from __future__ import division from mmtbx.ncs.ncs_search import res_alignment from mmtbx.ncs import ncs_search from iotbx import pdb import unittest import time import sys class TestSimpleAlignment(unittest.TestCase): """ Test alignment of closely similar sequences """ def setUp(self): a = "ssssAESSADKFKRQxxxHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQ" \ "NGRNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV" b = "AESSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQ" \ "NGRNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQkhIIIACDGNPYVPVHFDASVtttt" self.seq_a = list(a) self.seq_b = list(b) self.length_diff = len(b)/len(a) # Gaps needed for the inserted, not aligned, letters self.gaps_needed = 4 + 3 + 4 # pdb_obj = pdb.hierarchy.input(pdb_string=pdb_str) self.ph = pdb_obj.hierarchy cache = self.ph.atom_selection_cache() self.chain_a = self.ph.models()[0].chains()[0] self.chain_b = self.ph.models()[0].chains()[1] self.hierarchy_a = self.ph.select(cache.selection('chain A')) self.hierarchy_b = self.ph.select(cache.selection('chain B')) def test_1(self): print sys._getframe().f_code.co_name a = 'abcfadx' b = 'cabfa' seq_a = list(a) seq_b = list(b) # Test that aligned segments are at least min_contig_length long sel_a, sel_b, similarity = res_alignment( seq_a=seq_a, seq_b=seq_b, min_fraction_domain =0.1,min_contig_length=3) self.assertEqual([],list(sel_a)) self.assertEqual([],list(sel_b)) # Without length limitation sel_a, sel_b,similarity = res_alignment( seq_a=seq_a, seq_b=seq_b, min_fraction_domain =0.1,min_contig_length=2) self.assertEqual([0,1,3,4],list(sel_a)) self.assertEqual([1,2,3,4],list(sel_b)) def test_2(self): print sys._getframe().f_code.co_name sel_a, sel_b, similarity = res_alignment( self.seq_a, self.seq_b, min_fraction_domain=0.9,min_contig_length=0) expected_1 = [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119] expected_2 = [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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112] self.assertEqual(expected_1,list(sel_a)) self.assertEqual(expected_2,list(sel_b)) def test_3(self): print sys._getframe().f_code.co_name sel_a, sel_b, similarity = res_alignment( self.seq_a,self.seq_b,min_fraction_domain=0.95,min_contig_length=0) # difference is to large expected_1 = [] expected_2 = [] self.assertEqual(expected_1,list(sel_a)) self.assertEqual(expected_2,list(sel_b)) def test_search_ncs_relations(self): print sys._getframe().f_code.co_name chain_match_list = ncs_search.search_ncs_relations( ph=self.ph,min_fraction_domain=0.75,min_contig_length=3) [chain_a_id,chain_b_id,sel_a,sel_b,r1,r2,_] = chain_match_list[0] # self.assertEqual(chain_a_id,'A') self.assertEqual(chain_b_id,'B') # atoms_in_A = self.hierarchy_a.atoms().size() atoms_in_B = self.hierarchy_b.atoms().size() # atom count including water self.assertEqual(32,atoms_in_A) self.assertEqual(44,atoms_in_B) # self.assertEqual(sel_a.size(),25) self.assertEqual(sel_b.size(),25) # atom count including water self.assertEqual(32,atoms_in_A) self.assertEqual(44,atoms_in_B) # # number of waters is different as well expected_sel_a = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27] expected_sel_b = [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] self.assertEqual(list(sel_a), expected_sel_a) self.assertEqual(list(sel_b), expected_sel_b) # self.assertEqual(r1,[0, 1, 2, 3]) self.assertEqual(r2,[0, 1, 2, 3]) pdb_str = '''\ CRYST1 37.760 43.710 107.440 90.00 108.54 90.00 P 1 21 1 4 ATOM 1 N GLY A 1 10.100 14.506 -6.813 1.00 11.02 N ATOM 2 CA GLY A 1 9.618 15.911 -6.685 1.00 9.34 C ATOM 3 C GLY A 1 10.369 16.727 -7.707 1.00 7.85 C ATOM 4 O GLY A 1 11.481 16.388 -8.042 1.00 8.86 O ATOM 5 N LYS A 2 9.783 17.791 -8.213 1.00 7.53 N ATOM 6 CA LYS A 2 10.481 18.573 -9.209 1.00 7.43 C ATOM 7 C LYS A 2 10.199 20.063 -9.068 1.00 6.50 C ATOM 8 O LYS A 2 9.065 20.460 -8.837 1.00 4.58 O ATOM 9 CB LYS A 2 10.064 18.096 -10.596 1.00 10.22 C ATOM 10 CG LYS A 