from __future__ import absolute_import, division, print_function import time from iotbx.ncs import ncs_group_master_phil import iotbx.phil import iotbx.ncs import iotbx.pdb from libtbx.test_utils import approx_equal pdb_str_a_lot_of_ncs = """\ ATOM 0 N VALAa 175 4.326 -59.034 -15.595 1.00105.80 N ATOM 1 CA VALAa 175 5.525 -58.206 -15.617 1.00 86.22 C ATOM 2 C VALAa 175 6.348 -58.476 -14.358 1.00 61.80 C ATOM 3 O VALAa 175 5.879 -59.158 -13.445 1.00 58.55 O TER ATOM 4 N THRAb 174 -15.180 -65.753 -17.549 1.00113.31 N ATOM 5 CA THRAb 174 -14.857 -64.334 -17.581 1.00120.94 C ATOM 6 C THRAb 174 -15.877 -63.524 -16.808 1.00109.70 C ATOM 7 O THRAb 174 -15.828 -62.302 -16.798 1.00110.07 O TER ATOM 8 N LYSAc 30 -75.643 8.901 124.736 1.00205.41 N ATOM 9 CA LYSAc 30 -74.928 10.142 125.003 1.00200.32 C ATOM 10 C LYSAc 30 -75.558 11.283 124.229 1.00198.69 C ATOM 11 O LYSAc 30 -74.919 11.832 123.330 1.00194.89 O ATOM 12 N THRAc 31 -76.807 11.640 124.555 1.00163.49 N ATOM 13 CA THRAc 31 -77.445 12.728 123.826 1.00162.32 C ATOM 14 C THRAc 31 -76.491 13.902 123.640 1.00160.35 C ATOM 15 O THRAc 31 -76.874 15.060 123.806 1.00158.76 O TER ATOM 16 N VALAd 175 148.055 93.347 -15.595 1.00105.80 N ATOM 17 CA VALAd 175 147.227 94.546 -15.617 1.00 86.22 C ATOM 18 C VALAd 175 147.496 95.369 -14.358 1.00 61.80 C ATOM 19 O VALAd 175 148.179 94.900 -13.445 1.00 58.55 O TER ATOM 20 N THRAe 174 154.774 73.841 -17.549 1.00113.31 N ATOM 21 CA THRAe 174 153.355 74.164 -17.581 1.00120.94 C ATOM 22 C THRAe 174 152.544 73.144 -16.808 1.00109.70 C ATOM 23 O THRAe 174 151.323 73.193 -16.798 1.00110.07 O TER ATOM 24 N LYSAf 30 80.120 13.378 124.736 1.00205.41 N ATOM 25 CA LYSAf 30 78.879 14.093 125.003 1.00200.32 C ATOM 26 C LYSAf 30 77.738 13.463 124.229 1.00198.69 C ATOM 27 O LYSAf 30 77.189 14.102 123.330 1.00194.89 O ATOM 28 N THRAf 31 77.381 12.214 124.555 1.00163.49 N ATOM 29 CA THRAf 31 76.293 11.576 123.826 1.00162.32 C ATOM 30 C THRAf 31 75.119 12.530 123.640 1.00160.35 C ATOM 31 O THRAf 31 73.961 12.147 123.806 1.00158.76 O TER ATOM 32 N VALAg 175 29.987 84.695 -15.595 1.00105.80 N ATOM 33 CA VALAg 175 30.815 83.496 -15.617 1.00 86.22 C ATOM 34 C VALAg 175 30.545 82.672 -14.358 1.00 61.80 C ATOM 35 O VALAg 175 29.863 83.142 -13.445 1.00 58.55 O TER ATOM 36 N THRAh 174 23.268 104.201 -17.549 1.00113.31 N ATOM 37 CA THRAh 174 24.687 103.878 -17.581 1.00120.94 C ATOM 38 C THRAh 174 25.497 104.898 -16.808 1.00109.70 C ATOM 39 O THRAh 174 26.719 104.849 -16.798 1.00110.07 O TER ATOM 40 N LYSAi 30 97.922 164.664 124.736 1.00205.41 N ATOM 41 CA LYSAi 30 99.163 163.949 125.003 1.00200.32 C ATOM 42 C LYSAi 30 100.304 164.579 124.229 1.00198.69 C ATOM 43 O LYSAi 30 100.853 163.940 123.330 1.00194.89 O ATOM 44 N THRAi 31 100.661 165.828 124.555 1.00163.49 N ATOM 45 CA THRAi 31 101.749 166.466 123.826 1.00162.32 C ATOM 46 C THRAi 31 102.923 165.512 123.640 1.00160.35 C ATOM 47 O THRAi 31 104.081 165.895 123.806 1.00158.76 O TER ATOM 48 N VALAj 175 93.347 148.055 15.595 1.00105.80 N ATOM 49 CA VALAj 175 94.546 147.227 15.617 1.00 86.22 C ATOM 50 C VALAj 175 95.369 147.496 14.358 1.00 61.80 C ATOM 51 O VALAj 175 94.900 148.179 13.445 1.00 58.55 O TER ATOM 52 N THRAk 174 73.841 154.774 17.549 1.00113.31 N ATOM 53 CA THRAk 174 74.164 153.355 17.581 1.00120.94 C ATOM 54 C THRAk 174 73.144 152.544 16.808 1.00109.70 C ATOM 55 O THRAk 174 73.193 151.323 16.798 1.00110.07 O TER ATOM 56 N LYSAl 30 13.378 80.120-124.736 1.00205.41 N ATOM 57 CA LYSAl 30 14.093 78.879-125.003 1.00200.32 C ATOM 58 C LYSAl 30 13.462 77.738-124.229 1.00198.69 C ATOM 59 O LYSAl 30 14.102 77.189-123.330 1.00194.89 O ATOM 60 N THRAl 31 12.213 77.381-124.555 1.00163.49 N ATOM 61 CA THRAl 31 11.576 76.293-123.826 1.00162.32 C ATOM 62 C THRAl 31 12.530 75.119-123.640 1.00160.35 C ATOM 63 O THRAl 31 12.147 73.961-123.806 1.00158.76 O TER ATOM 64 N VALAm 175 84.695 29.987 15.595 1.00105.80 N ATOM 65 CA VALAm 175 83.496 30.815 15.617 1.00 86.22 C ATOM 66 C VALAm 175 82.672 30.545 14.358 1.00 61.80 C ATOM 67 O VALAm 175 83.142 29.863 13.445 1.00 58.55 O TER ATOM 68 N THRAn 174 104.201 23.268 17.549 1.00113.31 N ATOM 69 CA THRAn 174 103.878 24.687 17.581 1.00120.94 C ATOM 70 C THRAn 174 104.898 25.497 16.808 1.00109.70 C ATOM 71 O THRAn 174 104.849 26.719 16.798 1.00110.07 O TER ATOM 72 N LYSAo 30 164.664 97.921-124.736 1.00205.41 N ATOM 73 CA LYSAo 30 163.948 99.162-125.003 1.00200.32 C ATOM 74 C LYSAo 30 164.579 100.303-124.229 1.00198.69 C ATOM 75 O LYSAo 30 163.940 100.852-123.330 1.00194.89 O ATOM 76 N THRAo 31 165.828 100.660-124.555 1.00163.49 N ATOM 77 CA THRAo 31 166.466 101.748-123.826 1.00162.32 C ATOM 78 C THRAo 31 165.512 102.922-123.640 1.00160.35 C ATOM 79 O THRAo 31 165.895 104.080-123.806 1.00158.76 O TER ATOM 80 N VALAp 175 -4.326 59.034 -15.595 1.00105.80 N ATOM 81 CA VALAp 175 -5.525 58.206 -15.617 1.00 86.22 C ATOM 82 C VALAp 175 -6.348 58.476 -14.358 1.00 61.80 C ATOM 83 O VALAp 175 -5.879 59.158 -13.445 1.00 58.55 O TER ATOM 84 N THRAq 174 15.180 65.753 -17.549 1.00113.31 N ATOM 85 CA THRAq 174 14.857 64.334 -17.581 1.00120.94 C ATOM 86 C THRAq 174 15.877 63.524 -16.808 1.00109.70 C ATOM 87 O THRAq 174 15.828 62.302 -16.798 1.00110.07 O TER ATOM 88 N LYSAr 30 75.643 -8.901 124.736 1.00205.41 N ATOM 89 CA LYSAr 30 74.928 -10.142 125.003 1.00200.32 C ATOM 90 C LYSAr 30 75.558 -11.283 124.229 1.00198.69 C ATOM 91 O LYSAr 30 74.919 -11.832 123.330 1.00194.89 O ATOM 92 N THRAr 31 76.807 -11.640 124.555 1.00163.49 N ATOM 93 CA THRAr 31 77.445 -12.728 123.826 1.00162.32 C ATOM 94 C THRAr 31 76.491 -13.902 123.640 