from __future__ import absolute_import, division, print_function from scitbx.array_family import flex from scitbx.matrix import sqr from rstbx.diffraction.fastbragg import foo from rstbx.diffraction.fastbragg import detector,camera,crystal from rstbx.diffraction.fastbragg import fast_bragg_simulation import libtbx.load_env pdb_lines = """HEADER ELECTRON TRANSPORT 17-JAN-08 3BZ1 CRYST1 127.692 225.403 306.106 90.00 90.00 90.00 P 21 21 21 4 ATOM 100 CH2 TRP A 20 56.430 40.246 32.394 1.00 81.85 C ATOM 200 N PHE A 33 53.226 47.627 40.654 1.00 70.99 N ATOM 300 CD1 ILE A 46 45.639 29.364 40.352 1.00 64.65 C ATOM 400 CB ILE A 60 31.998 29.624 61.196 1.00 48.31 C ATOM 500 CZ TYR A 73 33.394 17.375 51.997 1.00 59.10 C ATOM 600 N ILE A 89 40.139 30.719 66.768 1.00 57.41 N ATOM 700 CB ALA A 100 48.660 18.955 63.036 1.00 50.19 C ATOM 800 OH TYR A 112 35.813 37.284 55.881 1.00 49.58 O ATOM 900 O CYS A 125 47.637 48.097 42.161 1.00 69.98 O ATOM 1000 CB ARG A 136 53.053 54.518 31.934 1.00 62.41 C ATOM 1100 O SER A 148 38.270 53.004 48.759 1.00 59.64 O ATOM 1200 OH TYR A 161 29.848 43.600 64.133 1.00 51.65 O ATOM 1300 CG1 ILE A 176 25.474 34.051 46.196 1.00 49.30 C ATOM 1400 C GLU A 189 24.280 45.586 66.763 1.00 54.83 C ATOM 1500 CB LEU A 200 25.906 59.092 53.794 1.00 57.65 C ATOM 1600 CD2 HIS A 215 26.386 60.725 30.820 1.00 66.14 C ATOM 1700 O GLU A 229 15.446 53.147 11.386 1.00 94.97 O ATOM 1800 OE1 GLN A 241 31.691 60.361 15.701 1.00 85.33 O ATOM 1900 CG TYR A 254 14.970 67.624 27.886 1.00 80.00 C ATOM 2000 CE1 PHE A 265 26.289 68.506 37.590 1.00 88.41 C ATOM 2100 N TRP A 278 29.660 62.229 43.659 1.00 63.59 N ATOM 2200 CG1 ILE A 290 29.934 48.592 56.874 1.00 56.42 C ATOM 2300 C ASN A 303 13.257 53.636 73.305 1.00 53.67 C ATOM 2400 CG2 THR A 316 7.855 57.090 68.127 1.00 58.80 C ATOM 2500 CB GLU A 329 19.451 40.098 69.217 1.00 49.38 C ATOM 2600 CA LEU A 341 25.291 40.222 77.420 1.00 58.62 C ATOM 2700 CD2 HIS B 9 10.231 39.622 13.536 1.00 61.64 C ATOM 2800 O HIS B 23 -1.741 36.161 13.565 1.00 73.51 O ATOM 2900 C MET B 37 -3.628 21.765 27.157 1.00 60.16 C ATOM 3000 N PRO B 50 -14.550 15.131 42.592 1.00 59.82 N ATOM 3100 CE2 PHE B 61 -3.211 29.588 31.858 1.00 36.72 C ATOM 3200 CG TRP B 75 -15.698 12.830 23.209 1.00 67.94 C ATOM 3300 CD PRO B 88 -20.869 13.773 26.882 1.00 88.90 C ATOM 3400 CG1 ILE B 101 -4.955 20.401 18.664 1.00 55.70 C ATOM 3500 CD2 HIS B 114 -3.854 35.717 4.227 1.00 76.12 C ATOM 3600 CD ARG B 124 1.132 49.272 -3.409 1.00 75.98 C ATOM 3700 CD LYS B 137 -13.446 52.508 4.977 1.00 81.73 C ATOM 3800 CB CYS B 150 -19.609 42.068 22.286 