from __future__ import division from mmtbx.ncs import ncs_search import iotbx.ncs import iotbx.pdb import unittest import sys class test_find_ncs_operators(unittest.TestCase): def test_two_chain_master(self): """ Testing one ncs group and master ncs with two chains of different length and chains are not in order """ print sys._getframe().f_code.co_name trans_obj = iotbx.ncs.input(pdb_string=test_pdb1) t = trans_obj.ncs_to_asu_selection self.assertEqual(t.keys(),['chain A or chain B']) self.assertEqual(t.values(),[['chain C or chain D', 'chain E or chain F']]) def test_three_chain_master(self): """ Test case of: Two groups, different number of chain in each group. two chains that are NOT ncs related """ print sys._getframe().f_code.co_name trans_obj = iotbx.ncs.input(pdb_string=test_pdb2) t = trans_obj.ncs_to_asu_selection self.assertEqual(t.keys(),['chain D', 'chain A']) self.assertEqual(t.values(),[['chain E'], ['chain B', 'chain C']]) # self.assertEqual(trans_obj.ncs_group_map[1][0],{'chain A'}) self.assertEqual(trans_obj.ncs_group_map[2][0],{'chain D'}) def test_master_build_from_two_related_chains(self): """ Test that minimal number of chains in master ncs are selected (not the minimal number of transformations) """ print sys._getframe().f_code.co_name trans_obj = iotbx.ncs.input(pdb_string=test_pdb3) t = trans_obj.ncs_to_asu_selection self.assertEqual(t.keys(),['chain A']) self.assertEqual(t.values(), [['chain B', 'chain C', 'chain D', 'chain E', 'chain F', 'chain G', 'chain H', 'chain I']]) def test_largest_common_ncs(self): """ Test that minimal number of transformations in master ncs are selected (not the minimal number of chains) """ print sys._getframe().f_code.co_name trans_obj = iotbx.ncs.input( pdb_string=test_pdb3, use_simple_ncs_from_pdb=False, use_minimal_master_ncs=False) t = trans_obj.ncs_to_asu_selection self.assertEqual(t.keys(),['chain A or chain B or chain C']) self.assertEqual(t.values(), [['chain D or chain E or chain F', 'chain G or chain H or chain I']]) def test_group_chains_by_domains_minimal_master_ncs_grouping(self): """ """ print sys._getframe().f_code.co_name # pdb_inp = iotbx.pdb.input(source_info=None, lines=test_pdb3) ph = pdb_inp.construct_hierarchy() # chain_match_list = ncs_search.search_ncs_relations( ph=ph,min_contig_length=0,min_fraction_domain=0) # make sure that all possible chains compared model = ph.models()[0] chain_ids = list({x.id for x in model.chains()}) chain_ids = sorted(chain_ids) n_chains = len(chain_ids) self.assertEqual(n_chains,9) self.assertEqual(len(chain_match_list),36) # match_dict = ncs_search.clean_chain_matching(chain_match_list,ph) # Test minimal master NCS transform_to_group,match_dict = ncs_search.minimal_master_ncs_grouping( match_dict=match_dict) group_dict = ncs_search.build_group_dict( transform_to_group,match_dict) self.assertEqual(len(group_dict),1) gr_obj = group_dict[('A',)] self.assertEqual(len(gr_obj.transforms),len(gr_obj.copies)) self.assertEqual(len(gr_obj.iselections),len(gr_obj.copies)) expected = [['A'], ['B'], ['C'], ['D'], ['E'], ['F'], ['G'], ['H'], ['I']] self.assertEqual(gr_obj.copies,expected) tr = gr_obj.transforms[0] self.assertTrue(tr.r.is_r3_identity_matrix()) self.assertTrue(tr.t.is_col_zero()) tr = gr_obj.transforms[1] self.assertFalse(tr.r.is_r3_identity_matrix()) self.assertFalse(tr.t.is_col_zero()) def test_group_chains_by_domains_minimal_NCS_operators(self): """ Test minimal NCS operators """ print sys._getframe().f_code.co_name pdb_inp = iotbx.pdb.input(source_info=None, lines=test_pdb3) ph = pdb_inp.construct_hierarchy() # chain_match_list = ncs_search.search_ncs_relations( ph=ph,min_contig_length=0,min_fraction_domain=0) # match_dict = ncs_search.clean_chain_matching(chain_match_list,ph) # transform_to_group,match_dict = ncs_search.minimal_ncs_operators_grouping( match_dict=match_dict) group_dict = ncs_search.build_group_dict( transform_to_group,match_dict) self.assertEqual(len(group_dict),1) gr_obj = group_dict[('A', 'B', 'C')] self.assertEqual(len(gr_obj.transforms),len(gr_obj.copies)) self.assertEqual(len(gr_obj.iselections),len(gr_obj.copies)) expected = [['A', 'B', 'C'], ['D', 'E', 'F'], ['G', 'H', 'I']] self.assertEqual(gr_obj.copies,expected) tr = gr_obj.transforms[0] self.assertTrue(tr.r.is_r3_identity_matrix()) self.assertTrue(tr.t.is_col_zero()) tr = gr_obj.transforms[1] self.assertFalse(tr.r.is_r3_identity_matrix()) self.assertFalse(tr.t.is_col_zero()) test_pdb1 = '''\ CRYST1 577.812 448.715 468.790 90.00 90.00 90.00 P 1 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 TER ATOM 7 CA LYS B 157 11.545 9.413 8.000 1.00 72.27 C ATOM 8 CA LYS B 158 12.277 10.718 8.343 1.00 75.78 C ATOM 9 CA LYS B 159 11.349 11.791 8.809 1.00 75.88 C TER ATOM 7 CA LYS F 157 2.154 3.953 16.298 1.00 72.27 C ATOM 8 CA LYS F 158 2.014 3.732 17.811 1.00 75.78 C ATOM 9 CA LYS F 159 2.558 2.413 18.250 1.00 75.88 C TER ATOM 7 CA LYS D 157 4.334 10.965 12.119 1.00 72.27 C ATOM 8 CA LYS D 158 4.057 11.980 13.238 1.00 75.78 C ATOM 9 CA LYS D 159 3.177 11.427 14.310 1.00 75.88 C TER ATOM 1 CA LYS C 151 6.855 8.667 15.730 1.00 44.22 C ATOM 2 CA LYS C 152 5.891 8.459 14.655 1.00 49.42 C ATOM 3 CA LYS C 153 6.103 7.155 13.858 1.00 46.15 C ATOM 4 CA LYS C 154 5.138 6.438 13.633 1.00 52.97 C ATOM 5 CA LYS C 155 5.801 9.685 13.736 1.00 41.68 C ATOM 6 CA LYS C 156 4.731 9.594 12.667 1.00 55.55 C TER ATOM 1 CA LYS E 151 6.987 4.106 17.432 1.00 44.22 C ATOM 2 CA LYS E 152 6.017 3.539 16.502 1.00 49.42 C ATOM 3 CA LYS E 153 6.497 3.492 15.036 1.00 46.15 C ATOM 4 CA LYS E 154 6.348 2.458 14.400 1.00 52.97 C ATOM 5 CA LYS E 155 4.647 4.221 16.634 1.00 41.68 C ATOM 6 CA LYS E 156 3.552 3.605 15.788 1.00 55.55 C TER ''' test_pdb2 = '''\ CRYST1 577.812 448.715 468.790 90.00 90.00 90.00 P 1 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 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 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 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 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 TER ''' test_pdb3 = '''\ ATOM 1 N THR A 1 13.014 18.419 8.520 1.00 20.00 N ATOM 2 CA THR A 1 12.903 17.061 8.000 1.00 20.00 C ATOM 3 C THR A 1 12.978 16.033 9.124 1.00 20.00 C ATOM 4 O THR A 1 13.793 16.157 10.038 1.00 20.00 O TER ATOM 1 N THR C 1 10.325 8.000 14.368 1.00 20.00 N ATOM 2 CA THR C 1 10.111 8.702 13.108 1.00 20.00 C ATOM 3 C THR C 1 11.313 9.570 12.750 1.00 20.00 C ATOM 4 O THR C 1 11.885 10.241 13.609 1.00 20.00 O TER ATOM 1 N THR D 1 -0.430 15.458 18.495 1.00 20.00 N ATOM 2 CA THR D 1 0.086 15.020 17.204 1.00 20.00 C ATOM 3 C THR D 1 1.440 14.334 17.355 1.00 20.00 C ATOM 4 O THR D 1 2.297 14.791 18.111 1.00 20.00 O TER ATOM 1 N THR E 1 1.895 8.366 19.752 1.00 20.00 N ATOM 2 CA THR E 1 1.682 9.068 18.491 1.00 20.00 C ATOM 3 C THR E 1 2.884 9.935 18.133 1.00 20.00 C ATOM 4 O THR E 1 3.455 10.606 18.993 1.00 20.00 O TER ATOM 1 N THR F 1 8.346 7.308 15.936 1.00 20.00 N ATOM 2 CA THR F 1 7.054 7.796 15.467 1.00 20.00 C ATOM 3 C THR F 1 6.884 9.281 15.767 1.00 20.00 C ATOM 4 O THR F 1 7.237 9.751 16.849 1.00 20.00 O TER ATOM 1 N THR G 1 0.609 -0.560 24.094 1.00 20.00 N ATOM 2 CA THR G 1 0.395 0.142 22.834 1.00 20.00 C ATOM 3 C THR G 1 1.598 1.009 22.476 1.00 20.00 C ATOM 4 O THR G 1 2.169 1.680 23.335 1.00 20.00 O TER ATOM 1 N THR H 1 7.061 -1.617 20.279 1.00 20.00 N ATOM 2 CA THR H 1 5.768 -1.130 19.810 1.00 20.00 C ATOM 3 C THR H 1 5.599 0.356 20.109 1.00 20.00 C ATOM 4 O THR H 1 5.950 0.825 21.191 1.00 20.00 O TER ATOM 1 N THR I 1 8.722 4.822 16.665 1.00 20.00 N ATOM 2 CA THR I 1 7.494 4.036 16.653 1.00 20.00 C ATOM 3 C THR I 1 6.628 4.350 17.868 1.00 20.00 C ATOM 4 O THR I 1 7.130 4.482 18.984 1.00 20.00 O TER ATOM 1 N THR B 1 8.000 15.093 13.112 1.00 20.00 N ATOM 2 CA THR B 1 8.516 14.654 11.820 1.00 20.00 C ATOM 3 C THR B 1 9.870 13.968 11.972 1.00 20.00 C ATOM 4 O THR B 1 10.727 14.426 12.727 1.00 20.00 O TER ''' 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 = ['test_master_build_from_two_related_chains'] suite = unittest.TestSuite(map(test_find_ncs_operators,tests)) return suite if __name__=='__main__': # use for individual tests # unittest.TextTestRunner().run(run_selected_tests()) # Use to run all tests unittest.main()