1.00160.35 C ATOM 95 O THRAr 31 76.874 -15.060 123.806 1.00158.76 O TER ATOM 96 N VALAs 175 -59.034 4.326 15.595 1.00105.80 N ATOM 97 CA VALAs 175 -58.206 5.525 15.617 1.00 86.22 C ATOM 98 C VALAs 175 -58.476 6.348 14.358 1.00 61.80 C ATOM 99 O VALAs 175 -59.158 5.879 13.445 1.00 58.55 O TER ATOM 100 N THRAt 174 -65.753 -15.180 17.549 1.00113.31 N ATOM 101 CA THRAt 174 -64.334 -14.857 17.581 1.00120.94 C ATOM 102 C THRAt 174 -63.524 -15.877 16.808 1.00109.70 C ATOM 103 O THRAt 174 -62.302 -15.828 16.798 1.00110.07 O TER ATOM 104 N LYSAu 30 8.901 -75.643-124.736 1.00205.41 N ATOM 105 CA LYSAu 30 10.142 -74.928-125.003 1.00200.32 C ATOM 106 C LYSAu 30 11.283 -75.558-124.229 1.00198.69 C ATOM 107 O LYSAu 30 11.832 -74.919-123.330 1.00194.89 O ATOM 108 N THRAu 31 11.640 -76.807-124.555 1.00163.49 N ATOM 109 CA THRAu 31 12.728 -77.445-123.826 1.00162.32 C ATOM 110 C THRAu 31 13.902 -76.491-123.640 1.00160.35 C ATOM 111 O THRAu 31 15.060 -76.874-123.806 1.00158.76 O TER ATOM 112 N VALAv 175 59.034 -4.326 15.595 1.00105.80 N ATOM 113 CA VALAv 175 58.206 -5.525 15.617 1.00 86.22 C ATOM 114 C VALAv 175 58.476 -6.348 14.358 1.00 61.80 C ATOM 115 O VALAv 175 59.158 -5.879 13.445 1.00 58.55 O TER ATOM 116 N THRAw 174 65.753 15.180 17.549 1.00113.31 N ATOM 117 CA THRAw 174 64.334 14.857 17.581 1.00120.94 C ATOM 118 C THRAw 174 63.524 15.877 16.808 1.00109.70 C ATOM 119 O THRAw 174 62.302 15.828 16.798 1.00110.07 O TER ATOM 120 N LYSAx 30 -8.901 75.643-124.736 1.00205.41 N ATOM 121 CA LYSAx 30 -10.142 74.928-125.003 1.00200.32 C ATOM 122 C LYSAx 30 -11.283 75.558-124.229 1.00198.69 C ATOM 123 O LYSAx 30 -11.832 74.919-123.330 1.00194.89 O ATOM 124 N THRAx 31 -11.640 76.807-124.555 1.00163.49 N ATOM 125 CA THRAx 31 -12.728 77.445-123.826 1.00162.32 C ATOM 126 C THRAx 31 -13.902 76.491-123.640 1.00160.35 C ATOM 127 O THRAx 31 -15.060 76.874-123.806 1.00158.76 O TER """ def get_ncs_groups(phil_str, pdb_str, **kwargs): phil_groups = ncs_group_master_phil.fetch( iotbx.phil.parse(phil_str)).extract() pdb_inp = iotbx.pdb.input(lines=pdb_str,source_info=None) ncs_inp = iotbx.ncs.input(hierarchy = pdb_inp.construct_hierarchy(), ncs_phil_groups=phil_groups.ncs_group, **kwargs) return ncs_inp.get_ncs_restraints_group_list() def exercise_1(): """ Simple selections, no tricks. Make sure reference and selections are what user want. All three chains are NCS-related. """ phil_str1=""" ncs_group { reference = chain E selection = chain F } """ phil_str2=""" ncs_group { reference = chain E selection = chain F selection = chain G } """ phil_str3=""" ncs_group { reference = chain G selection = chain E } """ phil_str4=""" ncs_group { reference = chain G selection = chain F selection = chain E } """ pdb_str = """\ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY E 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY E 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY E 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY E 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY F 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY F 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY F 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY F 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 N GLY G 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CA GLY G 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C GLY G 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 O GLY G 34 189.986 271.004 173.508 1.00 0.00 O TER """ ncs_groups = get_ncs_groups(phil_str1, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1 assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3] assert list(ncs_groups[0].copies[0].iselection) == [4, 5, 6, 7] # print "master isel:", list(ncs_groups[0].master_iselection) # print "copy isel:", list(ncs_groups[0].copies[0].iselection) # print "="*80 ncs_groups = get_ncs_groups(phil_str2, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3] assert list(ncs_groups[0].copies[0].iselection) == [4, 5, 6, 7] assert list(ncs_groups[0].copies[1].iselection) == [8, 9, 10, 11] # print "master isel:", list(ncs_groups[0].master_iselection) # print "copy isel:", list(ncs_groups[0].copies[0].iselection) # print "copy isel:", list(ncs_groups[0].copies[1].iselection) # print "="*80 ncs_groups = get_ncs_groups(phil_str3, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1 assert list(ncs_groups[0].master_iselection) == [8, 9, 10, 11] assert list(ncs_groups[0].copies[0].iselection) == [0, 1, 2, 3] # print "master isel:", list(ncs_groups[0].master_iselection) # print "copy isel:", list(ncs_groups[0].copies[0].iselection) # print "="*80 ncs_groups = get_ncs_groups(phil_str4, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert list(ncs_groups[0].master_iselection) == [8, 9, 10, 11] assert list(ncs_groups[0].copies[0].iselection) == [4, 5, 6, 7] assert list(ncs_groups[0].copies[1].iselection) == [0, 1, 2, 3] # print "master isel:", list(ncs_groups[0].master_iselection) # print "copy isel:", list(ncs_groups[0].copies[0].iselection) # print "copy isel:", list(ncs_groups[0].copies[1].iselection) # print "="*80 def exercise_2(): """ User tries to define non-matching groups. A matches B, but C doesn't match anything """ phil_str1=""" ncs_group { reference = chain A selection = chain C } """ phil_str2=""" ncs_group { reference = chain A selection = chain B selection = chain C } """ pdb_str = """\ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY B 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 N TYR C 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CA