1.00 71.10 C ATOM 3900 N PRO B 164 -25.221 27.178 25.947 1.00 78.19 N ATOM 4000 CB SER B 177 -24.093 23.363 37.543 1.00 69.60 C ATOM 4100 CZ PHE B 190 -23.890 49.302 34.563 1.00 82.38 C ATOM 4200 C ALA B 204 -24.194 46.989 25.481 1.00 68.99 C ATOM 4300 CD2 LEU B 218 -21.126 54.934 7.329 1.00 70.45 C ATOM 4400 CG ARG B 230 2.163 61.215 14.361 1.00 77.19 C ATOM 4500 CB ALA B 244 -6.668 48.852 25.158 1.00 60.23 C ATOM 4600 CZ2 TRP B 257 -3.347 36.591 46.798 1.00 52.77 C ATOM 4700 C THR B 271 -8.867 33.510 49.162 1.00 53.31 C ATOM 4800 CD GLN B 281 -13.383 29.920 62.401 1.00 67.13 C ATOM 4900 CA SER B 294 -33.026 21.366 66.399 1.00 69.25 C ATOM 5000 OE2 GLU B 307 -14.800 13.540 54.306 1.00 68.45 O ATOM 5100 CD PRO B 319 -5.922 31.146 48.057 1.00 47.82 C ATOM 5200 N ASP B 334 0.902 19.258 50.198 1.00 44.55 N ATOM 5300 CA ARG B 347 -10.219 20.652 76.188 1.00 61.50 C ATOM 5400 CG ARG B 358 -7.285 29.120 62.704 1.00 50.92 C ATOM 5500 CB LEU B 370 -4.691 26.163 73.320 1.00 50.59 C ATOM 5600 CE2 PHE B 383 13.890 27.916 70.647 1.00 33.21 C ATOM 5700 N GLN B 395 -1.283 20.760 81.492 1.00 56.45 N ATOM 5800 N GLN B 409 -14.069 9.629 68.475 1.00 59.62 N ATOM 5900 O ALA B 421 -2.576 22.480 66.140 1.00 57.75 O ATOM 6000 C ASP B 433 -0.960 11.201 49.784 1.00 55.09 C ATOM 6100 N SER B 446 -2.763 27.862 44.195 1.00 50.25 N ATOM 6200 C PHE B 458 2.089 42.286 31.803 1.00 53.50 C ATOM 6300 CA HIS B 469 5.917 52.473 21.275 1.00 65.93 C ATOM 6400 C GLY B 481 18.369 63.066 15.911 1.00 86.80 C ATOM 6500 C GLU C 29 42.829 84.391 42.151 1.00 96.99 C ATOM 6600 N LEU C 42 49.063 79.537 47.972 1.00 80.65 N ATOM 6700 C HIS C 56 47.160 76.079 63.881 1.00 75.29 C ATOM 6800 CD1 LEU C 69 40.241 76.971 80.264 1.00 73.46 C ATOM 6900 CB MET C 81 37.685 59.675 83.702 1.00 66.57 C ATOM 7000 N THR C 94 47.149 59.964 83.079 1.00 72.30 N ATOM 7100 CG2 THR C 108 39.735 68.134 90.385 1.00 84.58 C ATOM 7200 CA SER C 121 49.614 80.118 74.233 1.00 71.01 C ATOM 7300 CB ARG C 135 50.883 92.723 59.014 1.00 88.70 C ATOM 7400 CA GLY C 148 62.945 81.923 53.170 1.00 86.41 C ATOM 7500 OG1 THR C 159 69.683 71.849 55.898 1.00 76.62 O ATOM 7600 CG LEU C 173 64.970 62.992 74.939 1.00 75.86 C ATOM 7700 CE2 TYR C 186 46.358 53.614 86.921 1.00 54.85 C ATOM 7800 O THR C 200 65.438 52.726 87.800 1.00 81.03 O ATOM 7900 CZ TYR C 212 57.265 45.691 74.323 1.00 64.32 C ATOM 8000 CG2 VAL C 225 48.991 48.489 68.817 1.00 54.23 C ATOM 8100 CG TRP C 239 66.638 53.123 72.325 1.00 79.64 C ATOM 8200 CB ILE C 252 71.570 69.941 60.611 1.00 88.29 C ATOM 8300 CD1 PHE C 264 60.724 60.118 48.299 1.00 79.04 C ATOM 8400 