from __future__ import division from iotbx.ncs.ncs_preprocess import selection_string_from_selection from iotbx.ncs.ncs_preprocess import get_clean_selection_string from scitbx.array_family import flex from iotbx import pdb import unittest import sys class TestNcsPreprocessingFunctions(unittest.TestCase): """ Test utility functions in ncs_preprocess.py""" def test_get_clean_selection_string(self): """ Check get_clean_selection_string """ print sys._getframe().f_code.co_name ch_sel = 'chain A' res_selection1 = ['resseq 1:10'] res_id = '27c' s = '(resid ' + res_id + ' and (name ' atom_name = [x for x in [' CA',' N']] atom_str = ' or name '.join(atom_name) s = s + atom_str + ')' res_selection2 = ['resseq 1:10',s] result1 = get_clean_selection_string(ch_sel,[]) result2 = get_clean_selection_string(ch_sel,res_selection1) result3 = get_clean_selection_string(ch_sel,res_selection2) self.assertEqual(result1,'chain A') self.assertEqual(result2,'chain A and resseq 1:10') expt = 'chain A and (resseq 1:10 or (resid 27c and (name CA or name N))' self.assertEqual(result3,expt) def test_selection_string_from_selection(self): """ Test selection_string_from_selection """ print sys._getframe().f_code.co_name pdb_inp = pdb.hierarchy.input(pdb_string=test_pdb_1) isel1 = flex.size_t([12, 13, 14, 15, 16, 17, 18]) isel2 = flex.size_t([12, 13, 14, 16, 17, 18]) isel3 = flex.size_t([12, 13, 14, 15, 16, 17]) sel_str1 = selection_string_from_selection(pdb_inp,isel1) sel_str2 = selection_string_from_selection(pdb_inp,isel2) sel_str3 = selection_string_from_selection(pdb_inp,isel3) self.assertEqual(sel_str1,'chain D') self.assertEqual(sel_str2,'(chain D and (resseq 1:3 or resseq 5:7))') self.assertEqual(sel_str3,'(chain D and resseq 1:6)') # atom_cache = pdb_inp.hierarchy.atom_selection_cache().selection sel1 = list(atom_cache(sel_str1).iselection()) sel2 = list(atom_cache(sel_str2).iselection()) sel3 = list(atom_cache(sel_str3).iselection()) # self.assertEqual(sel1,list(isel1)) self.assertEqual(sel2,list(isel2)) self.assertEqual(sel3,list(isel3)) def test_selection_string_from_selection(self): """ Test selection_string_from_selection """ print sys._getframe().f_code.co_name pdb_inp = pdb.hierarchy.input(pdb_string=test_pdb_2) l1 = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25, 26,27,28,29,30,31] l2 = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17 ,20,21,22,23,24,25, 26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42] isel1 = flex.size_t(l1) isel2 = flex.size_t(l2) sel_str1 = selection_string_from_selection(pdb_inp,isel1) sel_str2 = selection_string_from_selection(pdb_inp,isel2) self.assertEqual(sel_str1,'chain A or (chain B and resseq 153:154)') s = '(chain A and (resseq 151 or (resid 152 and (name N or name CA or ' s += 'name C or name O or name CB or name CG or name CD or name NE or ' s += 'name CZ )))) or chain B' self.assertEqual(sel_str2,s) # atom_cache = pdb_inp.hierarchy.atom_selection_cache().selection sel1 = list(atom_cache(sel_str1).iselection()) sel2 = list(atom_cache(sel_str2).iselection()) # self.assertEqual(sel1,list(isel1)) self.assertEqual(sel2,list(isel2)) test_pdb_1 = '''\ 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 END ''' test_pdb_2 = '''\ CRYST1 41.870 78.240 85.900 90.00 90.00 90.00 P 2 21 21 8 SCALE1 0.023883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011641 0.00000 ATOM 1 N LYS A 151 16.915 16.113 -32.818 1.00 44.22 N ATOM 2 CA LYS A 151 16.266 15.939 -34.113 1.00 49.42 C ATOM 3 C LYS A 151 15.248 14.780 -34.161 1.00 46.15 C ATOM 4 O LYS A 151 14.149 14.982 -34.658 1.00 52.97 O ATOM 5 CB LYS A 151 17.295 15.845 -35.249 1.00 41.68 C ATOM 6 CG LYS A 151 16.696 15.787 -36.639 1.00 55.55 C ATOM 7 CD LYS A 151 17.694 16.193 -37.723 1.00 72.27 C ATOM 8 CE LYS A 151 18.426 17.498 -37.380 1.00 75.78 C ATOM 9 NZ LYS A 151 17.498 18.571 -36.914 1.00 75.88 N ATOM 10 N ARG A 152 15.575 13.584 -33.658 1.00 41.11 N ATOM 11 CA ARG A 152 14.545 12.524 -33.623 1.00 39.90 C ATOM 12 C ARG A 152 14.775 11.251 -32.810 1.00 33.61 C ATOM 13 O ARG A 152 15.911 10.847 -32.533 1.00 34.25 O ATOM 14 CB ARG A 152 14.096 12.135 -35.040 1.00 41.02 C ATOM 15 CG ARG A 152 15.094 11.299 -35.813 1.00 45.33 C ATOM 16 CD ARG A 152 14.593 11.085 -37.231 1.00 44.56 C ATOM 17 NE ARG A 152 13.434 10.190 -37.278 1.00 44.10 N ATOM 18 CZ ARG A 152 12.734 9.937 -38.378 1.00 49.14 C ATOM 19 NH1 ARG A 152 13.064 10.532 -39.521 1.00 44.79 N ATOM 20 NH2 ARG A 152 11.700 9.097 -38.335 1.00 45.30 N ATOM 21 N ALA B 153 13.656 10.621 -32.456 1.00 30.81 N ATOM 22 CA ALA B 153 13.619 9.397 -31.651 1.00 29.91 C ATOM 23 C ALA B 153 14.208 8.219 -32.409 1.00 31.80 C ATOM 24 O ALA B 153 14.248 8.241 -33.644 1.00 31.66 O ATOM 25 CB ALA B 153 12.176 9.082 -31.250 1.00 29.44 C ATOM 26 N PRO B 154 14.636 7.168 -31.680 1.00 30.22 N ATOM 27 CA PRO B 154 15.163 5.989 -32.375 1.00 28.83 C ATOM 28 C PRO B 154 14.085 5.348 -33.254 1.00 33.21 C ATOM 29 O PRO B 154 12.885 5.472 -32.970 1.00 26.91 O ATOM 30 CB PRO B 154 15.534 5.028 -31.234 1.00 27.52 C ATOM 31 CG PRO B 154 15.512 5.870 -29.971 1.00 30.59 C ATOM 32 CD PRO B 154 14.507 6.943 -30.231 1.00 27.77 C ATOM 33 N TYR B 155 14.519 4.680 -34.318 1.00 28.01 N ATOM 34 CA TYR B 155 13.603 3.970 -35.194 1.00 26.28 C ATOM 35 C TYR B 155 14.387 2.846 -35.845 1.00 32.08 C ATOM 36 O TYR B 155 15.623 2.936 -35.993 1.00 29.48 O ATOM 37 CB TYR B 155 13.028 4.912 -36.264 1.00 29.02 C ATOM 38 CG TYR B 155 14.088 5.528 -37.164 1.00 36.38 C ATOM 39 CD1 TYR B 155 14.789 6.670 -36.769 1.00 29.69 C ATOM 40 CD2 TYR B 155 14.403 4.957 -38.401 1.00 38.19 C ATOM 41 CE1 TYR B 155 15.760 7.237 -37.584 1.00 37.04 C ATOM 42 CE2 TYR B 155 15.376 5.518 -39.226 1.00 43.21 C ATOM 43 CZ TYR B 155 16.051 6.654 -38.804 1.00 41.97 C END ''' 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_processing_of_asu_2'] suite = unittest.TestSuite(map(TestNcsPreprocessingFunctions,tests)) return suite if __name__=='__main__': # use for individual tests # unittest.TextTestRunner().run(run_selected_tests()) # Use to run all tests unittest.main()