TYR C 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C TYR C 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 O TYR C 34 189.986 271.004 173.508 1.00 0.00 O TER """ ncs_groups = get_ncs_groups(phil_str1, pdb_str) assert len(ncs_groups) == 0 ncs_groups = get_ncs_groups(phil_str2, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1 assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3] assert list(ncs_groups[0].copies[0].iselection) == [4, 5, 6, 7] def exercise_3(): """ User can split one chain into ncs groups """ phil_str1=""" ncs_group { reference = chain A and resid 34 selection = chain A and resid 35 } """ pdb_str = """\ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O ATOM 5 N GLY A 35 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY A 35 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY A 35 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY A 35 249.986 144.872 173.510 1.00 0.00 O TER """ ncs_groups = get_ncs_groups(phil_str1, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1 assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3] assert list(ncs_groups[0].copies[0].iselection) == [4, 5, 6, 7] def exercise_4(): """ User can specify multiple chains in one selection """ pdb_str = """\ 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 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 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 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 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 """ phil_str1=""" ncs_group { reference = chain A or chain B selection = chain C or chain D selection = chain E or chain F } """ phil_str2=""" ncs_group { reference = chain E or chain F selection = chain C or chain D selection = chain A or chain B } """ phil_str3=""" ncs_group { reference = chain A or chain B selection = chain C or chain D } """ phil_str4=""" ncs_group { reference = chain A selection = chain C selection = chain E } """ ncs_groups = get_ncs_groups(phil_str1, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3, 4, 5, 6, 7, 8] assert list(ncs_groups[0].copies[0].iselection) == [9, 10, 11, 12, 13, 14, 15, 16, 17] assert list(ncs_groups[0].copies[1].iselection) == [18, 19, 20, 21, 22, 23, 24, 25, 26] ncs_groups = get_ncs_groups(phil_str2, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert list(ncs_groups[0].master_iselection) == [18, 19, 20, 21, 22, 23, 24, 25, 26] assert list(ncs_groups[0].copies[0].iselection) == [9, 10, 11, 12, 13, 14, 15, 16, 17] assert list(ncs_groups[0].copies[1].iselection) == [0, 1, 2, 3, 4, 5, 6, 7, 8] ncs_groups = get_ncs_groups(phil_str3, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1 assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3, 4, 5, 6, 7, 8] assert list(ncs_groups[0].copies[0].iselection) == [9, 10, 11, 12, 13, 14, 15, 16, 17] ncs_groups = get_ncs_groups(phil_str4, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3, 4, 5] assert list(ncs_groups[0].copies[0].iselection) == [9, 10, 11, 12, 13, 14] assert list(ncs_groups[0].copies[1].iselection) == [18, 19, 20, 21, 22, 23] def exercise_5(): """ User can specify selections for pdb file with blank chain ids, but with segids. Inputs are same as in exercise_1(), except chains renamed to segID. XXX. Currenly will not be outputted correctly, but should work fine. """ phil_str1=""" ncs_group { reference = segid seg1 selection = segid seg2 } """ phil_str2=""" ncs_group { reference = segid seg1 selection = segid seg2 selection = segid seg3 } """ phil_str3=""" ncs_group { reference = segid seg3 selection = segid seg1 } """ phil_str4=""" ncs_group { reference = segid seg3 selection = segid seg2 selection = segid seg1 } """ pdb_str = """\ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY 34 125.208 211.886 175.417 1.00 0.00 seg1 N ATOM 2 CA GLY 34 125.035 211.123 174.168 1.00 0.00 seg1 C ATOM 3 C GLY 34 126.386 210.806 173.507 1.00 0.00 seg1 C ATOM 4 O GLY 34 127.304 211.628 173.503 1.00 0.00 seg1 O TER ATOM 5 N GLY 34 251.532 143.432 175.422 1.00 0.00 seg2 N ATOM 6 CA GLY 34 252.120 143.948 174.173 1.00 0.00 seg2 C ATOM 7 C GLY 34 251.212 144.998 173.512 1.00 0.00 seg2 C ATOM 8 O GLY 34 249.986 144.872 173.510 1.00 0.00 seg2 O TER ATOM 9 N GLY 34 189.583 273.076 175.423 1.00 0.00 seg3 N ATOM 10 CA GLY 34 188.804 273.006 174.173 1.00 0.00 seg3 C ATOM 11 C GLY 34 188.920 271.622 173.510 1.00 0.00 seg3 C ATOM 12 O GLY 34 189.986 271.004 173.508 1.00 0.00 seg3 O TER """ ncs_groups = get_ncs_groups(phil_str1, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1 assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3] assert list(ncs_groups[0].copies[0].iselection) == [4, 5, 6, 7] ncs_groups = get_ncs_groups(phil_str2, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3] assert list(ncs_groups[0].copies[0].iselection) == [4, 5, 6, 7] assert list(ncs_groups[0].copies[1].iselection) == [8, 9, 10, 11] ncs_groups = get_ncs_groups(phil_str3, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1 assert list(ncs_groups[0].master_iselection) == [8, 9, 10, 11] assert list(ncs_groups[0].copies[0].iselection) == [0, 1, 2, 3] ncs_groups = get_ncs_groups(phil_str4, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert list(ncs_groups[0].master_iselection) == [8, 9, 10, 11] assert list(ncs_groups[0].copies[0].iselection) == [4, 5, 6, 7] assert list(ncs_groups[0].copies[1].iselection) == [0, 1, 2, 3] def exercise_6(): """ Automatic water filtering. Chains A, B, C, D are NCS-related even with water molecule """ phil_str1=""" ncs_group { reference = chain A selection = chain B } """ pdb_str = """\ CRYST1 18.415 14.419 12.493 90.00 90.00 90.00 P 1 ATOM 1 N THR A 1 11.782 12.419 4.645 1.00 10.00 N ATOM 2 CA THR A 1 11.671 11.061 4.125 1.00 10.00 C ATOM 3 C THR A 1 11.746 10.033 5.249 1.00 10.00 C ATOM 4 O THR A 1 12.561 10.157 6.163 1.00 10.00 O ATOM 5 CB THR A 1 12.772 10.760 3.092 1.00 10.00 C ATOM 6 OG1 THR A 1 12.672 11.682 2.000 1.00 10.00 O ATOM 7 O HOH A 2 12.635 9.340 2.565 1.00 10.00 O TER ATOM 1 N THR D 1 13.010 5.595 10.010 1.00 10.00 N ATOM 2 CA THR D 1 14.035 5.945 9.034 1.00 10.00 C ATOM 3 C THR D 1 15.310 6.423 9.720 1.00 10.00 C ATOM 4 O THR D 1 16.415 6.054 9.323 1.00 10.00 O ATOM 5 CB THR D 1 13.543 7.038 8.066 1.00 10.00 C ATOM 6 OG1 THR D 1 13.237 8.229 8.802 1.00 10.00 O ATOM 7 O HOH D 2 12.300 6.572 7.323 1.00 10.00 O TER ATOM 1 N THR B 1 6.768 9.093 9.237 1.00 10.00 N ATOM 2 CA THR B 1 7.284 8.654 7.945 1.00 10.00 C ATOM 3 C THR B 1 8.638 7.968 8.097 1.00 10.00 C ATOM 4 O THR B 1 9.495 8.426 8.852 1.00 10.00 O ATOM 5 CB THR B 1 7.423 9.832 6.963 1.00 10.00 C ATOM 6 OG1 THR B 1 6.144 10.446 6.765 1.00 10.00 O ATOM 7 O HOH B 2 7.962 9.350 5.625 1.00 10.00 O TER ATOM 1 N THR C 1 9.093 2.000 10.493 1.00 10.00 N ATOM 2 CA THR C 1 8.879 2.702 9.233 1.00 10.00 C ATOM 3 C THR C 1 10.081 3.570 8.875 1.00 10.00 C ATOM 4 O THR C 1 10.652 4.241 9.734 1.00 10.00 O ATOM 5 CB THR C 1 7.618 3.584 9.284 1.00 10.00 C ATOM 6 OG1 THR C 1 6.472 2.770 9.559 1.00 10.00 O ATOM 7 O HOH C 2 7.417 4.305 7.960 1.00 10.00 O TER """ ncs_groups = get_ncs_groups(phil_str1, pdb_str) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1 assert list(ncs_groups[0].master_iselection) == [0,1,2,3,4,5] assert list(ncs_groups[0].copies[0].iselection) == [14,15,16,17,18,19] # Here we modifying default exclude_selection parameter to keep waters p = iotbx.ncs.input.get_default_params() p.ncs_search.exclude_selection=None ncs_groups = get_ncs_groups(phil_str1, pdb_str, params=p.ncs_search) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1 assert list(ncs_groups[0].master_iselection) == [0,1,2,3,4,5,6], list(ncs_groups[0].master_iselection) assert list(ncs_groups[0].copies[0].iselection) == [14,15,16,17,18,19,20] def exercise_7(): """ extraction from exercise_00 form tst_ncs_input.py """ pdb_str1 = """ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY B 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 N GLY C 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CA GLY C 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C GLY C 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 O GLY C 34 189.986 271.004 173.508 1.00 0.00 O TER """ pdb_str2 = """ CRYST1 399.000 399.000 399.000 90.00 90.00 90.00 P 1 ATOM 1 O HOH S 1 109.583 203.076 175.423 1.00 0.00 O TER ATOM 1 N GLY A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CA GLY A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C GLY A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 O GLY A 34 127.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N GLY B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CA GLY B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C GLY B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 O GLY B 34 249.986 144.872 173.510 1.00 0.00 O TER ATOM 9 N GLY C 34 189.583 273.076 175.423 1.00 0.00 N ATOM 10 CA GLY C 34 188.804 273.006 174.173 1.00 0.00 C ATOM 11 C GLY C 34 188.920 271.622 173.510 1.00 0.00 C ATOM 12 O GLY C 34 189.986 271.004 173.508 1.00 0.00 O TER ATOM 9 O TYR D 4 189.583 273.076 175.423 1.00 0.00 O TER """ phil_str1 = """ ncs_group { reference = chain A selection = chain B selection = chain C } """ ncs_groups = get_ncs_groups(phil_str1, pdb_str1) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert list(ncs_groups[0].master_iselection) == [0,1,2,3] assert list(ncs_groups[0].copies[0].iselection) == [4,5,6,7] assert list(ncs_groups[0].copies[1].iselection) == [8,9,10,11] ncs_groups = get_ncs_groups(phil_str1, pdb_str2) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert list(ncs_groups[0].master_iselection) == [1,2,3,4] assert list(ncs_groups[0].copies[0].iselection) == [5,6,7,8] assert list(ncs_groups[0].copies[1].iselection) == [9,10,11,12] def exercise_8(): """ Here user tries to supply non-valid group along with valid group. Full list of valid NCS groups is in exercise_11, phil_str1. """ phil_str1 = """\ ncs_group { reference = chain Aa selection = chain Ae } """ phil_str2 = """\ ncs_group { reference = chain Aa selection = chain Ae } ncs_group { reference = chain As selection = chain Av } """ pdb_h = iotbx.pdb.input( source_info=None,lines=pdb_str_a_lot_of_ncs.split('\n')).\ construct_hierarchy() # show file: # pdb_h.write_pdb_file("user_ncs_phil_ex11.pdb") asc = pdb_h.atom_selection_cache() ncs_groups = get_ncs_groups(phil_str1, pdb_str_a_lot_of_ncs) assert len(ncs_groups)==0 # One group is ok ncs_groups = get_ncs_groups(phil_str2, pdb_str_a_lot_of_ncs) assert len(ncs_groups)==1 assert len(ncs_groups[0].copies) == 1 assert approx_equal(ncs_groups[0].master_iselection, asc.iselection("chain As")) assert approx_equal(ncs_groups[0].copies[0].iselection, asc.iselection("chain Av")) def exercise_9(): """ Here user's groups should be modified to exclude a residue or atom pdb_str is has good NCS, remarked atoms shows introduced discrepancies """ pdb_str = """\ ATOM 1 CB MET-- 1 52.886 1.976 9.011 1.00 41.44 C ATOM 2 CG MET-- 1 53.271 0.996 10.102 1.00 47.36 C ATOM 3 SD MET-- 1 55.066 1.105 10.320 1.00 54.87 S ATOM 4 CE MET-- 1 55.198 1.758 11.963 1.00 52.95 C ATOM 5 C MET-- 1 51.257 