CG LEU C 276 48.684 64.549 53.259 1.00 64.89 C ATOM 8500 CG2 VAL C 290 41.832 54.897 72.981 1.00 57.48 C ATOM 8600 CZ PHE C 301 44.591 57.265 86.195 1.00 70.05 C ATOM 8700 C THR C 316 30.583 36.329 87.074 1.00 59.01 C ATOM 8800 CG2 VAL C 328 35.267 26.607 88.411 1.00 63.86 C ATOM 8900 CB ARG C 343 41.831 23.983 76.148 1.00 51.02 C ATOM 9000 CA ARG C 357 38.290 34.957 71.104 1.00 61.60 C ATOM 9100 C GLU C 367 46.540 37.293 87.483 1.00 64.97 C ATOM 9200 O ILE C 380 37.697 30.576 92.067 1.00 67.63 O ATOM 9300 O ARG C 391 35.039 45.120 86.966 1.00 60.78 O ATOM 9400 CD1 LEU C 404 27.268 58.766 66.001 1.00 57.48 C ATOM 9500 CB PHE C 419 27.493 55.491 79.223 1.00 67.79 C ATOM 9600 CD1 PHE C 431 40.201 52.507 60.945 1.00 57.40 C ATOM 9700 CG TRP C 443 43.756 64.474 45.968 1.00 75.60 C ATOM 9800 CA LYS C 457 46.056 69.932 33.682 1.00 75.97 C ATOM 9900 CG PRO C 470 53.283 49.954 20.292 1.00 81.53 C ATOM 10000 CG TRP D 21 -0.801 81.734 29.348 1.00 77.02 C ATOM 10100 CB TRP D 32 -0.735 70.313 28.373 1.00 71.40 C ATOM 10200 C LEU D 45 3.971 67.431 50.438 1.00 56.33 C ATOM 10300 NE1 TRP D 58 -3.948 56.069 71.824 1.00 63.14 N ATOM 10400 O CYS D 71 9.769 64.233 65.991 1.00 66.26 O ATOM 10500 CG MET D 85 -9.271 51.951 57.279 1.00 61.82 C ATOM 10600 CD GLN D 98 -20.334 58.870 58.371 1.00 79.48 C ATOM 10700 O TRP D 111 -1.668 57.883 50.989 1.00 55.61 O ATOM 10800 N GLY D 124 1.991 62.768 35.633 1.00 65.92 N ATOM 10900 CG LEU D 135 7.056 71.817 23.809 1.00 70.97 C ATOM 11000 CA PRO D 149 10.850 54.606 39.091 1.00 55.93 C ATOM 11100 CB PRO D 161 -0.735 47.345 49.987 1.00 48.29 C ATOM 11200 CZ PHE D 173 3.153 56.984 49.943 1.00 50.71 C ATOM 11300 CZ PHE D 185 7.181 43.691 50.494 1.00 37.45 C ATOM 11400 C HIS D 197 17.164 41.521 43.801 1.00 50.10 C ATOM 11500 CA ILE D 213 33.634 55.063 37.092 1.00 69.26 C ATOM 11600 N GLY D 226 43.193 75.028 28.981 1.00 80.84 N ATOM 11700 CG GLN D 239 28.634 70.306 20.768 1.00 96.48 C ATOM 11800 C PHE D 252 42.989 51.474 30.264 1.00 69.10 C ATOM 11900 CA LYS D 264 30.303 56.876 23.582 1.00 65.51 C ATOM 12000 N VAL D 274 21.376 49.633 32.352 1.00 59.67 N ATOM 12100 CA GLY D 288 5.063 38.350 43.091 1.00 51.26 C ATOM 12200 CB SER D 300 17.107 20.052 47.341 1.00 49.18 C ATOM 12300 OE1 GLU D 312 25.457 24.792 61.967 1.00 56.19 O ATOM 12400 O GLY D 324 11.625 37.142 65.784 1.00 50.64 O ATOM 12500 CE1 HIS D 336 -2.635 43.943 61.172 1.00 62.69 C ATOM 12600 CG ARG D 348 13.912 33.212 72.962 1.00 50.25 C ATOM 12700 CA ASP E 12 18.164 91.898 42.777 1.00 89.88 C ATOM 12800 CG HIS E 23 9.724 89.213 52.411 1.00 85.44 C ATOM 12900 