2 10.871 18.687 -11.722 1.00 11.46 C ATOM 11 CD LYS A 2 10.092 18.615 -13.014 1.00 19.76 C ATOM 12 CE LYS A 2 9.725 17.195 -13.381 1.00 20.40 C ATOM 13 NZ LYS A 2 10.922 16.324 -13.540 1.00 26.54 N ATOM 14 N ILE A 3 11.226 20.875 -9.282 1.00 6.47 N ATOM 15 CA ILE A 3 11.128 22.321 -9.186 1.00 4.49 C ATOM 16 C ILE A 3 12.072 22.938 -10.224 1.00 4.38 C ATOM 17 O ILE A 3 13.107 22.372 -10.517 1.00 3.75 O ATOM 18 CB ILE A 3 11.550 22.813 -7.771 1.00 2.00 C ATOM 19 CG1 ILE A 3 11.272 24.308 -7.617 1.00 2.44 C ATOM 20 CG2 ILE A 3 13.048 22.554 -7.541 1.00 2.00 C ATOM 21 CD1 ILE A 3 11.435 24.816 -6.208 1.00 2.18 C ATOM 22 N THR A 4 11.699 24.079 -10.788 1.00 4.32 N ATOM 23 CA THR A 4 12.543 24.760 -11.751 1.00 7.18 C ATOM 24 C THR A 4 12.633 26.205 -11.328 1.00 5.50 C ATOM 25 O THR A 4 11.602 26.824 -11.045 1.00 5.90 O ATOM 26 CB THR A 4 11.950 24.736 -13.155 1.00 8.96 C ATOM 27 OG1 THR A 4 11.629 23.389 -13.508 1.00 14.82 O ATOM 28 CG2 THR A 4 12.954 25.288 -14.146 1.00 10.81 C TER ATOM 1492 N GLY B 3 30.298 10.660 57.402 1.00 8.41 N ATOM 1493 CA GLY B 3 30.111 9.211 57.319 1.00 6.72 C ATOM 1494 C GLY B 3 30.875 8.547 58.431 1.00 6.27 C ATOM 1495 O GLY B 3 31.907 9.064 58.860 1.00 6.95 O ATOM 1496 N LYS B 4 30.353 7.443 58.946 1.00 6.16 N ATOM 1497 CA LYS B 4 31.044 6.737 60.009 1.00 9.57 C ATOM 1498 C LYS B 4 30.699 5.272 59.908 1.00 8.82 C ATOM 1499 O LYS B 4 29.544 4.909 59.671 1.00 10.99 O ATOM 1500 CB LYS B 4 30.681 7.309 61.385 1.00 15.37 C ATOM 1501 CG LYS B 4 31.286 6.548 62.561 1.00 17.25 C ATOM 1502 CD LYS B 4 30.583 6.873 63.875 1.00 19.93 C ATOM 1503 CE LYS B 4 30.944 8.264 64.374 1.00 25.63 C ATOM 1504 NZ LYS B 4 32.411 8.433 64.713 1.00 32.30 N ATOM 1505 N ILE B 5 31.719 4.436 60.038 1.00 6.78 N ATOM 1506 CA ILE B 5 31.566 3.002 59.948 1.00 2.83 C ATOM 1507 C ILE B 5 32.501 2.424 60.999 1.00 3.23 C ATOM 1508 O ILE B 5 33.516 3.037 61.326 1.00 5.50 O ATOM 1509 CB ILE B 5 31.947 2.522 58.541 1.00 2.00 C ATOM 1513 N THR B 6 32.140 1.279 61.559 1.00 2.00 N ATOM 1514 CA THR B 6 32.944 0.619 62.593 1.00 2.91 C ATOM 1515 C THR B 6 33.142 -0.836 62.182 1.00 2.66 C ATOM 1516 O THR B 6 32.180 -1.560 61.883 1.00 2.00 O ATOM 1517 CB THR B 6 32.226 0.656 63.970 1.00 5.04 C ATOM 1518 OG1 THR B 6 31.894 2.006 64.303 1.00 7.93 O ATOM 1519 CG2 THR B 6 33.099 0.080 65.064 1.00 5.59 C ATOM 1520 N PHE B 7 34.393 -1.258 62.142 1.00 3.13 N ATOM 1521 CA PHE B 7 34.709 -2.610 61.743 1.00 4.16 C ATOM 1522 C PHE B 7 35.004 -3.435 62.989 1.00 7.18 C ATOM 1523 O PHE B 7 35.698 -2.951 63.889 1.00 8.29 O ATOM 1524 CB PHE B 7 35.936 -2.591 60.832 1.00 4.23 C ATOM 1525 CG PHE B 7 35.889 -1.521 59.766 1.00 5.16 C ATOM 1526 CD1 PHE B 7 35.279 -1.760 58.545 1.00 4.71 C ATOM 1527 CD2 PHE B 7 36.474 -0.268 59.990 1.00 4.91 C ATOM 1528 CE1 PHE B 7 35.248 -0.782 57.557 1.00 5.29 C ATOM 1529 CE2 PHE B 7 36.447 0.709 59.016 1.00 3.36 C ATOM 1530 CZ PHE B 7 35.826 0.443 57.791 1.00 8.22 C TER HETATM 2976 O HOH A 200 -5.015 35.539 13.500 1.00 13.39 O HETATM 2977 O HOH A 201 27.397 33.353 -7.193 1.00 42.92 O HETATM 2978 O HOH A 202 9.999 12.737 -8.741 1.00 22.09 O HETATM 2979 O HOH A 203 20.918 31.300 9.008 1.00 11.57 O HETATM 3128 O HOH B 303 38.892 -4.641 42.351 1.00 28.05 O HETATM 3129 O HOH B 304 23.863 8.189 55.409 1.00 9.33 O HETATM 3130 O HOH B 305 37.020 0.527 42.707 1.00 6.39 O HETATM 3131 O HOH B 306 29.889 -7.894 21.701 1.00 17.26 O HETATM 3132 O HOH B 307 36.038 -0.748 40.367 1.00 8.62 O HETATM 3133 O HOH B 308 31.840 -18.209 58.265 1.00 34.09 O HETATM 3134 O HOH B 309 21.378 -6.597 55.543 1.00 21.44 O HETATM 3135 O HOH B 310 39.908 -13.756 54.831 1.00 11.05 O 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_search_ncs_relations'] suite = unittest.TestSuite(map(TestSimpleAlignment,tests)) return suite if __name__=='__main__': # use for individual tests # unittest.TextTestRunner().run(run_selected_tests()) # Use to run all tests t0 = time.time() unittest.main() print 'Test took {0:.3f} sec'.format(time.time()-t0)