3.002 7.473 1.00 32.90 C ATOM 6 O MET-- 1 51.643 3.028 6.297 1.00 33.11 O ATOM 7 N MET-- 1 51.320 0.535 7.805 1.00 38.36 N ATOM 8 CA MET-- 1 51.486 1.834 8.434 1.00 36.79 C ATOM 9 N ILE-- 2 50.621 4.010 8.052 1.00 27.46 N ATOM 10 CA ILE-- 2 50.330 5.240 7.341 1.00 22.07 C ATOM 11 CB ILE-- 2 49.096 5.952 7.960 1.00 23.08 C ATOM 12 CG2 ILE-- 2 48.824 7.256 7.244 1.00 21.31 C remark ATOM 13 CG1 ILE-- 2 47.841 5.109 7.800 1.00 23.53 C ATOM 14 CD1 ILE-- 2 46.598 5.779 8.421 1.00 26.20 C ATOM 15 C ILE-- 2 51.562 6.118 7.509 1.00 19.91 C ATOM 16 O ILE-- 2 51.955 6.341 8.645 1.00 17.98 O ATOM 17 N LYS-- 3 52.103 6.642 6.398 1.00 18.18 N ATOM 18 CA LYS-- 3 53.229 7.583 6.418 1.00 17.08 C ATOM 19 CB LYS-- 3 54.076 7.396 5.144 1.00 19.78 C ATOM 20 CG LYS-- 3 55.276 8.374 5.088 1.00 23.29 C ATOM 21 CD LYS-- 3 55.948 8.330 3.717 1.00 29.04 C ATOM 22 CE LYS-- 3 57.288 7.627 3.791 1.00 31.30 C ATOM 23 NZ LYS-- 3 57.822 7.350 2.460 1.00 34.23 N ATOM 24 C LYS-- 3 52.675 9.012 6.481 1.00 14.59 C ATOM 25 O LYS-- 3 51.877 9.404 5.627 1.00 15.75 O ATOM 26 N VAL-- 4 53.044 9.811 7.492 1.00 12.13 N ATOM 27 CA VAL-- 4 52.594 11.201 7.600 1.00 10.72 C ATOM 28 CB VAL-- 4 51.792 11.417 8.905 1.00 12.27 C ATOM 29 CG1 VAL-- 4 51.313 12.867 9.013 1.00 11.73 C ATOM 30 CG2 VAL-- 4 50.586 10.433 8.913 1.00 12.18 C ATOM 31 C VAL-- 4 53.878 12.034 7.643 1.00 11.26 C ATOM 32 O VAL-- 4 54.859 11.624 8.278 1.00 12.24 O ATOM 33 N GLU-- 5 53.857 13.160 6.937 1.00 9.99 N ATOM 34 CA GLU-- 5 55.027 14.050 6.987 1.00 11.22 C ATOM 35 CB GLU-- 5 55.705 14.042 5.622 1.00 12.79 C ATOM 36 CG GLU-- 5 56.999 14.908 5.598 1.00 16.55 C ATOM 37 CD GLU-- 5 57.945 14.693 4.429 1.00 18.73 C ATOM 38 OE1 GLU-- 5 57.591 14.045 3.458 1.00 18.89 O ATOM 39 OE2 GLU-- 5 59.066 15.182 4.506 1.00 21.35 O ATOM 40 C GLU-- 5 54.642 15.472 7.371 1.00 11.49 C ATOM 41 O GLU-- 5 53.646 15.977 6.854 1.00 12.69 O TER ATOM 1 CB MET G 1 0.115 20.271 3.107 1.00 41.44 ATOM 2 CG MET G 1 0.717 21.085 1.978 1.00 47.36 ATOM 3 SD MET G 1 1.424 22.584 2.709 1.00 54.87 ATOM 4 CE MET G 1 3.156 22.361 2.406 1.00 52.95 ATOM 5 C MET G 1 -1.177 18.359 3.971 1.00 32.90 ATOM 6 O MET G 1 -2.072 18.689 4.760 1.00 33.11 ATOM 7 N MET G 1 -1.968 19.642 1.989 1.00 38.36 ATOM 8 CA MET G 1 -0.810 19.133 2.704 1.00 36.79 ATOM 9 N ILE G 2 -0.401 17.300 4.154 1.00 27.46 ATOM 10 CA ILE G 2 -0.542 16.440 5.313 1.00 22.07 ATOM 11 CB ILE G 2 -0.020 15.011 5.001 1.00 23.08 ATOM 12 CG2 ILE G 2 -0.128 14.130 6.226 1.00 21.31 ATOM 13 CG1 ILE G 2 -0.860 14.345 3.923 1.00 23.53 ATOM 14 CD1 ILE G 2 -0.357 12.928 3.575 1.00 26.20 ATOM 15 C ILE G 2 0.314 17.068 6.404 1.00 19.91 ATOM 16 O ILE G 2 1.490 17.289 6.152 1.00 17.98 ATOM 17 N LYS G 3 -0.264 17.284 7.595 1.00 18.18 ATOM 18 CA LYS G 3 0.465 17.790 8.764 1.00 17.08 ATOM 19 CB LYS G 3 -0.488 18.627 9.640 1.00 19.78 ATOM 20 CG LYS G 3 0.212 19.180 10.906 1.00 23.29 ATOM 21 CD LYS G 3 -0.806 19.795 11.864 1.00 29.04 ATOM 22 CE LYS G 3 -0.702 21.306 11.871 1.00 31.30 ATOM 23 NZ LYS G 3 -1.826 21.917 12.577 1.00 34.23 ATOM 24 C LYS G 3 1.006 16.597 9.561 1.00 14.59 ATOM 25 O LYS G 3 0.239 15.716 9.954 1.00 15.75 ATOM 26 N VAL G 4 2.324 16.510 9.792 1.00 12.13 ATOM 27 CA VAL G 4 2.914 15.426 10.581 1.00 10.72 ATOM 28 CB VAL G 4 3.918 14.613 9.730 1.00 12.27 remark ATOM 29 CG1 VAL G 4 4.527 13.474 10.552 1.00 11.73 ATOM 30 CG2 VAL G 4 3.172 14.059 8.481 1.00 12.18 ATOM 31 C VAL G 4 3.657 16.123 11.725 1.00 11.26 ATOM 32 O VAL G 4 4.277 17.173 11.509 1.00 12.24 ATOM 33 N GLU G 5 3.545 15.548 12.918 1.00 9.99 ATOM 34 CA GLU G 5 4.289 16.118 14.052 1.00 11.22 ATOM 35 CB GLU G 5 3.293 16.720 15.036 1.00 12.79 ATOM 36 CG GLU G 5 3.995 17.409 16.243 1.00 16.55 ATOM 37 CD GLU G 5 3.146 18.345 17.086 1.00 18.73 ATOM 38 OE1 GLU G 5 1.934 18.369 16.952 1.00 18.89 ATOM 39 OE2 GLU G 5 3.723 19.072 17.886 1.00 21.35 ATOM 40 C GLU G 5 5.146 15.072 14.750 1.00 11.49 ATOM 41 O GLU G 5 4.666 13.961 14.970 1.00 12.69 """ phil_str1 = """\ ncs_group { reference = chain -- selection = chain G } """ phil_str2 = """\ ncs_group { reference = chain G selection = chain '--' } """ pdb_h = iotbx.pdb.input( source_info=None,lines=pdb_str.split('\n')).\ construct_hierarchy() # show file: # pdb_h.write_pdb_file("user_ncs_phil_ex9.pdb") asc = pdb_h.atom_selection_cache() p = iotbx.ncs.input.get_default_params() p.ncs_search.exclude_selection = None ncs_groups = get_ncs_groups(phil_str1,pdb_str, params=p.ncs_search) assert len(ncs_groups)==1 assert len(ncs_groups[0].copies) == 1 assert approx_equal(ncs_groups[0].master_iselection, asc.iselection("chain '--' and not ((resid 2 or resid 4) and name CG1)")) assert approx_equal(ncs_groups[0].copies[0].iselection, asc.iselection("chain G and not ((resid 2 or resid 4) and name CG1)")) ncs_groups = get_ncs_groups(phil_str2,pdb_str, params=p.ncs_search) assert len(ncs_groups)==1 assert len(ncs_groups[0].copies) == 1 assert approx_equal(ncs_groups[0].master_iselection, asc.iselection("chain G and not ((resid 2 or resid 4) and name CG1)")) assert approx_equal(ncs_groups[0].copies[0].iselection, asc.iselection("chain '--' and not ((resid 2 or resid 4) and name CG1)")) def exercise_10(): """ Include water if requested by user. Oleg. Not anymore. Just fixing Previously was exercise_18 in tst_ncs_input """ pdb_str_15 = """ ATOM 1 N1 XXX A 34 125.208 211.886 175.417 1.00 0.00 N ATOM 2 CT XXX A 34 125.035 211.123 174.168 1.00 0.00 C ATOM 3 C XXX A 34 126.386 210.806 173.507 1.00 0.00 C ATOM 4 K XXX A 34 127.304 211.628 173.503 1.00 0.00 K ATOM 1 O HOH A 35 135.208 211.886 175.417 1.00 0.00 O ATOM 2 O HOH A 36 135.035 