CB LEU E 36 -0.117 81.291 67.900 1.00 70.26 C ATOM 13000 CG2 THR E 49 -1.179 64.296 67.834 1.00 61.18 C ATOM 13100 CB ARG E 61 -2.323 49.122 79.882 1.00 88.20 C ATOM 13200 CD LYS E 73 -17.743 60.195 61.429 1.00 74.64 C ATOM 13300 N VAL F 11 15.993 96.516 32.978 1.00 95.73 N ATOM 13400 O ALA F 22 5.710 78.633 45.555 1.00 73.32 O ATOM 13500 C GLY F 35 6.641 77.242 64.377 1.00 67.22 C ATOM 13600 CA ARG H 4 -6.132 42.027 -7.866 1.00 90.52 C ATOM 13700 ND2 ASN H 15 -6.361 49.254 1.776 1.00 81.21 N ATOM 13800 CA LEU H 30 -18.790 65.525 21.049 1.00 73.95 C ATOM 13900 CG LEU H 42 -14.264 53.453 33.427 1.00 79.57 C ATOM 14000 CD1 ILE H 54 -20.487 50.335 50.523 1.00 68.77 C ATOM 14100 CA GLU I 2 58.092 23.554 57.876 1.00 71.08 C ATOM 14200 CG PHE I 14 61.361 36.617 43.358 1.00 66.86 C ATOM 14300 C GLY I 26 62.908 55.772 38.054 1.00 78.38 C ATOM 14400 O PRO J 9 24.648 91.273 51.531 1.00 78.21 O ATOM 14500 CB VAL J 23 19.540 80.157 65.363 1.00 69.47 C ATOM 14600 CD1 LEU J 36 5.079 66.010 73.040 1.00 74.63 C ATOM 14700 CE2 PHE K 18 34.702 85.604 85.570 1.00 81.28 C ATOM 14800 CA PHE K 32 37.105 79.841 61.828 1.00 68.56 C ATOM 14900 C PHE K 45 35.499 84.515 44.358 1.00 84.69 C ATOM 15000 CB VAL L 10 19.568 40.277 10.480 1.00 81.89 C ATOM 15100 N LEU L 23 25.370 37.709 29.295 1.00 48.48 N ATOM 15200 CG PHE L 35 15.700 26.715 36.587 1.00 57.45 C ATOM 15300 CB ALA M 10 14.779 24.043 33.437 1.00 50.93 C ATOM 15400 CD1 ILE M 23 27.117 29.969 19.939 1.00 68.61 C ATOM 15500 OG1 THR O 30 59.852 28.238 88.273 1.00 86.55 O ATOM 15600 CB LYS O 44 52.660 18.801 77.543 1.00 63.87 C ATOM 15700 CG2 ILE O 58 49.231 3.465 101.214 1.00 92.18 C ATOM 15800 CA LEU O 71 45.849 12.711 81.045 1.00 67.23 C ATOM 15900 CE LYS O 83 29.412 -3.685 52.037 1.00 91.64 C ATOM 16000 CA LEU O 96 43.140 15.192 64.970 1.00 64.05 C ATOM 16100 CD GLN O 108 40.291 18.746 93.673 1.00 84.07 C ATOM 16200 C VAL O 122 38.086 10.051 93.162 1.00 68.13 C ATOM 16300 CA GLN O 135 38.800 12.567 60.896 1.00 54.37 C ATOM 16400 C VAL O 148 36.165 10.783 83.952 1.00 59.64 C ATOM 16500 CA ILE O 162 53.767 2.333 94.433 1.00 84.28 C ATOM 16600 CG2 VAL O 174 32.148 7.788 78.609 1.00 58.15 C ATOM 16700 N GLY O 187 16.598 24.287 64.445 1.00 52.49 N ATOM 16800 CD PRO O 201 5.762 22.790 55.974 1.00 49.53 C ATOM 16900 CG LYS O 214 16.607 16.684 70.039 1.00 46.98 C ATOM 17000 CA VAL O 227 52.726 3.511 85.940 1.00 79.62 C ATOM 17100 CA GLU O 242 44.541 3.458 77.560 1.00 70.49 C ATOM 17200 O GLU O 255 26.874 6.548 65.762 1.00 58.69 O ATOM 17300 CA ALA O 267 49.743 12.180 89.104 1.00 75.32 C ATOM 17400 CA PHE T 8 