def contact():
base_dir = expanduser("~")
global form
form = Lintools_Input()
if request.method == 'POST':
traj_files = request.form["trajectory_path"].rsplit(",")
global output_name
output_name = request.form["output_name"]
inputs = request.form
global lintools
lintools = Lintools(
inputs["topology_path_hidden"],
[base_dir + x for x in traj_files if traj_files != [u'']], None,
"resid " + str(inputs["ligand_selection"].rsplit(",")[0]) +
" and segid " + inputs["ligand_selection"].rsplit(",")[1],
inputs["residueOffset"],
float(inputs["distance_cutoff"]), [None], [None], [None],
float(inputs["analysis_cutoff"]), "amino", inputs["output_name"],
False)
lintools.save_files()
lintools.data_input_and_res_time_analysis()
lintools.analysis_of_prot_lig_interactions()
lintools.plot_residues()
lintools.draw_figure()
lintools.remove_files()
return redirect(url_for('input'))
elif request.method == 'GET':
return render_template('contact.html', form=form)
class TestBasic2(TestCase):
def setUp(self):
self.test_svg = TEST2
self.output_name = "test2_1"
self.lintools = Lintools(AMI_GRO, [AMI_XTC], None, "resname UNK", 30,
3.5, [1], [None], [None], 0.3, "clock",
self.output_name, False)
self.lintools.save_files()
self.lintools.data_input_and_res_time_analysis()
self.lintools.analysis_of_prot_lig_interactions()
self.lintools.plot_residues()
self.lintools.write_config_file(None)
self.lintools.draw_figure()
def tearDown(self):
self.lintools.remove_files()
del self.lintools
def test_ami_clocks(self):
#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 TestBasic3(TestCase):
def setUp(self):
u = MDAnalysis.Universe(PDB_4XP1)
lig_name = u.select_atoms("resname LDP")
self.test_svg = TEST3
self.output_name = "test3_1"
self.lintools = Lintools(PDB_4XP1, [], LDP_MOL2, lig_name, 0, 3.5, [1],
[None], [None], 0.3, "domains",
self.output_name)
self.lintools.save_files()
self.lintools.data_input_and_res_time_analysis()
self.lintools.analysis_of_prot_lig_interactions(False)
self.lintools.plot_residues()
self.lintools.draw_figure()
def tearDown(self):
self.lintools.remove_files()
del self.lintools
def test_ldp_domains(self):
#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 TestBasic3(TestCase):
def setUp(self):
self.test_svg = TEST3
self.output_name = "test3_1"
self.lintools = Lintools(PDB_4XP1,[],None,"resname LDP",0,3.5,[1],[None],[None],0.3,0,"domains",self.output_name,False)
self.lintools.save_files()
self.lintools.data_input_and_res_time_analysis()
self.lintools.analysis_of_prot_lig_interactions()
self.lintools.plot_residues()
self.lintools.write_config_file(None)
self.lintools.draw_figure()
def tearDown(self):
self.lintools.remove_files()
del self.lintools
def test_ldp_domains(self):
#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