211.123 174.168 1.00 0.00 O ATOM 3 O HOH A 37 136.386 210.806 173.507 1.00 0.00 O ATOM 4 O HOH A 38 137.304 211.628 173.503 1.00 0.00 O TER ATOM 5 N1 XXX B 34 251.532 143.432 175.422 1.00 0.00 N ATOM 6 CT XXX B 34 252.120 143.948 174.173 1.00 0.00 C ATOM 7 C XXX B 34 251.212 144.998 173.512 1.00 0.00 C ATOM 8 K XXX B 34 249.986 144.872 173.510 1.00 0.00 K ATOM 5 O HOH B 35 271.532 143.432 175.422 1.00 0.00 O ATOM 6 O HOH B 36 272.120 143.948 174.173 1.00 0.00 O ATOM 7 O HOH B 37 271.212 144.998 173.512 1.00 0.00 O ATOM 8 O HOH B 38 279.986 144.872 173.510 1.00 0.00 O TER """ phil_str=""" ncs_group { reference = chain A selection = chain B } """ ### user-supplied p = iotbx.ncs.input.get_default_params() p.ncs_search.exclude_selection = None ncs_groups = get_ncs_groups(phil_str,pdb_str_15, params=p.ncs_search) # group 1 assert len(ncs_groups)==1 assert len(ncs_groups[0].copies) == 1 # chain A assert list(ncs_groups[0].master_iselection) == [0, 1, 2, 3, 4, 5, 6, 7] # chain B assert list(ncs_groups[0].copies[0].iselection) == [8,9,10,11,12,13,14,15] def exercise_11(): """ Two-letter chain ids. Also testing user selections for multiple chains. """ phil_str1 = """\ ncs_group { reference = chain Aa or chain Ab or chain Ac selection = chain Ad or chain Ae or chain Af selection = chain Ag or chain Ah or chain Ai selection = chain Aj or chain Ak or chain Al selection = chain Am or chain An or chain Ao selection = chain Ap or chain Aq or chain Ar selection = chain As or chain At or chain Au selection = chain Av or chain Aw or chain Ax }""" phil_str2 = """\ ncs_group { reference = chain Aa or chain Ab selection = chain Ad or chain Ae selection = chain Ag or chain Ah selection = chain Aj or chain Ak selection = chain Am or chain An selection = chain Ap or chain Aq selection = chain As or chain At selection = chain Av or chain Aw }""" phil_str3 = """\ ncs_group { reference = chain Aj selection = chain Am selection = chain Ap } """ phil_str4 = """\ ncs_group { reference = chain Aj selection = chain Am selection = chain Ap } ncs_group { reference = chain Aa selection = chain Ad selection = chain Av } """ pdb_h = iotbx.pdb.input( source_info=None,lines=pdb_str_a_lot_of_ncs.split('\n')).\ construct_hierarchy() # show file: # pdb_h.write_pdb_file("user_ncs_phil_ex11.pdb") asc = pdb_h.atom_selection_cache() ncs_groups = get_ncs_groups(phil_str1, pdb_str_a_lot_of_ncs) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 7 assert ncs_groups[0].master_iselection == asc.iselection( "chain Aa or chain Ab or chain Ac") for i, s_str in enumerate([ "chain Ad or chain Ae or chain Af", "chain Ag or chain Ah or chain Ai", "chain Aj or chain Ak or chain Al", "chain Am or chain An or chain Ao", "chain Ap or chain Aq or chain Ar", "chain As or chain At or chain Au", "chain Av or chain Aw or chain Ax"]): assert approx_equal(ncs_groups[0].copies[i].iselection, asc.iselection(s_str)) # Now we want only 2 chains from each selection ncs_groups = get_ncs_groups(phil_str2, pdb_str_a_lot_of_ncs) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 7 assert ncs_groups[0].master_iselection == asc.iselection( "chain Aa or chain Ab") for i, s_str in enumerate([ "chain Ad or chain Ae", "chain Ag or chain Ah", "chain Aj or chain Ak", "chain Am or chain An", "chain Ap or chain Aq", "chain As or chain At", "chain Av or chain Aw"]): assert approx_equal(ncs_groups[0].copies[i].iselection, asc.iselection(s_str)) # User is greedy ncs_groups = get_ncs_groups(phil_str3, pdb_str_a_lot_of_ncs) assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 2 assert approx_equal(ncs_groups[0].master_iselection, asc.iselection("chain Aj")) assert approx_equal(ncs_groups[0].copies[0].iselection, asc.iselection("chain Am")) assert approx_equal(ncs_groups[0].copies[1].iselection, asc.iselection("chain Ap")) # Two groups ncs_groups = get_ncs_groups(phil_str4, pdb_str_a_lot_of_ncs) assert len(ncs_groups) == 2 assert len(ncs_groups[0].copies) == 2 assert len(ncs_groups[1].copies) == 2 assert approx_equal(ncs_groups[0].master_iselection, asc.iselection("chain Aj")) assert approx_equal(ncs_groups[0].copies[0].iselection, asc.iselection("chain Am")) assert approx_equal(ncs_groups[0].copies[1].iselection, asc.iselection("chain Ap")) assert approx_equal(ncs_groups[1].master_iselection, asc.iselection("chain Aa")) assert approx_equal(ncs_groups[1].copies[0].iselection, asc.iselection("chain Ad")) assert approx_equal(ncs_groups[1].copies[1].iselection, asc.iselection("chain Av")) def exercise_12(): """ User's ncs_group is separated into several groups by validation procedure. """ pdb_str = """\ CRYST1 595.620 595.620 595.620 90.00 90.00 90.00 I 2 3 SCALE1 0.001679 0.000000 0.000000 0.00000 SCALE2 0.000000 0.001679 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001679 0.00000 ATOM 266 N LEU 1 20 -63.533-187.068-206.553 1.00 47.37 N ATOM 267 CA LEU 1 20 -64.594-187.999-206.894 1.00 38.42 C ATOM 268 C LEU 1 20 -64.792-189.093-205.863 1.00 40.45 C ATOM 269 O LEU 1 20 -65.844-189.739-205.864 1.00 37.26 O ATOM 270 CB LEU 1 20 -64.312-188.680-208.230 1.00 38.09 C ATOM 271 CG LEU 1 20 -63.920-187.774-209.381 1.00 40.19 C ATOM 272 CD1 LEU 1 20 -63.950-188.678-210.596 1.00 39.43 C ATOM 273 CD2 LEU 1 20 -64.787-186.534-209.581 1.00 33.28 C ATOM 285 N THR 1 21 -63.827-189.307-204.987 1.00 45.58 N ATOM 286 CA THR 1 21 -63.813-190.421-204.050 1.00 39.34 C ATOM 287 C THR 1 21 -63.827-189.887-202.615 1.00 39.90 C ATOM 288 O THR 1 21 -63.742-188.677-202.358 1.00 36.18 O ATOM 289 CB THR 1 21 -62.584-191.313-204.320 1.00 49.62 C ATOM 