30.107 24.156 33.778 1.00 58.16 C ATOM 17500 CE2 PHE T 19 37.073 30.806 23.807 1.00 66.58 C ATOM 17600 O LYS T 31 38.930 53.026 9.904 1.00104.23 O ATOM 17700 O GLY U 48 2.470 14.492 84.844 1.00 53.19 O ATOM 17800 OD1 ASN U 61 17.430 27.269 88.022 1.00 64.67 O ATOM 17900 CG PRO U 73 20.509 34.023 98.785 1.00 68.36 C ATOM 18000 CG GLU U 86 13.983 7.114 98.623 1.00 75.48 C ATOM 18100 N ARG U 100 16.728 26.887 112.613 1.00 79.81 N ATOM 18200 CA HIS U 111 5.985 23.384 97.418 1.00 66.26 C ATOM 18300 OE1 GLU U 123 25.495 13.972 83.507 1.00 74.96 O ATOM 18400 O GLU V 28 -1.415 59.687 86.032 1.00 69.71 O ATOM 18500 N GLY V 42 1.728 48.438 106.910 1.00 77.83 N ATOM 18600 O GLU V 54 16.395 61.529 91.352 1.00 67.27 O ATOM 18700 C HIS V 67 18.618 48.373 86.041 1.00 51.86 C ATOM 18800 CA ARG V 81 9.654 43.737 90.640 1.00 59.19 C ATOM 18900 CA ASN V 94 8.577 49.578 100.936 1.00 64.63 C ATOM 19000 OG1 THR V 106 19.762 41.352 102.868 1.00 66.61 O ATOM 19100 CA PRO V 119 27.043 49.726 96.368 1.00 53.71 C ATOM 19200 NE ARG V 131 34.037 57.790 98.066 1.00 77.69 N ATOM 19300 N ILE V 145 11.653 52.943 92.598 1.00 57.53 N ATOM 19400 CA GLY V 157 10.349 43.420 85.728 1.00 62.22 C ATOM 19500 C ILE y 25 27.680 83.976 70.831 1.00 93.60 C ATOM 19600 C LEU y 39 36.215 96.397 55.160 1.00 88.39 C ATOM 19700 C LYS X 17 -23.484 62.051 48.307 1.00 73.05 C ATOM 19800 C GLY X 31 -12.949 75.783 36.869 1.00 78.68 C ATOM 19900 N LYS X 45 0.108 87.147 24.605 1.00 94.37 N ATOM 20000 CB UNK Y 15 -2.576 94.042 54.728 1.00100.98 C ATOM 20100 C PHE Z 5 40.041 89.364 89.872 1.00 91.94 C ATOM 20200 O VAL Z 18 39.978 94.277 69.809 1.00 76.44 O ATOM 20300 CB ASP Z 32 47.282 103.853 60.501 1.00100.60 C ATOM 20400 N SER Z 44 48.888 94.580 73.401 1.00 86.76 N ATOM 20500 CD2 LEU Z 57 44.301 89.773 91.041 1.00 78.59 C HETATM20600 C2 CLA A 362 31.764 47.668 47.431 1.00 60.44 C HETATM20700 NB CLA A 363 29.710 41.445 46.930 1.00 45.58 N HETATM20800 C7 CLA D 364 16.133 64.229 46.053 1.00 76.65 C HETATM20900 CBB PHO D 355 14.716 56.516 46.747 1.00 56.43 C HETATM21000 C14 CLA A 366 66.544 40.085 54.813 1.00 90.68 C HETATM21100 C4C CLA B 511 -26.404 52.016 32.721 1.00 96.16 C HETATM21200 C19 CLA B 512 -3.098 50.381 41.085 1.00 83.96 C HETATM21300 C1D CLA B 514 -5.234 38.699 29.202 1.00 71.34 C HETATM21400 CHC CLA B 516 -20.209 32.957 21.111 1.00 89.96 C HETATM21500 CAD CLA B 517 2.554 21.339 34.550 1.00 55.30 C HETATM21600 C3A CLA B 519 -10.472 56.508 18.414 1.00 84.57 C HETATM21700 O2D CLA B 520 -10.650 46.894 16.518 1.00 72.71 O HETATM21800 CGA CLA B 522 -3.932 39.345 15.732 1.00 83.81 C