from __future__ import absolute_import, division, print_function import os, sys import time #import libtbx.load_env from mmtbx import monomer_library import mmtbx.monomer_library.server from cctbx.array_family import flex import mmtbx.model import mmtbx.monomer_library.pdb_interpretation from six.moves import cStringIO as StringIO #from mmtbx import utils #from libtbx.utils import format_cpu_times from mmtbx import conformation_dependent_library as cdl from mmtbx.conformation_dependent_library import cdl_utils, cdl_setup from mmtbx.conformation_dependent_library.cdl_database import cdl_database from six.moves import range filenames = { "cdl_test_1.pdb" : [ [ "IleVal_nonxpro", "NonPGIV_nonxpro", "Gly_nonxpro", ], [ (-100, 110), ( -70, 150), ( -80, 160), ], [ ["B", 30, 122.93], ["B", 177, 120.94], ["B", 16, 120.64], ], ], "cdl_test_2.pdb" : [ [ "NonPGIV_nonxpro", "NonPGIV_nonxpro", "NonPGIV_nonxpro", "NonPGIV_nonxpro", ], [ ( 170, -40), (-110, 160), ( 170, -40), (-110, 160), ], [ ["I", 10921, 121.54], ["B", 85, 122.92], ["I", 10921, 121.54], ["B", 85, 122.92], ], ], "cdl_test_3.pdb" : [ [ "NonPGIV_nonxpro", "NonPGIV_xpro", "Pro_nonxpro", "Gly_nonxpro", ], [ (-130, 20), (-120, 90), ( -50, 130), ( 90, 0), ], [ ["B", 24, 122.14], ["B", 7, 123.30], ["B", 21, 119.93], ["B", 79, 122.05], ], ], "cdl_test_4.pdb" : [ [ "IleVal_xpro", "Pro_nonxpro", "IleVal_xpro", "Pro_nonxpro", ], [ (-150, 150), ( -70, 140), (-150, 150), ( -70, 140), ], [ ["I", 81, 122.13], ["B", 44, 119.76], ["I", 81, 122.13], ["B", 44, 119.76], ], ], "cdl_test_5.pdb" : [ [ "Gly_xpro", "Pro_xpro", "Pro_nonxpro", "Gly_nonxpro", ], [ ( 170, 70), ( -30, 160), ( -30, 160), (-180,-160), ], [ ["I", 44, 121.87], ["I", 12, 120.38], ["I", 639, 119.84], ["B", 7, 120.51], ], ], "cdl_test_7.pdb" : [ [ "NonPGIV_nonxpro", # A "NonPGIV_nonxpro", "NonPGIV_nonxpro", "NonPGIV_nonxpro", # B "NonPGIV_nonxpro", "NonPGIV_nonxpro", ], [ (-110, 100), ( -60, -30), ( -60, -30), (-110, 100), ( -50, -40), ( -70, -20), ], [ ["B", 46, 123.14], ["B", 718, 120.28], ["B", 718, 120.28], ["B", 46, 123.14], ["B", 254, 120.38], ["B", 436, 120.72], ], [ (27, 28, 29), (29, 28, 27), (28, 29), (11, 27, 28), (28, 27, 11), (11, 27), (27, 28), ], ], "cdl_test_8.pdb" : [ [ "NonPGIV_xpro", ], [ ( -70, 130), ], [ ['B', 15, 120.67], ], [ True, ], ], "cdl_test_9.pdb" : [ [ 'IleVal_nonxpro', ], [ None, ], [ None, ], ] } output_filenames = { "cdl_test_1.pdb" : """CRYST1 78.400 78.400 36.970 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012755 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012755 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027049 0.00000 ATOM 1 N LYS A 1 2.978 10.061 9.810 1.00 18.67 N ATOM 2 CA LYS A 