from __future__ import absolute_import, division, print_function import mmtbx.monomer_library.pdb_interpretation as pdb_interpretation from libtbx.utils import null_out from datetime import datetime import iotbx.phil import unittest import shutil import os from six.moves import map __author__ = 'Youval Dar' # control if temp folder will be deleted after test DEBUG_MODE = False test_pdb_str = '''\ CRYST1 577.812 448.715 468.790 90.00 90.00 90.00 P 1 SCALE1 0.001731 0.000000 0.000000 0.00000 SCALE2 0.000000 0.002229 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002133 0.00000 ATOM 1 CA LYS A 151 10.766 9.333 12.905 1.00 44.22 C ATOM 2 CA LYS A 152 10.117 9.159 11.610 1.00 49.42 C ATOM 3 CA LYS A 153 9.099 8.000 11.562 1.00 46.15 C ATOM 4 CA LYS A 154 8.000 8.202 11.065 1.00 52.97 C ATOM 5 CA LYS A 155 11.146 9.065 10.474 1.00 41.68 C ATOM 6 CA LYS A 156 10.547 9.007 9.084 1.00 55.55 C ATOM 7 CA LYS A 157 11.545 9.413 8.000 1.00 72.27 C ATOM 8 CA LYS A 158 12.277 10.718 8.343 1.00 75.78 C ATOM 9 CA LYS A 159 11.349 11.791 8.809 1.00 75.88 C TER ATOM 222 CA LEU X 40 94.618 -5.253 91.582 1.00 87.10 C ATOM 223 CA ARG X 41 62.395 51.344 80.786 1.00107.25 C ATOM 224 CA ARG X 42 62.395 41.344 80.786 1.00107.25 C TER ATOM 1 CA THR D 1 8.111 11.080 10.645 1.00 20.00 C ATOM 2 CA THR D 2 8.000 9.722 10.125 1.00 20.00 C ATOM 3 CA THR D 3 8.075 8.694 11.249 1.00 20.00 C ATOM 4 CA THR D 4 8.890 8.818 12.163 1.00 20.00 C ATOM 5 CA THR D 5 9.101 9.421 9.092 1.00 20.00 C ATOM 6 CA THR D 6 9.001 10.343 8.000 1.00 20.00 C ATOM 7 CA THR D 7 8.964 8.000 8.565 1.00 20.00 C TER ATOM 1 CA LYS B 151 6.855 8.667 15.730 1.00 44.22 C ATOM 2 CA LYS B 152 5.891 8.459 14.655 1.00 49.42 C ATOM 3 CA LYS B 153 6.103 7.155 13.858 1.00 46.15 C ATOM 4 CA LYS B 154 5.138 6.438 13.633 1.00 52.97 C ATOM 5 CA LYS B 155 5.801 9.685 13.736 1.00 41.68 C ATOM 6 CA LYS B 156 4.731 9.594 12.667 1.00 55.55 C ATOM 7 CA LYS B 157 4.334 10.965 12.119 1.00 72.27 C ATOM 8 CA LYS B 158 4.057 11.980 13.238 1.00 75.78 C ATOM 9 CA LYS B 159 3.177 11.427 14.310 1.00 75.88 C TER ATOM 1 CA LYS C 151 6.987 4.106 17.432 1.00 44.22 C ATOM 2 CA LYS C 152 6.017 3.539 16.502 1.00 49.42 C ATOM 3 CA LYS C 153 6.497 3.492 15.036 1.00 46.15 C ATOM 4 CA LYS C 154 6.348 2.458 14.400 1.00 52.97 C ATOM 5 CA LYS C 155 4.647 4.221 16.634 1.00 41.68 C ATOM 6 CA LYS C 156 3.552 3.605 15.788 1.00 55.55 C ATOM 7 CA LYS C 157 2.154 3.953 16.298 1.00 72.27 C ATOM 8 CA LYS C 158 2.014 3.732 17.811 1.00 75.78 C ATOM 9 CA LYS C 159 2.558 2.413 18.250 1.00 75.88 C TER ATOM 222 CA LEU Y 40 194.618 5.253 81.582 1.00 87.10 C ATOM 223 CA ARG Y 41 162.395 41.344 70.786 1.00107.25 C ATOM 224 CA ARG Y 42 162.395 31.344 70.786 1.00107.25 C TER ATOM 1 CA THR E 1 8.111 -10.645 11.080 1.00 20.00 C ATOM 2 CA THR E 2 8.000 -10.125 9.722 1.00 20.00 C ATOM 3 CA THR E 3 8.075 -11.249 8.694 1.00 20.00 C ATOM 4 CA THR E 4 8.890 -12.163 8.818 1.00 20.00 C ATOM 5 CA THR E 5 9.101 -9.092 9.421 1.00 20.00 C ATOM 6 CA THR E 6 9.001 -8.000 10.343 1.00 20.00 C ATOM 7 CA THR E 7 8.964 -8.565 8.000 1.00 20.00 C TER ''' master_params = '''\ include scope mmtbx.monomer_library.pdb_interpretation.master_params_str ''' class TestPDBinterpretationNCSSearch(unittest.TestCase): def setUp(self): """ Create temporary folder for temp files produced during test """ self.current_dir = os.getcwd() now = datetime.now().strftime("%I%p_%m_%d_%Y") test_name = self.__class__.__name__ self.tempdir = '{}_{}'.format(test_name, now) if not os.path.isdir(self.tempdir): os.mkdir(self.tempdir) os.chdir(self.tempdir) # open('test.pdb','w').write(test_pdb_str) def test_calling_pdb_interpretation(self): """ Make sure can create NCS object and change search parameters """ params_phil = iotbx.phil.parse( input_string=master_params, process_includes=True) params = params_phil.extract() # Turn on NCS search and adjust one of the parameters params.ncs_search.enabled = True pdb_processed_file = pdb_interpretation.run( args=['test.pdb'], params=params, log=null_out()) ncs_obj = pdb_processed_file.ncs_obj self.assertEqual(ncs_obj.number_of_ncs_groups,2) def tearDown(self): """ remove temp files and folder When DEBUG_MODE = True, the temporary folder will not be deleted """ os.chdir(self.current_dir) if not DEBUG_MODE: try: shutil.rmtree(self.tempdir) except Exception: pass def run_selected_tests(): """ Run selected tests 1) List in "tests" the names of the particular test you want to run 2) Comment out unittest.main() 3) Un-comment unittest.TextTestRunner().run(run_selected_tests()) """ tests = ['some_test_name'] suite = unittest.TestSuite(list(map(TestPDBinterpretationNCSSearch, tests))) return suite if __name__ == '__main__': # use for individual tests # DEBUG_MODE = True # unittest.TextTestRunner().run(run_selected_tests()) # Use to run all tests unittest.main(verbosity=0)