def run_single_file(input_filename,
min_len_nt,
results_foldername,
display_plots=False,
print_to_console=True):
coordinates, edges, faces, edge_length_vec, file_name, \
staple_name, singleXOs = ply_to_input(
input_filename, results_foldername, min_len_nt)
scaf_seq = [] # Using default scaffold sequence
scaf_name = [] # Using default scaffold name
full_file_name = DX_cage_design( # noqa: F841
coordinates,
edges,
faces,
edge_length_vec,
file_name,
staple_name,
singleXOs,
scaf_seq,
scaf_name,
results_foldername,
print_to_console=print_to_console)
if display_plots:
from matplotlib import pyplot as plt
plt.show()
def test_unused_vertex_is_removed(self):
coordinates, edges, faces, edge_length_vec, file_name, staple_name, \
singleXOs = ply_to_input("01_tetrahedron", '', min_len_nt=52)
# Note there are 5 coordinates in the starting file:
assert len(coordinates) == 4
assert len(faces) == 4 # Shouldn't have changed
# Started as coordinates[4]:
assert list(coordinates[3]) == [0.577350, 0.000000, -0.204124]
# Started as [1, 2, 4]
assert faces[3] == [1, 2, 3]
def test_arbitrary_face_is_correct(self):
coordinates, edges, faces, edge_length_vec, file_name, staple_name, \
singleXOs = ply_to_input("01_tetrahedron", '', min_len_nt=52)
assert faces[11] == [3, 9, 4]
def test_arbitrary_coordinate_is_correct(self):
coordinates, edges, faces, edge_length_vec, file_name, staple_name, \
singleXOs = ply_to_input("01_tetrahedron", '', min_len_nt=52)
assert list(coordinates[-5]) == [0.851000, -0.618000, -0.526000]
def test_list_lengths_are_correct(self):
coordinates, edges, faces, edge_length_vec, file_name, staple_name, \
singleXOs = ply_to_input("05_icosahedron", '', min_len_nt=52)
assert len(coordinates) == 12
assert len(faces) == 20
def test_plot_function_is_not_called_if_results_foldername_not_set(
self, plotter_mock):
ply_to_input("01_tetrahedron", results_foldername='i_am_defined')
assert plotter_mock.call_count == 1
def test_single_xos_used_when_min_len_nt_is_long(self):
coordinates, edges, faces, edge_length_vec, file_name, staple_name, \
singleXOs = ply_to_input("01_tetrahedron", '', min_len_nt=43)
assert singleXOs == 1
def test_arbitrary_coordinate_is_correct(self):
coordinates, edges, faces, edge_length_vec, file_name, staple_name, \
singleXOs = ply_to_input("01_tetrahedron", '', min_len_nt=52)
assert list(coordinates[1]) == [-0.288675, -0.500000, -0.204124]