1 2.042 10.475 8.681 1.00 18.31 C ATOM 3 C LYS A 1 2.170 11.990 8.529 1.00 19.54 C ATOM 4 O LYS A 1 2.174 12.724 9.562 1.00 18.93 O ATOM 5 CB LYS A 1 0.614 10.079 9.071 1.00 18.68 C ATOM 6 CG LYS A 1 -0.468 10.538 8.055 1.00 20.33 C ATOM 7 CD LYS A 1 -1.793 9.976 8.472 1.00 23.73 C ATOM 8 CE LYS A 1 -2.857 10.739 7.745 1.00 27.82 C ATOM 9 NZ LYS A 1 -4.139 9.932 7.827 1.00 35.12 N ATOM 10 N VAL A 2 2.301 12.446 7.281 1.00 20.08 N ATOM 11 CA VAL A 2 2.189 13.827 6.988 1.00 19.50 C ATOM 12 C VAL A 2 0.780 14.077 6.459 1.00 20.53 C ATOM 13 O VAL A 2 0.455 13.617 5.317 1.00 21.79 O ATOM 14 CB VAL A 2 3.230 14.266 5.965 1.00 19.74 C ATOM 15 CG1 VAL A 2 3.079 15.706 5.710 1.00 19.95 C ATOM 16 CG2 VAL A 2 4.675 13.969 6.492 1.00 20.88 C ATOM 17 N PHE A 3 -0.025 14.816 7.224 1.00 19.86 N ATOM 18 CA PHE A 3 -1.383 15.190 6.817 1.00 19.37 C ATOM 19 C PHE A 3 -1.385 16.251 5.760 1.00 19.48 C ATOM 20 O PHE A 3 -0.541 17.116 5.732 1.00 19.87 O ATOM 21 CB PHE A 3 -2.184 15.760 7.983 1.00 17.99 C ATOM 22 CG PHE A 3 -2.764 14.735 8.851 1.00 19.05 C ATOM 23 CD1 PHE A 3 -1.965 14.098 9.821 1.00 17.66 C ATOM 24 CD2 PHE A 3 -4.096 14.381 8.763 1.00 17.74 C ATOM 25 CE1 PHE A 3 -2.519 13.100 10.640 1.00 19.73 C ATOM 26 CE2 PHE A 3 -4.613 13.367 9.590 1.00 16.68 C ATOM 27 CZ PHE A 3 -3.842 12.762 10.524 1.00 20.53 C ATOM 28 N GLY A 4 -2.390 16.210 4.856 1.00 21.93 N ATOM 29 CA GLY A 4 -2.669 17.427 4.119 1.00 20.88 C ATOM 30 C GLY A 4 -3.440 18.425 4.971 1.00 20.46 C ATOM 31 O GLY A 4 -4.063 18.017 5.942 1.00 20.59 O ATOM 32 N ARG A 5 -3.452 19.702 4.585 1.00 20.64 N ATOM 33 CA ARG A 5 -4.145 20.738 5.384 1.00 22.42 C ATOM 34 C ARG A 5 -5.629 20.426 5.653 1.00 23.55 C ATOM 35 O ARG A 5 -6.065 20.496 6.804 1.00 22.39 O ATOM 36 CB ARG A 5 -4.019 22.075 4.644 1.00 23.43 C ATOM 37 CG ARG A 5 -4.695 23.187 5.211 1.00 21.72 C ATOM 38 CD ARG A 5 -4.439 24.429 4.291 1.00 23.07 C ATOM 39 NE ARG A 5 -4.978 24.334 2.924 1.00 26.36 N ATOM 40 CZ ARG A 5 -6.256 24.606 2.606 1.00 29.93 C ATOM 41 NH1 ARG A 5 -7.155 25.021 3.533 1.00 29.05 N ATOM 42 NH2 ARG A 5 -6.634 24.532 1.335 1.00 30.26 N END """, "cdl_test_2.pdb" : """CRYST1 59.140 59.140 186.740 90.00 90.00 120.00 P 32 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016909 0.009762 0.000000 0.00000 SCALE2 0.000000 0.019525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005355 0.00000 ATOM 3708 N ARG A 238 -3.155 2.964 9.280 1.00 26.44 N ANISOU 3708 N ARG A 238 2310 4436 3302 1501 -44 -636 N ATOM 3709 CA ARG A 238 -2.158 2.016 9.755 1.00 38.30 C ANISOU 3709 CA ARG A 238 2311 6253 5989 1912 86 1184 C ATOM 3710 C ARG A 238 -2.826 0.771 10.333 1.00 40.52 C ANISOU 3710 C ARG A 238 4415 4937 6042 2589 1562 468 C ATOM 3711 O