from __future__ import absolute_import, division, print_function from iotbx.ncs import format_80 from libtbx.utils import null_out from datetime import datetime from scitbx import matrix import iotbx.ncs as ncs from iotbx import pdb import iotbx.phil import unittest import shutil import os from iotbx.ncs import ncs_group_master_phil import mmtbx.ncs.ncs import mmtbx.model from libtbx.test_utils import approx_equal from six.moves import range from six.moves import map __author__ = 'Youval' import libtbx.load_env have_phenix = False if libtbx.env.has_module(name="phenix"): from phenix.command_line import simple_ncs_from_pdb have_phenix = True class TestNcsGroupPreprocessing(unittest.TestCase): """ Test spec and phil, NCS and ASU information processing""" def setUp(self): """ Create temporary folder for temp files produced during test """ self.currnet_dir = os.getcwd() now = datetime.now().strftime("%I%p_%m_%d_%Y") self.tempdir = 'TestNcsGroupPreprocessing_{}'.format(now) if not os.path.isdir(self.tempdir): os.mkdir(self.tempdir) os.chdir(self.tempdir) self.pdb_inp = pdb.input(source_info=None, lines=test_pdb_ncs_spec) self.ph = self.pdb_inp.construct_hierarchy() self.pdb_inp = pdb.input(source_info=None, lines=test_pdb_ncs_spec) def test_phil_processing(self): """ Verify that phil parameters are properly processed need to supply exclude_selection=None because model consist only from UNK residues. """ # print sys._getframe().f_code.co_name # read file and create pdb object pdb_inp = pdb.input(source_info=None, lines=pdb_test_data2) phil_groups = ncs_group_master_phil.fetch( iotbx.phil.parse(pdb_test_data2_phil)).extract() p = iotbx.ncs.input.get_default_params() p.ncs_search.exclude_selection=None p.ncs_search.minimum_number_of_atoms_in_copy=0 trans_obj = iotbx.ncs.input( ncs_phil_groups=phil_groups.ncs_group, hierarchy=pdb_inp.construct_hierarchy(), params=p.ncs_search) nrgl = trans_obj.get_ncs_restraints_group_list() # nrgl._show() sels = nrgl.get_array_of_str_selections() assert sels == [["chain 'A'", "chain 'D'", "chain 'G'"], ["chain 'B' or chain 'C'", "chain 'E' or chain 'F'", "chain 'H' or chain 'I'"]] def test_superpos_pdb(self): """ verify creation of transformations using superpose_pdb need to supply exclude_selection=None because model consist only from UNK residues. """ # print sys._getframe().f_code.co_name # read file and create pdb object pdb_inp = pdb.input(source_info=None, lines=pdb_test_data1) phil_groups = ncs_group_master_phil.fetch( iotbx.phil.parse(pdb_test_data1_phil)).extract() p = iotbx.ncs.input.get_default_params() p.ncs_search.exclude_selection=None p.ncs_search.minimum_number_of_atoms_in_copy=0 trans_obj = ncs.input( ncs_phil_groups=phil_groups.ncs_group, hierarchy=pdb_inp.construct_hierarchy(), params=p.ncs_search) nrgl = trans_obj.get_ncs_restraints_group_list() # nrgl._show() sels = nrgl.get_array_of_str_selections() assert sels == [["chain 'A'", "chain 'C'", "chain 'E'"], ["chain 'B'", "chain 'D'", "chain 'F'"]] self.assertTrue(approx_equal(nrgl[0].copies[0].r, matrix.sqr( [0.309017,-0.809017,0.5,0.809017,0.5,0.309017,-0.5,0.309017,0.809017]), eps=0.01)) def test_spec_reading(self): """ verify creating and processing spec This is ncs.ncs - specific functionality """ if have_phenix: xrs = self.pdb_inp.xray_structure_simple() xrs_unit_cell = xrs.orthorhombic_unit_cell_around_centered_scatterers( buffer_size=8) self.ph.adopt_xray_structure(xrs_unit_cell) of = open("test_ncs_spec.pdb", "w") print(self.ph.as_pdb_string(crystal_symmetry=xrs.crystal_symmetry()), file=of) of.close() # create a spec file ncs_from_pdb=simple_ncs_from_pdb.run( args=["pdb_in=test_ncs_spec.pdb", "write_spec_files=True"], log=null_out()) else: print("phenix not available, skipping test_spec_reading()") pass def test_processing_of_asu_2(self): """ processing complete ASU If MTRIX records are present, they are ignored This maybe ncs.ncs - specific functionality, not clear yet. """ # print