def setUp(self):
u = MDAnalysis.Universe(FILE2)
lig_name = u.select_atoms("resname UNK")
self.output_name = "test3"
self.test_svg = TEST3_SVG
self.lintools = Lintools(FILE2, [TRAJ_20_FR, TRAJ_50_FR], lig_name, 30,
3.5, 50, "clock", None, False, False, False,
True, None, "test3")
self.lintools.get_info_about_input_and_analyse()
self.lintools.plot_residues()
self.lintools.draw_molecule_and_figure(tests=True)
def setUp(self):
u = MDAnalysis.Universe(FILE1)
lig_name = u.select_atoms("resname LDP")
self.output_name = "test2"
self.test_svg = TEST2_SVG
self.lintools = Lintools(FILE1, None, lig_name, 0, 3.5, 30, "domains",
DOM_FILE_4XP1, False, False, False, True,
None, "test2")
self.lintools.get_info_about_input_and_analyse()
self.lintools.plot_residues()
self.lintools.draw_molecule_and_figure(tests=True)
class TestBasic3(TestCase):
def setUp(self):
u = MDAnalysis.Universe(FILE2)
lig_name = u.select_atoms("resname UNK")
self.output_name = "test3"
self.test_svg = TEST3_SVG
self.lintools = Lintools(FILE2, [TRAJ_20_FR, TRAJ_50_FR], lig_name, 30,
3.5, 50, "clock", None, False, False, False,
True, None, "test3")
self.lintools.get_info_about_input_and_analyse()
self.lintools.plot_residues()
self.lintools.draw_molecule_and_figure(tests=True)
def tearDown(self):
self.lintools.remove_files()
del self.lintools
file_list = ["test3.svg", "test3_config.txt"]
for f in file_list:
if os.path.isfile(f) == True:
os.remove(f)
def test_two_trajectories_clock(self):
# Is the molecule mol2 file produced?
assert_equal(os.path.isfile("LIG_test.mol2"), True)
#Is the final svg file produced?
assert_equal(os.path.isfile(self.output_name + ".svg"), True)
if os.path.isfile(self.output_name + ".svg") == True:
with open(self.test_svg, "r") as test:
testlines = test.readlines()
with open(self.output_name + ".svg", "r") as output:
lines = output.readlines()
i = 0
for line in lines:
assert_equal(testlines[i], lines[i])
i += 1
class TestBasic2(TestCase):
def setUp(self):
u = MDAnalysis.Universe(FILE1)
lig_name = u.select_atoms("resname LDP")
self.output_name = "test2"
self.test_svg = TEST2_SVG
self.lintools = Lintools(FILE1, None, lig_name, 0, 3.5, 30, "domains",
DOM_FILE_4XP1, False, False, False, True,
None, "test2")
self.lintools.get_info_about_input_and_analyse()
self.lintools.plot_residues()
self.lintools.draw_molecule_and_figure(tests=True)
def tearDown(self):
self.lintools.remove_files()
del self.lintools
file_list = ["test2.svg", "test2_config.txt"]
for f in file_list:
if os.path.isfile(f) == True:
os.remove(f)
def test_4xp1_domains(self):
# Is the molecule mol2 file produced?
assert_equal(os.path.isfile("LIG_test.mol2"), True)
#Is the final svg file produced?
assert_equal(os.path.isfile(self.output_name + ".svg"), True)
if os.path.isfile(self.output_name + ".svg") == True:
with open(self.test_svg, "r") as test:
testlines = test.readlines()
with open(self.output_name + ".svg", "r") as output:
lines = output.readlines()
i = 0
for line in lines:
assert_equal(testlines[i], lines[i])
i += 1
class TestBasic4(TestCase):
def setUp(self):
u = MDAnalysis.Universe(FILE2)
lig_name = u.select_atoms("resname UNK")
self.output_name = "test4"
self.test_svg = TEST4_SVG
self.lintools = Lintools(FILE2, [TRAJ_20_FR, TRAJ_50_FR], lig_name, 30,
3.5, 50, "clock", None, False, True, False,
False, None, "test4")
self.lintools.get_info_about_input_and_analyse()
self.lintools.plot_residues()
self.lintools.draw_molecule_and_figure(tests=True)
def tearDown(self):
self.lintools.remove_files()
del self.lintools
file_list = ["test4.svg", "test4_config.txt"]
for f in file_list:
if os.path.isfile(f) == True:
os.remove(f)
def test_two_trajectories_clock2(self):
# Is the molecule mol2 file produced?
assert_equal(os.path.isfile("LIG_test.mol2"), True)
#Is the final svg file produced?
assert_equal(os.path.isfile(self.output_name + ".svg"), True)
if os.path.isfile(self.output_name + ".svg") == True:
with open(self.test_svg, "r") as test:
testlines = test.readlines()
with open(self.output_name + ".svg", "r") as output:
lines = output.readlines()
i = 0
for line in lines:
if i == 1166: # This line contains an url which changes with every itiaration and cannot be tested
continue
else:
assert_equal(testlines[i], lines[i])
i += 1
test.close()
output.close()
#Is the residue info file produced?
self.resinfo_file = RESINFO_ILE340
assert_equal(os.path.isfile("ILE340.svg"), True)
#Compare
with open(self.resinfo_file, "r") as test:
testlines2 = test.readlines()
with open("ILE340.svg", "r") as output:
lines2 = output.readlines()
i = 0
for line in lines:
if i == 1 or i == 6: # This line contains an url which changes with every itiaration and cannot be tested
continue
else:
assert_equal(testlines2[i], lines2[i])
i += 1