290 OG1 THR 1 21 -61.390-190.515-204.234 1.00 52.31 O ATOM 291 CG2 THR 1 21 -62.664-191.988-205.729 1.00 38.87 C ATOM 299 N ARG 1 22 -63.976-190.808-201.669 1.00 47.15 N ATOM 300 CA ARG 1 22 -64.297-190.439-200.299 1.00 45.35 C ATOM 301 C ARG 1 22 -63.888-191.595-199.403 1.00 44.05 C ATOM 302 O ARG 1 22 -64.251-192.746-199.674 1.00 47.23 O ATOM 303 CB ARG 1 22 -65.799-190.145-200.267 1.00 50.32 C ATOM 304 CG ARG 1 22 -66.470-189.595-199.030 1.00 48.26 C ATOM 305 CD ARG 1 22 -67.916-189.242-199.482 1.00 71.42 C ATOM 306 NE ARG 1 22 -68.807-188.659-198.474 1.00 89.96 N ATOM 307 CZ ARG 1 22 -70.012-188.139-198.752 1.00 89.76 C ATOM 308 NH1 ARG 1 22 -70.490-188.125-200.004 1.00 72.83 N ATOM 309 NH2 ARG 1 22 -70.755-187.629-197.765 1.00 72.15 N ATOM 323 N ALA 1 23 -63.090-191.310-198.380 1.00 31.79 N ATOM 324 CA ALA 1 23 -62.661-192.357-197.458 1.00 37.78 C ATOM 325 C ALA 1 23 -63.777-192.758-196.478 1.00 41.29 C ATOM 326 O ALA 1 23 -64.556-191.929-195.997 1.00 41.52 O ATOM 327 CB ALA 1 23 -61.432-191.902-196.679 1.00 34.84 C ATOM 333 N LEU 1 24 -63.865-194.045-196.194 1.00 37.34 N ATOM 334 CA LEU 1 24 -64.861-194.553-195.277 1.00 27.60 C ATOM 335 C LEU 1 24 -64.182-195.423-194.245 1.00 35.82 C ATOM 336 O LEU 1 24 -63.148-196.034-194.520 1.00 42.04 O ATOM 337 CB LEU 1 24 -65.902-195.408-195.995 1.00 41.37 C ATOM 338 CG LEU 1 24 -66.637-194.703-197.121 1.00 45.57 C ATOM 339 CD1 LEU 1 24 -67.524-195.709-197.954 1.00 28.75 C ATOM 340 CD2 LEU 1 24 -67.430-193.557-196.482 1.00 26.24 C ATOM 352 N PRO 1 25 -64.769-195.542-193.072 1.00 43.07 N ATOM 353 CA PRO 1 25 -64.203-196.455-192.080 1.00 45.02 C ATOM 354 C PRO 1 25 -64.368-197.875-192.575 1.00 28.49 C ATOM 355 O PRO 1 25 -65.337-198.184-193.276 1.00 23.83 O ATOM 356 CB PRO 1 25 -65.031-196.189-190.827 1.00 42.63 C ATOM 357 CG PRO 1 25 -66.337-195.696-191.405 1.00 34.61 C ATOM 358 CD PRO 1 25 -65.960-194.851-192.567 1.00 25.43 C TER ATOM A0BF2 N THRGA 20 -52.224 -82.892-121.524 1.00 32.92 N ATOM A0BF3 CA THRGA 20 -53.561 -83.049-120.966 1.00 35.79 C ATOM A0BF4 C THRGA 20 -54.347 -84.185-121.629 1.00 43.91 C ATOM A0BF5 O THRGA 20 -55.534 -84.024-121.903 1.00 55.90 O ATOM A0BF6 CB THRGA 20 -54.363 -81.742-121.088 1.00 32.17 C ATOM A0BF7 OG1 THRGA 20 -54.607 -81.451-122.480 1.00 27.96 O ATOM A0BF8 CG2 THRGA 20 -53.683 -80.551-120.374 1.00 31.79 C ATOM A0BFG N GLUGA 21 -53.739 -85.326-121.965 1.00 56.34 N ATOM A0BFH CA GLUGA 21 -54.586 -86.501-122.243 1.00 51.10 C ATOM A0BFI C GLUGA 21 -54.919 -87.215-120.943 1.00 54.73 C ATOM A0BFJ O GLUGA 21 -54.108 -87.260-120.010 1.00 42.85 O ATOM A0BFK CB GLUGA 21 -54.002 -87.549-123.220 1.00 30.90 C ATOM A0BFL CG GLUGA 21 -54.033 -87.190-124.724 1.00 50.79 C ATOM A0BFM CD GLUGA 21 -52.748 -86.608-125.203 1.00 85.38 C ATOM A0BFN OE1 GLUGA 21 -52.055 -85.975-124.369 1.00 95.33 O ATOM A0BFO OE2 GLUGA 21 -52.502 -86.706-126.435 1.00 76.32 O ATOM A0BFV N GLYGA 22 -56.107 -87.813-120.913 1.00 62.38 N ATOM A0BFW CA GLYGA 22 -56.653 -88.413-119.710 1.00 46.07 C ATOM A0BFX C GLYGA 22 -57.080 -87.396-118.680 1.00 65.93 C ATOM A0BFY O GLYGA 22 -56.984 -87.663-117.475 1.00 63.56 O ATOM A0BG2 N SERGA 23 -57.542 -86.227-119.121 1.00 75.27 N ATOM A0BG3 CA SERGA 23 -57.933 -85.143-118.234 1.00 63.26 C ATOM A0BG4 C SERGA 23 -59.451 -85.070-118.142 1.00 85.09 C ATOM A0BG5 O SERGA 23 -60.193 -85.512-119.030 1.00 74.26 O ATOM A0BG6 CB SERGA 23 -57.360 -83.796-118.689 1.00 62.39 C ATOM A0BG7 OG SERGA 23 -55.986 -83.921-119.034 1.00 78.01 O ATOM A0BGD N THRGA 24 -59.887 -84.512-117.033 1.00103.11 N ATOM A0BGE CA THRGA 24 -61.286 -84.324-116.713 1.00 96.25 C ATOM A0BGF C THRGA 24 -61.901 -83.158-117.487 1.00 95.46 C ATOM A0BGG O THRGA 24 -63.067 -82.845-117.236 1.00 94.00 O ATOM A0BGH CB THRGA 24 -61.420 -84.124-115.185 1.00 96.30 C ATOM A0BGI OG1 THRGA 24 -62.797 -83.996-114.836 1.00102.74 O ATOM A0BGJ CG2 THRGA 24 -60.614 -82.887-114.622 1.00 80.83 C ATOM A0BGR N ILEGA 25 -61.158 -82.541-118.421 1.00 92.73 N ATOM A0BGS CA ILEGA 25 -61.639 -81.451-119.271 1.00 85.74 C ATOM A0BGT C ILEGA 25 -61.603 -81.911-120.740 1.00 81.39 C ATOM A0BGU O ILEGA 25 -60.740 -82.708-121.136 1.00 75.57 O ATOM A0BGV CB ILEGA 25 -60.844 -80.121-119.029 1.00 78.83 C ATOM A0BGW CG1 ILEGA 25 -60.850 -79.715-117.527 1.00 81.73 C ATOM A0BGX CG2 ILEGA 25 -61.406 -78.934-119.840 1.00 76.17 C ATOM A0BGY CD1 ILEGA 25 -59.934 -78.530-117.162 1.00 70.88 C TER ATOM A1OYJ N THRAB 20 -34.601-167.170-165.019 1.00 47.42 N ATOM A1OYK CA THRAB 20 -35.664-166.423-165.675 1.00 38.19 C ATOM A1OYL C THRAB 20 -36.920-166.289-164.808 1.00 43.55 C ATOM A1OYM O THRAB 20 -38.028-166.342-165.336 1.00 58.60 O ATOM A1OYN CB THRAB 20 -36.026-167.082-167.013 1.00 37.29 C ATOM A1OYO OG1 THRAB 20 -36.609-168.396-166.811 1.00 34.65 O ATOM A1OYP CG2 THRAB 20 -34.819-167.200-167.905 1.00 47.27 C ATOM A1OYX N GLUAB 21 -36.809-166.114-163.487 1.00 40.30 N ATOM A1OYY CA GLUAB 21 -37.997-165.653-162.772 1.00 40.72 C ATOM A1OYZ C GLUAB 21 -38.098-164.151-162.911 1.00 56.45 C ATOM A1OZ0 O GLUAB 21 -37.095-163.439-163.057 1.00 48.83 O ATOM A1OZ1 CB GLUAB 21 -38.090-166.019-161.270 1.00 35.24 C ATOM A1OZ2 CG GLUAB 21 -38.502-167.478-160.944 1.00 54.14 C ATOM A1OZ3 CD GLUAB 21 -37.345-168.335-160.677 1.00 80.61 C ATOM A1OZ4 OE1 GLUAB 21 -36.278-168.016-161.240 1.00 92.19 O ATOM A1OZ5 OE2 GLUAB 21 -37.542-169.372-160.000 1.00 74.27 O ATOM A1OZC N GLYAB 22 -39.335-163.681-162.903 1.00 58.92 N ATOM A1OZD CA GLYAB 22 -39.594-162.287-163.140 1.00 48.41 C ATOM A1OZE C GLYAB 22 -39.333-161.886-164.568 1.00 61.25 C ATOM A1OZF O GLYAB 22 -38.868-160.772-164.828 1.00 52.03 O ATOM A1OZJ N SERAB 23 -39.573-162.785-165.504 1.00 81.16 N ATOM A1OZK CA SERAB 23 -39.313-162.516-166.905 1.00 71.05 C ATOM A1OZL C SERAB 23 -40.624-162.236-167.624 1.00 79.99 C ATOM A1OZM O SERAB 23 -41.718-162.618-167.190 1.00 75.06 O ATOM A1OZN CB SERAB 23 -38.567-163.682-167.576 1.00 68.18 C ATOM A1OZO OG SERAB 23 -37.509-164.144-166.746 1.00 77.85 O ATOM A1OZU N THRAB 24 -40.481-161.521-168.708 1.00 89.58 N ATOM A1OZV CA THRAB 24 -41.586-161.179-169.573 1.00 91.58 C ATOM A1OZW C THRAB 24 -42.024-162.351-170.470 1.00 98.61 C ATOM A1OZX O THRAB 24 -42.893-162.146-171.321 1.00100.89 O ATOM A1OZY CB THRAB 24 -41.175-159.953-170.402 1.00 91.75 C ATOM A1OZZ OG1 THRAB 24 -42.261-159.554-171.238 1.00103.20 O ATOM A1P00 CG2 THRAB 24 -39.878-160.193-171.260 1.00 77.23 C ATOM A1P08 N ILEAB 25 -41.467-163.557-170.293 1.00 96.60 N ATOM A1P09 CA ILEAB 25 -41.834-164.747-171.060 1.00 81.06 C ATOM A1P0A C ILEAB 25 -42.395-165.793-170.099 1.00 77.96 C ATOM A1P0B O ILEAB 25 -41.993-165.860-168.929 1.00 71.48 O ATOM A1P0C CB ILEAB 25 -40.641-165.307-171.895 1.00 82.14 C ATOM A1P0D CG1 ILEAB 25 -40.019-164.206-172.805 1.00 85.32 C ATOM A1P0E CG2 ILEAB 25 -41.071-166.508-172.747 1.00 75.75 C ATOM A1P0F CD1 ILEAB 25 -38.682-164.562-173.521 1.00 64.61 C TER ATOM A1ZO1 N LEUFB 20 -117.661-248.006-174.897 1.00 48.46 N ATOM A1ZO2 CA LEUFB 20 -116.344-247.393-174.779 1.00 31.10 C ATOM A1ZO3 C LEUFB 20 -115.899-246.648-176.028 1.00 42.66 C ATOM A1ZO4 O LEUFB 20 -114.898-245.929-175.971 1.00 40.76 O ATOM A1ZO5 CB LEUFB 20 -115.276-248.441-174.508 1.00 31.04 C ATOM A1ZO6 CG LEUFB 20 -115.569-249.438-173.423 1.00 43.61 C ATOM A1ZO7 CD1 LEUFB 20 -114.283-250.230-173.234 1.00 48.24 C ATOM A1ZO8 CD2 LEUFB 20 -116.061-248.825-172.115 1.00 38.75 C ATOM A1ZOK N THRFB 21 -116.547-246.866-177.163 1.00 55.85 N ATOM A1ZOL CA THRFB 21 -116.140-246.297-178.441 1.00 43.47 C ATOM A1ZOM C THRFB 21 -117.270-245.418-178.984 1.00 51.67 C ATOM A1ZON O THRFB 21 -118.375-245.353-178.434 1.00 50.72 O ATOM A1ZOO CB THRFB 21 -115.774-247.401-179.425 1.00 33.43 C ATOM A1ZOP OG1 THRFB 21 -116.920-248.240-179.614 1.00 50.93 O ATOM A1ZOQ CG2 THRFB 21 -114.581-248.247-178.851 1.00 26.17 C ATOM A1ZOY N ARGFB 22 -116.980-244.715-180.072 1.00 49.13 N ATOM A1ZOZ CA ARGFB 22 -117.818-243.600-180.478 1.00 35.40 C ATOM A1ZP0 C ARGFB 22 -117.553-243.328-181.949 1.00 44.20 C ATOM A1ZP1 O ARGFB 22 -116.395-243.146-182.343 1.00 41.59 O ATOM A1ZP2 CB ARGFB 22 -117.441-242.430-179.578 1.00 49.27 C ATOM A1ZP3 CG ARGFB 22 -118.165-241.112-179.677 1.00 59.06 C ATOM A1ZP4 CD ARGFB 22 -117.649-240.290-178.480 1.00 81.73 C ATOM A1ZP5 NE ARGFB 22 -118.235-238.966-178.278 1.00 93.03 N ATOM A1ZP6 CZ ARGFB 22 -118.016-238.230-177.181 1.00 94.32 C ATOM A1ZP7 NH1 ARGFB 22 -117.217-238.667-176.191 1.00 76.59 N ATOM A1ZP8 NH2 ARGFB 22 -118.595-237.036-177.072 1.00 78.59 N ATOM A1ZPM N ALAFB 23 -118.604-243.290-182.762 1.00 39.74 N ATOM A1ZPN CA ALAFB 23 -118.401-243.076-184.189 1.00 40.06 C ATOM A1ZPO C ALAFB 23 -118.078-241.613-184.495 1.00 42.35 C ATOM A1ZPP O ALAFB 23 -118.587-240.687-183.861 1.00 44.55 O ATOM A1ZPQ CB ALAFB 23 -119.627-243.535-184.974 1.00 39.71 C ATOM A1ZPW N LEUFB 24 -117.174-241.404-185.439 1.00 44.81 N ATOM A1ZPX CA LEUFB 24 -116.769-240.066-185.835 1.00 35.11 C ATOM A1ZPY C LEUFB 24 -116.826-239.893-187.335 1.00 40.09 C ATOM A1ZPZ O LEUFB 24 -116.660-240.858-188.085 1.00 51.80 O ATOM A1ZQ0 CB LEUFB 24 -115.345-239.756-185.414 1.00 42.69 C ATOM A1ZQ1 CG LEUFB 24 -115.154-239.849-183.909 1.00 55.89 C ATOM A1ZQ2 CD1 LEUFB 24 -113.661-239.714-183.568 1.00 33.93 C ATOM A1ZQ3 CD2 LEUFB 24 -116.049-238.781-183.220 1.00 35.88 C ATOM A1ZQF N PROFB 25 -117.004-238.671-187.801 1.00 40.39 N ATOM A1ZQG CA PROFB 25 -117.007-238.457-189.243 1.00 49.95 C ATOM A1ZQH C PROFB 25 -115.622-238.648-189.848 1.00 35.64 C ATOM A1ZQI O PROFB 25 -114.604-238.253-189.273 1.00 21.90 O ATOM A1ZQJ CB PROFB 25 -117.529-237.028-189.377 1.00 36.12 C ATOM A1ZQK CG PROFB 25 -117.210-236.413-188.096 1.00 26.49 C ATOM A1ZQL CD PROFB 25 -117.424-237.464-187.089 1.00 32.95 C TER END """ phil_str1 = """\ ncs_group { reference = chain 1 selection = chain FB selection = chain AB selection = chain GA } """ pdb_h = iotbx.pdb.input( source_info=None,lines=pdb_str.split('\n')).\ construct_hierarchy() # show file: # pdb_h.write_pdb_file("user_ncs_phil_ex12.pdb") asc = pdb_h.atom_selection_cache() ncs_groups = get_ncs_groups(phil_str1, pdb_str) # ncs_groups._show() assert len(ncs_groups) == 2 assert len(ncs_groups[0].copies) == 1 assert len(ncs_groups[1].copies) == 1 # from iotbx.pdb.atom_selection import selection_string_from_selection # print list(ncs_groups[0].master_iselection) # print list(asc.iselection("chain 1")) # print selection_string_from_selection(pdb_h, ncs_groups[0].master_iselection) # print selection_string_from_selection(pdb_h, ncs_groups[0].copies[0].iselection) # STOP() assert approx_equal(ncs_groups[1].master_iselection, asc.iselection("chain AB")) assert approx_equal(ncs_groups[1].copies[0].iselection, asc.iselection("chain GA")) assert approx_equal(ncs_groups[0].master_iselection, asc.iselection("chain 1")) assert approx_equal(ncs_groups[0].copies[0].iselection, asc.iselection("chain FB")) if (__name__ == "__main__"): t0=time.time() exercise_1() exercise_2() exercise_3() exercise_4() # exercise_5() #temp disabled. Need to tweak selection_string_from_selection # in atom_selection.py exercise_6() exercise_7() exercise_8() exercise_9() exercise_10() exercise_11() exercise_12() print("Time: %6.4f"%(time.time()-t0)) print("OK")