HETATM21900 C4 CLA B 523 8.852 43.002 22.934 1.00 70.48 C HETATM22000 C2B CLA B 525 -14.006 41.766 8.133 1.00 97.68 C HETATM22100 C9 CLA B 526 -11.824 25.329 -0.631 1.00106.01 C HETATM22200 CBB CLA C 475 39.928 67.338 64.645 1.00 59.03 C HETATM22300 C14 CLA C 476 50.357 62.165 64.457 1.00 87.49 C HETATM22400 C4C CLA C 478 53.106 55.767 51.571 1.00 72.93 C HETATM22500 C19 CLA C 479 59.949 48.251 61.645 1.00100.03 C HETATM22600 C1D CLA C 481 42.030 67.462 48.801 1.00 85.05 C HETATM22700 CHC CLA C 483 44.314 69.269 63.901 1.00 50.61 C HETATM22800 CAD CLA C 484 43.342 83.454 49.029 1.00 82.21 C HETATM22900 C3A CLA C 486 61.049 84.971 60.287 1.00 97.06 C HETATM23000 FE HEM V 164 21.702 46.175 93.090 1.00 67.31 FE HETATM23100 C4 PL9 A 367 23.534 65.392 32.049 1.00 87.59 C HETATM23200 C14 BCR A 369 49.813 31.115 42.316 1.00 69.53 C HETATM23300 C38 BCR B 528 4.937 19.657 26.930 1.00 79.68 C HETATM23400 C14 BCR H 107 -21.140 55.848 30.373 1.00 89.39 C HETATM23500 C38 BCR K 112 25.295 79.179 53.876 1.00 74.98 C HETATM23600 C14 BCR Z 116 52.931 81.451 77.107 1.00 77.87 C HETATM23700 C3D DGD A 370 53.637 32.456 61.804 1.00 85.34 C HETATM23800 C28 LHG A 371 35.937 62.504 44.119 1.00 65.86 C HETATM23900 C3G DGD C 490 27.108 67.075 73.164 1.00 77.16 C HETATM24000 C6 LMG D 359 9.071 67.359 68.690 1.00 71.69 C HETATM24100 C4 LMG B 531 19.088 52.863 20.315 1.00 79.55 C HETATM24200 C4 LMG D 360 31.370 49.703 21.577 1.00 74.79 C HETATM24300 O47 SQD T 213 39.292 32.149 16.094 1.00 89.97 O HETATM24400 C5 LMG B 534 -5.220 3.042 32.449 1.00 88.99 C HETATM24500 C16 LMG M 217 31.439 29.591 17.567 1.00 80.15 C HETATM24600 C32 LMG C 492 29.124 71.911 68.040 1.00 81.16 C HETATM24700 C1 LHG A 374 26.048 76.110 36.215 1.00 94.79 C HETATM24800 C13 SQD F 224 -4.639 79.397 39.277 1.00 94.00 C HETATM24900 C5B LMT M 226 18.726 10.738 43.575 1.00 89.50 C HETATM25000 C12 LMT B 535 -16.566 32.829 12.754 1.00 71.46 C HETATM25100 C11 LMT B 536 -11.459 65.368 27.690 1.00 83.60 C """ def amplitudes_from_pdb(resolution,algorithm=None,anomalous=False): from iotbx import pdb pdb_inp = pdb.input(source_info=None,lines = pdb_lines) xray_structure = pdb_inp.xray_structure_simple() primitive_xray_structure = xray_structure.primitive_setting() P1_primitive_xray_structure = primitive_xray_structure.expand_to_p1() fcalc = P1_primitive_xray_structure.structure_factors( d_min=resolution, anomalous_flag=anomalous, algorithm=algorithm).f_calc() return fcalc.amplitudes() def tst_all(): F = foo() assert F == (1,2,3,4) size=1516 D = detector(slowpixels=1516,fastpixels=1516,pixel_size=0.00011) D.set_region_of_interest(0,int(0.6*size),int(0.4*size),int(0.6*size)) D.set_oversampling(1) C = camera() C.distance = 0.18166 C.Ybeam = 0.08338 C.Zbeam = 0.08338 C.lambda0 = 6.2E-10 C.dispersion = 0.002 C.dispsteps = 4 C.hdivrange = 0 C.vdivrange = 0 C.hdivstep = 1 C.vdivstep = 1 C.source_distance = 10. C.fluence = 1.E24 Amat = sqr((127.6895065259495, 0.6512077339887,-0.4403031342553, -1.1449112128916,225.3922539826207,1.8393136632579, 1.0680694468752,-2.4923062985132,306.0953037195841)) PSII = amplitudes_from_pdb(8.,"fft",True) from cctbx import crystal_orientation X = crystal() X.orientation = crystal_orientation.crystal_orientation( Amat,crystal_orientation.basis_type.direct) X.miller = PSII.indices() X.amplitudes = PSII.data() X.Na = 6; X.Nb = 6; X.Nc = 6 SIM = fast_bragg_simulation() SIM.set_detector(D) SIM.set_camera(C) SIM.set_crystal(X) SIM.sweep_over_detector() data = D.raw scale_factor = 55000./flex.max(data) #print "scale_factor",scale_factor fileout="intimage_001.img" SIM.to_smv_format(fileout=fileout, intfile_scale = scale_factor, saturation=40000) import os assert os.path.isfile(fileout) os.remove(fileout) #simulation is complete, now we'll autoindex the image fragment and verify # that the indexed cell is similar to the input cell. if (not libtbx.env.has_module("annlib")): print("Skipping some tests: annlib not available.") return # 1. Analysis of the image to identify the Bragg peak centers. # This step uses an inefficient algorithm and implementation and # is most time consuming; but the code is only for testing, not production from rstbx.diffraction.fastbragg.tst_utils_clustering import specific_libann_cluster M=specific_libann_cluster(scale_factor*data,intensity_cutoff = 25,distance_cutoff=17) # M is a dictionary of peak intensities indexed by pixel coordinates # 2. Now autoindex the pattern from rstbx.diffraction.fastbragg.tst_utils_clustering import index_wrapper SIM.C = C SIM.D = D ai,ref_uc = index_wrapper(M.keys(), SIM, PSII) tst_uc = ai.getOrientation().unit_cell() #print ref_uc # (127.692, 225.403, 306.106, 90, 90, 90) #print tst_uc # (106.432, 223.983, 303.102, 90.3185, 91.5998, 90.5231) # 3. Final assertion. In the given orientation, # the unit cell A vector is into the beam and is not well sampled, # so tolerances have to be fairly relaxed, 5%. # Labelit does better with the target_cell restraint, but this improved # algorithm is not used here for the test assert ref_uc.is_similar_to(tst_uc, relative_length_tolerance=0.20, absolute_angle_tolerance= 2.0) if __name__=="__main__": tst_all() print("OK")