import tempfile
from pygromos.files import coord as cnf
from pygromos.tests.test_files.general_file_functions import general_file_tests
from pygromos.tests.in_testfiles import in_test_file_path
from pygromos.tests.test_files import out_test_root_dir
in_file_path = in_test_file_path + "/cnf/in_cnf1.cnf"
in_file_renum_path = in_test_file_path + "/cnf/in_renumber_ligs.cnf"
root_out = tempfile.mkdtemp(dir=out_test_root_dir, prefix="cnf_")
out_path = root_out + "/out_cnf1.cnf"
out_red_path = root_out + "/out_cnf1_reduced.cnf"
[docs]class test_cnf(general_file_tests):
__test__ = True
in_file_path = in_test_file_path + "/cnf/in_cnf1.cnf"
root_out = root_out
class_type = cnf.Cnf
[docs] def test_parse(self):
cnf_file = self.class_type(self.in_file_path)
self.assertEqual(type(cnf_file), cnf.Cnf)
[docs] def test_delete_res(self):
cnf_file = cnf.Cnf(in_file_path)
cnf_file.delete_residue(resID=4, resName="4E96")
cnf_file.write(out_red_path)
[docs] def test_clean_posiResNumsByName(self):
cnf_file = cnf.Cnf(in_file_renum_path, clean_resiNumbers_by_Name=True)
cnf_file.clean_posiResNums()
residues = cnf_file.get_residues()
# print(residues)
self.assertEqual(2, len(residues), "Found more/less than two residues!")
self.assertEqual(2, list(residues["3U5L"].keys())[0], "Could not recognzize expected resNum for 3U5l = 2")
self.assertEqual(1, list(residues["3MXF"].keys())[0], "Could not recognzize expected resNum for 3MXF = 1")
self.assertEqual(31, residues["3U5L"][2], "Could not recognzize expected atom ammount for 3U5l = 2")
self.assertEqual(35, residues["3MXF"][1], "Could not recognzize expected atom ammount for 3MXF = 1")
[docs] def test_write_out(self):
cnf_file = cnf.Cnf(in_file_path)
cnf_file.write(out_path)
[docs] def test_visualize(self):
cnf_file = cnf.Cnf(in_file_path)
view = cnf_file.view
assert view is not None