def test_distance_alpha_c(self):
"""
test distance_alpha_c method
:return:
"""
centers = compute_geometry.center_mass_unit(False, unit_test_dir)
ris = compute_geometry.distance_alpha_c(centers,
False,
unit_test_dir)
self.assertEqual(ris['unit_27-48.pdb']['CA1'], 8.609722419859281)
def test_handedness(self):
"""
test handedness method
:return:
"""
centers = compute_geometry.center_mass_unit(False, unit_test_dir)
ris = compute_geometry.handedness(centers,
False,
unit_test_dir)
self.assertEquals(ris['unit_27-48.pdb'], 'L')
self.assertEquals(ris['unit_49-72.pdb'], 'L')
def test_curvature(self):
"""
test curvature method
:return:
"""
centers = compute_geometry.center_mass_unit(False, unit_test_dir)
ris = compute_geometry.curvature(centers,
False,
unit_test_dir)
self.assertEquals(ris['unit_27-48.pdb_unit_49-72.pdb'],
18.9001109414561)
def test_pitch(self):
"""
test pitch method
:return:
"""
centers = compute_geometry.center_mass_unit(False, unit_test_dir)
ris = compute_geometry.pitch(centers,
False,
unit_test_dir)
self.assertEquals(ris['unit_27-48.pdb_unit_49-72.pdb'],
11.498455699343008)
def test_twist(self):
"""
test twist method
:return:
"""
centers = compute_geometry.center_mass_unit(False, unit_test_dir)
ris = compute_geometry.twist(centers,
False,
unit_test_dir)
self.assertEquals(ris['unit_27-48.pdb_unit_49-72.pdb'],
0.9309720264364901)
def test_center_of_mass(self):
"""
test center_of_mass method
:return:
"""
ris = compute_geometry.center_mass_unit(False, unit_test_dir)
self.assertEquals(ris['unit_27-48.pdb'], (-54.48145734501918,
30.31792712426065,
15.1713042009396))
self.assertEquals(ris['unit_49-72.pdb'], (-50.468922194033716,
34.10473405182134,
10.878357331957995))
def test_distance_center_of_mass(self):
"""
test distance_center_of_mass method
:return:
"""
centers = compute_geometry.center_mass_unit(False, unit_test_dir)
ris = compute_geometry.distance_center_of_mass(centers,
False,
unit_test_dir)
self.assertEquals(ris['unit_27-48.pdb']['unit_49-72.pdb'],
6.990689369755643)
self.assertEquals(ris['unit_27-48.pdb']['unit_49-72.pdb'],
ris['unit_49-72.pdb']['unit_27-48.pdb'])
'message': 'Display the results with pymol?',
'default': False
},
]
answers = prompt(questions, style=style)
if answers['draw']:
# pymol
pymol.finish_launching()
for unit in os.listdir(unit_dir):
pymol.cmd.load(unit_dir + unit, unit)
centers = compute_geometry.center_mass_unit(answers['draw'], unit_dir)
if answers['center_of_mass']:
if answers['json']:
print(json.dumps(centers, indent=4, sort_keys=True))
else:
for unit in unit_dir_list:
keys = natural_keys(unit)
print("Center of mass of " + unit.split('.')[0] + " is: " +
str(centers[unit]))
if answers['center_of_mass_distance']:
ris = compute_geometry.distance_center_of_mass(centers,
answers['draw'],
unit_dir)
if answers['json']: