from __future__ import absolute_import, division, print_function from libtbx import easy_run import libtbx.load_env import os.path import time # taken from 3zee multiplied pdb_str = """\ CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 ATOM 114 N VALA1 13 28.866 7.875-103.684 1.00 0.00 N ATOM 115 CA VALA1 13 27.966 7.696-104.717 1.00 0.00 C ATOM 116 C VALA1 13 28.923 7.301-105.774 1.00 0.00 C ATOM 117 O VALA1 13 29.996 7.851-105.765 1.00 0.00 O ATOM 118 CB VALA1 13 27.357 9.044-105.115 1.00 0.00 C ATOM 119 CG1 VALA1 13 28.173 10.400-104.901 1.00 0.00 C ATOM 120 CG2 VALA1 13 26.772 9.026-106.573 1.00 0.00 C ATOM 121 N VALA1 14 28.597 6.282-106.581 1.00 0.00 N ATOM 122 CA VALA1 14 29.479 5.817-107.556 1.00 0.00 C ATOM 123 C VALA1 14 28.731 5.902-108.820 1.00 0.00 C ATOM 124 O VALA1 14 27.735 5.291-108.935 1.00 0.00 O ATOM 125 CB VALA1 14 29.816 4.426-107.266 1.00 0.00 C ATOM 126 CG1 VALA1 14 30.981 4.043-108.197 1.00 0.00 C ATOM 127 CG2 VALA1 14 30.218 4.344-105.790 1.00 0.00 C ATOM 128 N PROA1 15 29.286 6.585-109.794 1.00 0.00 N ATOM 129 CA PROA1 15 28.744 6.599-111.104 1.00 0.00 C ATOM 130 C PROA1 15 29.165 5.280-111.724 1.00 0.00 C ATOM 131 O PROA1 15 30.277 4.833-111.335 1.00 0.00 O ATOM 132 CB PROA1 15 29.324 7.870-111.770 1.00 0.00 C ATOM 133 CG PROA1 15 30.683 7.956-111.088 1.00 0.00 C ATOM 134 CD PROA1 15 30.341 7.551-109.692 1.00 0.00 C ATOM 135 N CYSA1 16 28.318 4.535-112.451 1.00 0.00 N ATOM 136 CA CYSA1 16 28.758 3.175-112.680 1.00 0.00 C ATOM 137 C CYSA1 16 28.739 2.854-114.087 1.00 0.00 C ATOM 138 O CYSA1 16 28.894 1.759-114.604 1.00 0.00 O ATOM 139 CB CYSA1 16 27.905 2.251-111.855 1.00 0.00 C ATOM 140 SG CYSA1 16 28.255 2.522-110.159 1.00 0.00 S ATOM 141 N GLYA1 17 28.299 3.834-114.840 1.00 0.00 N ATOM 142 CA GLYA1 17 27.972 3.877-116.194 1.00 0.00 C ATOM 143 C GLYA1 17 27.015 2.770-116.530 1.00 0.00 C ATOM 144 O GLYA1 17 25.791 3.024-116.400 1.00 0.00 O ATOM 145 N ASPA1 18 27.485 1.673-117.088 1.00 0.00 N ATOM 146 CA ASPA1 18 26.581 0.717-117.651 1.00 0.00 C ATOM 147 C ASPA1 18 26.603 -0.454-116.677 1.00 0.00 C ATOM 148 O ASPA1 18 25.726 -1.309-116.715 1.00 0.00 O ATOM 149 CB ASPA1 18 27.058 0.127-118.978 1.00 0.00 C ATOM 150 CG ASPA1 18 25.941 -0.447-119.867 1.00 0.00 C ATOM 151 OD1 ASPA1 18 25.283 -1.471-119.437 1.00 0.00 O ATOM 152 OD2 ASPA1 18 25.763 0.055-120.988 1.00 0.00 O ATOM 153 N GLYA1 19 27.598 -0.551-115.748 1.00 0.00 N ATOM 154 CA GLYA1 19 27.850 -1.623-114.809 1.00 0.00 C ATOM 155 C GLYA1 19 28.483 -2.857-115.392 1.00 0.00 C ATOM 156 O GLYA1 19 28.602 -3.897-114.714 1.00 0.00 O ATOM 157 N ARGA1 20 28.884 -2.776-116.690 1.00 0.00 N ATOM 158 CA ARGA1 20 29.503 -3.853-117.351 1.00 0.00 C ATOM 159 C ARGA1 20 30.956 -3.624-117.090 1.00 0.00 C ATOM 160 O ARGA1 20 31.604 -2.729-117.659 1.00 0.00 O ATOM 161 CB ARGA1 20 29.135 -3.792-118.837 1.00 0.00 C ATOM 162 CG ARGA1 20 27.632 -4.042-119.004 1.00 0.00 C ATOM 163 CD ARGA1 20 27.125 -5.547-118.721 1.00 0.00 C ATOM 164 NE ARGA1 20 27.534 -6.358-119.907 1.00 0.00 N ATOM 165 CZ ARGA1 20 28.739 -6.931-119.948 1.00 0.00 C ATOM 166 NH1 ARGA1 20 29.387 -7.363-118.805 1.00 0.00 N ATOM 167 NH2 ARGA1 20 29.293 -7.238-121.145 1.00 0.00 N ATOM 168 N META1 21 31.444 -4.500-116.136 1.00 0.00 N ATOM 169 CA META1 21 32.768 -4.515-115.553 1.00 0.00 C ATOM 170 C META1 21 32.830 -5.593-114.505 1.00 0.00 C ATOM 171 O META1 21 31.843 -5.906-113.868 1.00 0.00 O ATOM 172 CB META1 21 32.981 -3.224-114.734 1.00 0.00 C ATOM 173 CG META1 21 34.438 -2.959-114.287 1.00 0.00 C ATOM 174 SD META1 21 34.506 -2.151-112.763 1.00 0.00 S ATOM 175 CE META1 21 34.190 -0.475-113.397 1.00 0.00 C ATOM 176 N LYSA1 22 34.049 -6.099-114.200 1.00 0.00 N ATOM 177 CA LYSA1 22 34.284 -6.987-113.056 1.00 0.00 C ATOM 178 C LYSA1 22 34.369 -6.049-111.900 1.00 0.00 C ATOM 179 O LYSA1 22 34.435 -4.865-112.055 1.00 0.00 O ATOM 180 CB LYSA1 22 35.583 -7.836-113.206 1.00 0.00 C ATOM 181 CG LYSA1 22 35.330 -9.254-113.722 1.00 0.00 C ATOM 182 CD LYSA1 22 36.457 -10.351-113.280 1.00 0.00 C ATOM 183 CE LYSA1 22 35.864 -11.774-113.255 1.00 0.00 C ATOM 184 NZ LYSA1 22 36.511 -12.735-112.250 1.00 0.00 N TER ATOM 784 N VALA2 13 26.276 -14.311-100.152 1.00 0.00 N ATOM 785 CA VALA2 13 25.503 -13.817-101.185 1.00 0.00 C ATOM 786 C VALA2 13 25.920 -14.765-102.242 1.00 0.00 C ATOM 787 O VALA2 13 27.074 -15.112-102.233 1.00 0.00 O ATOM 788 CB VALA2 13 25.997 -12.423-101.583 1.00 0.00 C ATOM 789 CG1 VALA2 13 27.525 -12.011-101.369 1.00 0.00 C ATOM 790 CG2 VALA2 13 25.563 -12.031-103.041 1.00 0.00 C ATOM 791 N VALA2 14 24.979 -15.275-103.049 1.00 0.00 N ATOM 792 CA VALA2 14 25.293 -16.221-104.024 1.00 0.00 C ATOM 793 C VALA2 14 24.813 -15.641-105.288 1.00 0.00 C ATOM 794 O VALA2 14 23.671 -15.392-105.403 1.00 0.00 O ATOM 795 CB VALA2 14 24.573 -17.458-103.734 1.00 0.00 C ATOM 796 CG1 VALA2 14 25.148 -18.540-104.665 1.00 0.00 C ATOM 797 CG2 VALA2 14 24.806 -17.795-102.258 1.00 0.00 C ATOM 798 N PROA2 15 25.685 -15.533-106.262 1.00 0.00 N ATOM 799 CA PROA2 15 25.304 -15.148-107.572 1.00 0.00 C ATOM 800 C PROA2 15 24.695 -16.390-108.192 1.00 0.00 C ATOM 801 O PROA2 15 25.187 -17.483-107.803 1.00 0.00 O ATOM 802 CB PROA2 15 26.603 -14.632-108.238 1.00 0.00 C ATOM 803 CG PROA2 15 27.643 -15.511-107.556 1.00 0.00 C ATOM 804 CD PROA2 15 27.116 -15.567-106.160 1.00 0.00 C ATOM 805 N CYSA2 16 23.568 -16.341-108.919 1.00 0.00 N ATOM 806 CA CYSA2 16 22.944 -17.627-109.148 1.00 0.00 C ATOM 807 C CYSA2 16 22.707 -17.845-110.555 1.00 0.00 C ATOM 808 O CYSA2 16 22.061 -18.743-111.072 1.00 0.00 O ATOM 809 CB CYSA2 16 21.688 -17.702-108.323 1.00 0.00 C ATOM 810 SG CYSA2 16 22.128 -17.749-106.627 1.00 0.00 S ATOM 811 N GLYA2 17 23.069 -16.834-111.308 1.00 0.00 N ATOM 812 CA GLYA2 17 22.862 -16.576-112.662 1.00 0.00 C ATOM 813 C GLYA2 17 21.406 -16.712-112.998 1.00 0.00 C ATOM 814 O GLYA2 17 20.698 -15.681-112.868 1.00 0.00 O ATOM 815 N ASPA2 18 20.985 -17.829-113.556 1.00 0.00 N ATOM 816 CA ASPA2 18 19.670 -17.892-114.119 1.00 0.00 C ATOM 817 C ASPA2 18 18.875 -18.753-113.145 1.00 0.00 C ATOM 818 O ASPA2 18 17.651 -18.762-113.183 1.00 0.00 O ATOM 819 CB ASPA2 18 19.605 -18.648-115.446 1.00 0.00 C ATOM 820 CG ASPA2 18 18.403 -18.289-116.335 1.00 0.00 C ATOM 821 OD1 ASPA2 18 17.219 -18.571-115.905 1.00 0.00 O ATOM 822 OD2 ASPA2 18 18.622 -17.803-117.456 1.00 0.00 O ATOM 823 N GLYA2 19 19.526 -19.511-112.216 1.00 0.00 N ATOM 824 CA GLYA2 19 18.965 -20.459-111.277 1.00 0.00 C ATOM 825 C GLYA2 19 18.567 -21.788-111.860 1.00 0.00 C ATOM 826 O GLYA2 19 17.933 -22.621-111.182 1.00 0.00 O ATOM 827 N ARGA2 20 18.912 -22.007-113.158 1.00 0.00 N ATOM 828 CA ARGA2 20 18.614 -23.213-113.819 1.00 0.00 C ATOM 829 C ARGA2 20 19.820 -24.054-113.558 1.00 0.00 C ATOM 830 O ARGA2 20 20.907 -23.857-114.127 1.00 0.00 O ATOM 831 CB ARGA2 20 18.390 -22.914-115.305 1.00 0.00 C ATOM 832 CG ARGA2 20 17.132 -22.053-115.472 1.00 0.00 C ATOM 833 CD ARGA2 20 15.724 -22.788-115.189 1.00 0.00 C ATOM 834 NE ARGA2 20 15.458 -23.656-116.375 1.00 0.00 N ATOM 835 CZ ARGA2 20 15.930 -24.904-116.416 1.00 0.00 C ATOM 836 NH1 ARGA2 20 16.099 -25.664-115.273 1.00 0.00 N ATOM 837 NH2 ARGA2 20 16.117 -25.509-117.613 1.00 0.00 N ATOM 838 N META2 21 19.565 -25.024-112.604 1.00 0.00 N ATOM 839 CA META2 21 20.509 -25.952-112.021 1.00 0.00 C ATOM 840 C