sys._getframe().f_code.co_name # reading and processing the spec file trans_obj = ncs.input(hierarchy = self.pdb_inp.construct_hierarchy()) nrgl = trans_obj.get_ncs_restraints_group_list() # nrgl._show() sels = nrgl.get_array_of_str_selections() assert sels == [["chain 'A'", "chain 'B'", "chain 'C'"], ["chain 'D'", "chain 'E'"]] def test_print_ncs_phil_param(self): """ Verify correct printout of NCS phil parameters. need to supply exclude_selection=None because model consist only from UNK residues. """ # print sys._getframe().f_code.co_name pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_test_data2) phil_groups = ncs_group_master_phil.fetch( iotbx.phil.parse(pdb_test_data2_phil)).extract() p = iotbx.ncs.input.get_default_params() p.ncs_search.exclude_selection=None p.ncs_search.minimum_number_of_atoms_in_copy=0 trans_obj = ncs.input( ncs_phil_groups=phil_groups.ncs_group, hierarchy=pdb_inp.construct_hierarchy(), params = p.ncs_search) result = trans_obj.print_ncs_phil_param(write=False) # print "="*50 # print "resutl" # print result # print "="*50 test = (pdb_test_data2_phil == result) test = test or (pdb_test_data2_phil_reverse == result) self.assertTrue(test) # def test_finding_partial_ncs(self): # print sys._getframe().f_code.co_name params = ncs.input.get_default_params() params.ncs_search.chain_similarity_threshold = 0.2 ncs_inp = ncs.input( hierarchy=iotbx.pdb.input(source_info=None, lines=pdb_str).construct_hierarchy(), params = params.ncs_search) nrgl = ncs_inp.get_ncs_restraints_group_list() # nrgl._show() sels = nrgl.get_array_of_str_selections() print(sels) assert sels == [[ "(chain 'A' and (name N or name CA or name C or name O ))", "chain 'B'", "(chain 'C' and (name N or name CA or name C or name O ))"]] def test_format_string_longer_than_80(self): """ Check that strings longer that 80 characters are split correctly """ # print sys._getframe().f_code.co_name s = [str (x) for x in range(50)] s = ''.join(s) result = format_80(s) expected = '0123456789101112131415161718192021222324252627282930313233' \ '3435363738394041424344 \\ \n4546474849' self.assertEqual(result,expected) def tearDown(self): """ remove temp files and folder """ os.chdir(self.currnet_dir) shutil.rmtree(self.tempdir) pdb_str = """\ CRYST1 26.628 30.419 28.493 90.00 90.00 90.00 P 1 ATOM 1 N THR A 1 15.886 19.796 13.070 1.00 10.00 N ATOM 2 CA THR A 1 15.489 18.833 12.050 1.00 10.00 C ATOM 3 C THR A 1 15.086 17.502 12.676 1.00 10.00 C ATOM 4 O THR A 1 15.739 17.017 13.600 1.00 10.00 O ATOM 5 CB THR A 1 16.619 18.590 11.033 1.00 10.00 C ATOM 6 OG1 THR A 1 16.963 19.824 10.392 1.00 10.00 O ATOM 7 CG2 THR A 1 16.182 17.583 9.980 1.00 10.00 C TER 8 THR A 1 ATOM 1 N THR B 1 10.028 17.193 16.617 1.00 10.00 N ATOM 2 CA THR B 1 11.046 16.727 15.681 1.00 10.00 C ATOM 3 C THR B 1 12.336 16.360 16.407 1.00 10.00 C ATOM 4 O THR B 1 12.772 17.068 17.313 1.00 10.00 O remark ATOM 5 CB THR B 1 11.356 17.789 14.609 1.00 10.00 C remark ATOM 6 OG1 THR B 1 10.163 18.098 13.879 1.00 10.00 O remark ATOM 7 CG2 THR B 1 12.418 17.281 13.646 1.00 10.00 C TER 16 THR B 1 ATOM 1 N THR C 1 12.121 9.329 18.086 1.00 10.00 N ATOM 2 CA THR C 1 12.245 10.284 16.991 1.00 10.00 C ATOM 3 C THR C 1 13.707 10.622 16.718 1.00 10.00 C ATOM 4 O THR C 1 14.493 10.814 17.645 1.00 10.00 O ATOM 5 CB THR C 1 11.474 11.584 17.284 1.00 10.00 C ATOM 6 OG1 THR C 1 10.087 11.287 17.482 1.00 10.00 O ATOM 7 CG2 THR C 1 11.619 12.563 16.129 1.00 10.00 C TER 24 THR C 1 END """ pdb_test_data1="""\ ATOM 749 O UNK A 90 28.392 67.262 97.682 1.00 0.00 O ATOM 750 N UNK A 91 30.420 66.924 98.358 1.00 0.00 N TER ATOM 1495 N UNK B 67 33.124 2.704 114.920 1.00 0.00 N TER ATOM 749 O UNK C 90 3.199 86.786 85.616 1.00 0.00 O ATOM 750 N UNK C 91 4.437 88.467 85.044 1.00 0.00 N TER ATOM 1495 N UNK D 67 65.508 63.662 77.246 1.00 0.00 N TER ATOM 749 O UNK E 90 -26.415 72.437 94.483 1.00 0.00 O ATOM 750 N UNK E 91 -27.678 74.103 93.921 1.00 0.00 N TER ATOM 1495 N UNK F 67 7.362 108.699 