, 0],
[1, 2, 3],
[-1, -2, -3],
[4, 5, 6],
[-4, -5, -6],
[7, 8, 9],
[-7, -8, -9],
[10, 11, 12],
[-10, -11, -12],
]
]
)
self.assertItemsEqual(
[(1, 3), (5, 7)],
RMSDMatrixBuilder.process_group(
"first_equivalence", matrix_parameters, traj_handler, calc_selection_coordsets
),
)
self.assertItemsEqual(
[[(1, 3), (5, 7)], [(1, 5)]],
RMSDMatrixBuilder.process_symm_groups(matrix_parameters, traj_handler, calc_selection_coordsets),
)
def test_process_group(self):
matrix_parameters = {
"symmetries": {
"first_equivalence": {
"common":
"my common text",
"equivalences": [["one atom", "another atom"],
["yet another atom", "final atom"]]
},
"second_equivalence": {
"common": "my common text",
"equivalences": [["one atom", "yet another atom"]]
}
}
}
traj_handler = TrajectoryHandlerStub([
("my common text and one atom", numpy.array([[[1, 2, 3]]])),
("my common text and another atom", numpy.array([[[4, 5, 6]]])),
("my common text and yet another atom", numpy.array([[[7, 8,
9]]])),
("my common text and final atom", numpy.array([[[10, 11, 12]]]))
])
calc_selection_coordsets = numpy.array([[[0, 0, 0], [1, 2, 3],
[-1, -2, -3], [4, 5, 6],
[-4, -5, -6], [7, 8, 9],
[-7, -8, -9], [10, 11, 12],
[-10, -11, -12]]])
self.assertItemsEqual([(1, 3), (5, 7)],
RMSDMatrixBuilder.process_group(
"first_equivalence", matrix_parameters,
traj_handler, calc_selection_coordsets))
self.assertItemsEqual([[(1, 3), (5, 7)], [(1, 5)]],
RMSDMatrixBuilder.process_symm_groups(
matrix_parameters, traj_handler,
calc_selection_coordsets))