META2 21 19.807 -26.772-110.973 1.00 0.00 C ATOM 841 O META2 21 18.879 -26.314-110.336 1.00 0.00 O ATOM 842 CB META2 21 21.558 -25.168-111.202 1.00 0.00 C ATOM 843 CG META2 21 22.792 -25.985-110.755 1.00 0.00 C ATOM 844 SD META2 21 23.400 -25.450-109.231 1.00 0.00 S ATOM 845 CE META2 21 24.334 -24.022-109.865 1.00 0.00 C ATOM 846 N LYSA2 22 20.337 -27.981-110.668 1.00 0.00 N ATOM 847 CA LYSA2 22 19.891 -28.784-109.524 1.00 0.00 C ATOM 848 C LYSA2 22 20.602 -28.167-108.368 1.00 0.00 C ATOM 849 O LYSA2 22 21.470 -27.358-108.523 1.00 0.00 O ATOM 850 CB LYSA2 22 20.240 -30.297-109.674 1.00 0.00 C ATOM 851 CG LYSA2 22 19.076 -31.144-110.190 1.00 0.00 C ATOM 852 CD LYSA2 22 19.129 -32.716-109.748 1.00 0.00 C ATOM 853 CE LYSA2 22 17.715 -33.332-109.723 1.00 0.00 C ATOM 854 NZ LYSA2 22 17.517 -34.473-108.718 1.00 0.00 N TER END """ def exercise_04(prefix="tst_mi_map_test_06"): """ Actually will try to CCD. Same as 05, but with NCS copies. Should include actual check for success. """ # without cryst pdb_file = open("%s_start.pdb" % prefix, "w") pdb_file.write(pdb_str) pdb_file.close() cmd = " ".join([ "phenix.model_idealization", "%s_start.pdb" % prefix, "use_map_for_reference=True", "run_minimization_first=False", "run_minimization_last=False", "loop_idealization.minimize_whole=False", "loop_idealization.number_of_ccd_trials=1", "number_of_refinement_cycles=1", "n_macro=1", "debug=True", # ">%s.log" % prefix, ]) print(cmd) assert not easy_run.call(cmd) # assert os.path.isfile("%s_start.pdb_all_idealized.pdb" % prefix) res_log = open("%s_start.pdb.log" % prefix, "r") log_lines = res_log.readlines() res_log.close() # NCS constraints with map are not implemented yet # should be there for l in [ "Using ncs\n", "Idealizing chain A1\n", # 'Working on pdbres="VALA1 13 " OUTLIER\n', # "Using map as reference\n", # " Minimizing... (NCS)\n", # "Ramachandran outliers: 0.00 0.00 0.00 0.00 0.00\n", # "Rotamer outliers : 12.50 12.50 12.50 12.50 0.00 0.00\n", "All done.\n"]: assert l in log_lines, "'%s' not in log file." % l # should not be there for l in [ "Idealizing chain A2\n", 'Working on pdbres="VALA2 13 " OUTLIER\n']: assert l not in log_lines, "'%s' should not be in log file." % l if (__name__ == "__main__"): t0 = time.time() if (not libtbx.env.has_module(name="probe")): print("Skipping: probe not configured") else: exercise_04() print("Time: %.2f" % (time.time() - t0)) print("OK")