Example #1
0
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)
Example #2
0
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
Example #3
0
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
Example #4
0
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