def tearDown(self):
sys.argv = self.storeArgv
written_test_files = [
get_relative_path("test_{:s}.pdb".format(shape))
for shape in self.geometries.keys()
]
for file in written_test_files:
if os.path.exists(file):
os.remove(file)
def test_raises_execeptions(self):
flat_reference = Molecules(
get_relative_path("reference_files/test_classes/reference.pdb"))
baseshape = shapes.shape()
with self.assertRaises(NotImplementedError):
baseshape.gen_shape(flat_reference, 0)
with self.assertRaises(NotImplementedError):
baseshape.dimension_requirements()
with self.assertRaises(NotImplementedError):
baseshape.final_dimensions()
def test_shapes(self):
base_args = len(sys.argv)
for shape, geometry in self.geometries.items():
sys.argv.extend([
"-s", shape, "-o",
get_relative_path("test_{:s}.pdb".format(shape)), "-g"
])
sys.argv.extend(geometry)
bumpy.main()
success = PDBComp.compareAtomFields(
get_relative_path("test_{:s}.pdb".format(shape)),
get_relative_path(
"reference_files/test_shapes/test_{:s}.pdb".format(shape)))
if not success:
os.rename("test_{:s}.pdb".format(shape),
"failed_test_{:s}.pdb".format(shape))
self.assertTrue(success, "Failure in shape {:s}".format(shape))
sys.argv = sys.argv[:base_args]
def setUp(self):
self.invalidArgs = emptyArgs()
self.invalidArgs.s = "sphere"
self.invalidArgs.f = get_relative_path(
"reference_files/test_user_interface/reference.pdb")
self.invalidArgs.z = "10"
self.invalidArgs.o = "output.pdb"
self.invalidArgs.p = None
self.invalidArgs.n = None
# redirect stderr for text checking
self.stderr = std_checker()
self.stored_stderr = sys.stderr
sys.stderr = self.stderr
def setUp(self):
class args:
pass
self.validArgs = args()
self.validArgs.s = "sphere"
self.validArgs.f = get_relative_path(
"reference_files/test_user_interface/reference.pdb")
self.validArgs.z = "10"
self.validArgs.g = ["r_sphere:100"]
self.validArgs.o = "argument_check_output.pdb"
self.validArgs.p = None
self.validArgs.n = None
# redirect stderr for text checking
self.stderr = std_checker()
self.stored_stderr = sys.stderr
sys.stderr = self.stderr
def setUp(self):
self.geometries = {
'buckle': ['r_buckle:50', 'l_buckle:60'],
'capped_cylinder': ['r_cylinder:50', 'l_cylinder:60'],
'cylinder': ['r_cylinder:50', 'l_cylinder:60'],
'double_bilayer_cylinder':
['r_cylinder:50', 'l_cylinder:50', 'r_junction:40', 'l_flat:250'],
'flat_bilayer': ['x_dimension:50', 'y_dimension:40'],
'inner_quarter_torus': ['r_torus:75', 'r_tube:50'],
'outer_quarter_torus': ['r_torus:75', 'r_tube:50'],
'semicylinder_plane':
['r_cylinder:50', 'l_cylinder:30', 'r_junction:40', 'l_flat:50'],
'semisphere': ['r_sphere:50'],
'semisphere_plane': ['r_sphere:50', 'r_junction:30', 'l_flat:200'],
'sphere': ['r_sphere:50'],
'torus': ['r_torus:75', 'r_tube:50']
}
self.storeArgv = sys.argv
sys.argv = [
"bumpy.py", "-z", "10", "-f",
get_relative_path("reference_files/input/input_asymm.gro")
]
def test_dummy_topology(self):
sys.argv.extend(["-f", get_relative_path("reference_files/input/input_asymm.gro"),
"-p", "topol_with_dummy.top", "--gen_dummy_particles", "--dummy_grid_thickness", "50"])
bumpy.main()
self.assertTrue(FileComp.filesMatchExactly("topol_with_dummy.top",
get_relative_path("reference_files/test_topology/topol_with_dummy.top")))
def test_complex_topology(self):
sys.argv.extend(["-f", get_relative_path("reference_files/input/input_asymm.gro"),
"-p", "topol_complex.top"])
bumpy.main()
self.assertTrue(FileComp.filesMatchExactly("topol_complex.top",
get_relative_path("reference_files/test_topology/topol_complex.top")))
def setUp(self):
self.flat_reference = Molecules(
get_relative_path("reference_files/test_classes/reference.pdb"))
self.flat_reference.duplicate_laterally(
3, 3) # should be large enough for all shapes