ARG A 238 -2.916 0.609 11.567 1.00 70.06 O ANISOU 3711 O ARG A 238 13435 7190 5995 -711 -2846 3279 O ATOM 3712 CB ARG A 238 -1.347 2.771 10.834 1.00 46.30 C ANISOU 3712 CB ARG A 238 2187 7787 7618 1791 -1530 1440 C ATOM 3713 CG ARG A 238 -0.562 3.934 10.206 1.00 63.42 C ANISOU 3713 CG ARG A 238 4955 7689 11453 30 524 -36 C ATOM 3714 CD ARG A 238 -0.570 5.141 11.137 1.00 65.76 C ANISOU 3714 CD ARG A 238 3404 7864 13718 1672 3308 -1029 C ATOM 3715 NE ARG A 238 -1.611 6.058 10.682 1.00 74.79 N ANISOU 3715 NE ARG A 238 6336 7837 14243 1136 504 931 N ATOM 3716 CZ ARG A 238 -1.593 7.373 10.605 1.00 75.60 C ANISOU 3716 CZ ARG A 238 6297 7919 14508 415 192 1432 C ATOM 3717 NH1 ARG A 238 -0.527 8.069 10.982 1.00 80.12 N ANISOU 3717 NH1 ARG A 238 5536 10778 14127 -2180 3841 2359 N ATOM 3718 NH2 ARG A 238 -2.657 8.042 10.161 1.00 77.75 N ANISOU 3718 NH2 ARG A 238 5602 8669 15269 2476 3438 1117 N ATOM 3719 H ARG A 238 -3.639 3.361 9.870 1.00 31.73 H ATOM 3720 HA ARG A 238 -1.567 1.761 9.016 1.00 45.96 H ATOM 3721 HB2 ARG A 238 -1.950 3.114 11.511 1.00 55.56 H ATOM 3722 HB3 ARG A 238 -0.729 2.158 11.263 1.00 55.56 H ATOM 3723 HG2 ARG A 238 0.353 3.657 10.039 1.00 76.11 H ATOM 3724 HG3 ARG A 238 -0.964 4.176 9.357 1.00 76.11 H ATOM 3725 HD2 ARG A 238 -0.750 4.858 12.048 1.00 78.91 H ATOM 3726 HD3 ARG A 238 0.294 5.582 11.119 1.00 78.91 H ATOM 3727 HE ARG A 238 -2.343 5.685 10.427 1.00 89.75 H ATOM 3728 HH11 ARG A 238 0.168 7.661 11.282 1.00 96.14 H ATOM 3729 HH12 ARG A 238 -0.531 8.927 10.925 1.00 96.14 H ATOM 3730 HH21 ARG A 238 -3.364 7.615 9.921 1.00 93.29 H ATOM 3731 HH22 ARG A 238 -2.637 8.901 10.114 1.00 93.29 H ATOM 3732 N GLU A 239 -3.259 -0.180 9.507 1.00 61.01 N ANISOU 3732 N GLU A 239 8805 7109 7268 -465 1338 -107 N ATOM 3733 CA GLU A 239 -3.997 -1.358 9.938 1.00 54.21 C ANISOU 3733 CA GLU A 239 8081 6237 6280 626 1613 -200 C ATOM 3734 C GLU A 239 -4.598 -2.077 8.722 1.00 55.11 C ANISOU 3734 C GLU A 239 9152 5609 6177 510 1378 67 C ATOM 3735 O GLU A 239 -4.560 -3.307 8.677 1.00 57.38 O ANISOU 3735 O GLU A 239 9787 5373 6643 -1615 1558 1275 O ATOM 3736 CB AGLU A 239 -5.113 -0.987 10.921 0.39 51.07 C ANISOU 3736 CB AGLU A 239 7126 6478 5800 1665 682 270 C ATOM 3737 CB BGLU A 239 -5.114 -0.984 10.899 0.61 51.10 C ANISOU 3737 CB BGLU A 239 7361 6372 5685 1709 761 428 C ATOM 3738 CG AGLU A 239 -5.565 -2.004 11.946 0.39 43.33 C ANISOU 3738 CG AGLU A 239 5570 5396 5499 3079 821 -50 C ATOM 3739 CG BGLU A 239 -4.827 -1.259 12.366 0.61 48.99 C ANISOU 3739 CG BGLU A 239 6855 6082 5677 2131 459 -122 C ATOM 3740 CD AGLU A 239 -6.502 -1.466 13.020 0.39 45.82 C ANISOU 3740 CD AGLU A 239 6276 5460 5674 2634 906 -931 C ATOM 3741 CD BGLU A 239 -5.877 -0.539 13.204 0.61 