49.412 1.00 0.00 N TER """ pdb_str2="""\ CRYST1 106.820 62.340 114.190 90.00 90.00 90.00 P 21 21 21 16 SCALE1 0.009361 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008757 0.00000 ATOM 1 N GLU A 1 63.453 38.635 25.703 1.00134.43 N ATOM 2 CA GLU A 1 64.202 37.516 26.347 1.00134.43 C ATOM 3 C GLU A 1 64.256 36.311 25.412 1.00134.43 C ATOM 4 O GLU A 1 65.333 35.940 24.953 1.00134.43 O ATOM 5 CB GLU A 1 63.542 37.121 27.675 1.00207.79 C ATOM 6 CG GLU A 1 64.339 36.145 28.538 1.00207.79 C ATOM 7 CD GLU A 1 63.462 35.340 29.490 1.00207.79 C ATOM 8 OE1 GLU A 1 62.232 35.542 29.493 1.00207.79 O ATOM 9 OE2 GLU A 1 63.997 34.492 30.232 1.00207.79 O END """ pdb_test_data1_phil = '''\ ncs_group { reference = 'chain A' selection = 'chain C' selection = 'chain E' } ncs_group { reference = 'chain B' selection = 'chain D' selection = 'chain F' } ''' pdb_test_data2="""\ ATOM 749 O UNK A 90 28.392 67.262 97.682 1.00 0.00 O ATOM 750 N UNK B 91 30.420 66.924 98.358 1.00 0.00 N ATOM 750 N UNK X 93 38.420 76.924 58.358 1.00 0.00 N ATOM 1495 N UNK C 67 33.124 2.704 114.920 1.00 0.00 N TER ATOM 749 O UNK D 90 3.199 86.786 85.616 1.00 0.00 O ATOM 750 N UNK E 91 4.437 88.467 85.044 1.00 0.00 N ATOM 1495 N UNK F 67 65.508 63.662 77.246 1.00 0.00 N TER ATOM 749 O UNK G 90 -26.415 72.437 94.483 1.00 0.00 O ATOM 750 N UNK H 91 -27.678 74.103 93.921 1.00 0.00 N ATOM 1495 N UNK I 67 7.362 108.699 49.412 1.00 0.00 N TER """ pdb_test_data2_phil = '''\ ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' or chain 'C' selection = chain 'E' or chain 'F' selection = chain 'H' or chain 'I' } ''' pdb_test_data2_phil_reverse = '''\ ncs_group { reference = chain 'B' or chain 'C' selection = chain 'E' or chain 'F' selection = chain 'H' or chain 'I' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ''' test_phil_3 = '''\ ncs_group { reference = chain D and (resseq 1:7) selection = chain E and (resseq 1:7) } ncs_group { reference = chain A and (resseq 151:159) selection = chain B and (resseq 151:159) selection = chain C and (resseq 151:159) } ''' user_phil3 = '''\ ncs_group { reference = 'chain A' selection = 'chain B' selection = 'chain C' } ncs_group { reference = 'chain B' selection = 'chain D' } ''' user_phil4 = '''\ ncs_group { reference = 'chain A' selection = 'chain C' selection = 'chain D' } ncs_group { reference = 'chain B' selection = 'chain D' } ''' user_phil5 = '''\ ncs_group { reference = 'chain A' selection = 'chain C' selection = 'chain D' } ncs_group { reference = 'chain C' selection = 'chain E' } ''' test_pdb_ncs_spec = '''\ 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 ''' test_ncs_spec = '''\ Summary of NCS information Fri Jun 13 13:18:12 2014 C:\Phenix\Dev\Work\work\junk new_ncs_group new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 10.5384 9.4098 10.2058 CHAIN A RMSD 0.0 MATCHING 9 RESSEQ 151:159 new_operator rota_matrix 0.4966 0.8679 -0.0102 rota_matrix -0.6436 0.3761 0.6666 rota_matrix 0.5824 -0.3245 0.7453 tran_orth -0.0003 -0.0002 0.0003 center_orth 5.1208 9.3744 13.7718 CHAIN B RMSD 0.0005 MATCHING 9 RESSEQ 151:159 new_operator rota_matrix -0.3180 0.7607 0.5659 rota_matrix -0.1734 -0.6334 0.7541 rota_matrix 0.9321 0.1416 0.3334 tran_orth 0.0002 0.0004 -0.0006 center_orth 4.5304 3.5021 16.4612 CHAIN C RMSD 0.0005 MATCHING 9 RESSEQ 151:159 new_ncs_group new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 8.5917 9.4397 9.9770 CHAIN D RMSD 0.0 MATCHING 7 RESSEQ 1:7 new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 -0.0000 1.0000 rota_matrix 0.0000 -1.0000 -0.0000 tran_orth 0.0000 -0.0000 0.0000 center_orth 8.5917 -9.9770 9.4397 CHAIN E RMSD 0.0 MATCHING 7 RESSEQ 1:7 ''' 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_finding_partial_ncs'] suite = unittest.TestSuite(list(map(TestNcsGroupPreprocessing,tests))) return suite if __name__=='__main__': # use for individual tests # unittest.TextTestRunner().run(run_selected_tests()) # Use to run all tests unittest.main(verbosity=0)