49.31 C ANISOU 3741 CD BGLU A 239 7487 5254 5994 1837 445 -878 C ATOM 3742 OE1AGLU A 239 -6.171 -0.475 13.703 0.39 42.67 O ANISOU 3742 OE1AGLU A 239 5740 4028 6446 3819 -363 -267 O ATOM 3743 OE1BGLU A 239 -6.510 0.403 12.702 0.61 49.13 O ANISOU 3743 OE1BGLU A 239 6944 5966 5758 2026 402 -741 O ATOM 3744 OE2AGLU A 239 -7.604 -2.032 13.226 0.39 42.34 O ANISOU 3744 OE2AGLU A 239 5022 6899 4165 3057 -24 -1587 O ATOM 3745 OE2BGLU A 239 -6.056 -0.967 14.344 0.61 45.41 O ANISOU 3745 OE2BGLU A 239 9181 2709 5363 1565 407 -2132 O ATOM 3746 H GLU A 239 -3.092 -0.093 8.668 1.00 73.21 H ATOM 3747 HA AGLU A 239 -3.376 -1.969 10.387 1.00 65.05 H ATOM 3748 HB2AGLU A 239 -4.825 -0.196 11.402 0.39 61.28 H ATOM 3749 HB2BGLU A 239 -5.304 -0.038 10.795 0.61 61.32 H ATOM 3750 HB3AGLU A 239 -5.890 -0.734 10.398 0.39 61.28 H ATOM 3751 HB3BGLU A 239 -5.913 -1.472 10.645 0.61 61.32 H ATOM 3752 HG2AGLU A 239 -6.013 -2.730 11.483 0.39 52.00 H ATOM 3753 HG2BGLU A 239 -4.861 -2.213 12.538 0.61 58.79 H ATOM 3754 HG3AGLU A 239 -4.781 -2.375 12.379 0.39 52.00 H ATOM 3755 HG3BGLU A 239 -3.941 -0.938 12.597 0.61 58.79 H ATOM 3756 N GLN A 240 -5.123 -1.256 7.820 1.00 51.78 N ANISOU 3756 N GLN A 240 7881 5786 6005 1303 1976 -299 N ATOM 3757 CA GLN A 240 -5.815 -1.651 6.579 1.00 48.42 C ANISOU 3757 CA GLN A 240 7439 5291 5667 1037 2360 0 C ATOM 3758 C GLN A 240 -4.914 -1.631 5.369 1.00 50.22 C ANISOU 3758 C GLN A 240 6823 6557 5702 323 2152 622 C ATOM 3759 O GLN A 240 -4.600 -0.753 4.598 1.00 48.60 O ANISOU 3759 O GLN A 240 3660 8042 6764 1632 953 2651 O ATOM 3760 CB GLN A 240 -7.093 -0.780 6.473 1.00 49.78 C ANISOU 3760 CB GLN A 240 7780 4950 6185 1171 1880 -549 C ATOM 3761 CG GLN A 240 -8.174 -1.308 7.405 1.00 42.82 C ANISOU 3761 CG GLN A 240 6648 3396 6227 2273 855 1000 C ATOM 3762 CD GLN A 240 -9.333 -0.374 7.653 1.00 41.20 C ANISOU 3762 CD GLN A 240 7296 3924 4435 2729 687 401 C ATOM 3763 OE1 GLN A 240 -9.512 0.675 7.010 1.00 34.35 O ANISOU 3763 OE1 GLN A 240 6339 2251 4461 1271 -2237 -1012 O ATOM 3764 NE2 GLN A 240 -10.148 -0.767 8.636 1.00 55.98 N ANISOU 3764 NE2 GLN A 240 6092 7850 7330 1793 1349 1644 N ATOM 3765 H GLN A 240 -5.053 -0.413 7.975 1.00 62.13 H ATOM 3766 HA GLN A 240 -6.110 -2.578 6.699 1.00 58.10 H ATOM 3767 HB2 GLN A 240 -6.882 0.138 6.707 1.00 59.74 H ATOM 3768 HB3 GLN A 240 -7.419 -0.790 5.559 1.00 59.74 H ATOM 3769 HG2 GLN A 240 -8.521 -2.135 7.034 1.00 51.39 H ATOM 3770 HG3 GLN A 240 -7.765 -1.521 8.258 1.00 51.39 H ATOM 3771 HE21 GLN A 240 -10.830 -0.288 8.847 1.00 67.18 H ATOM 3772 HE22 GLN A 240 -9.990 -1.500 9.057 1.00 67.18 H ATOM 3773 N MET A 248 -4.937 2.701 4.182 1.00 37.29 N ANISOU 3773 N MET A 248 5297 3715 5155 2607 -2235 -1151 N ATOM 3774 CA MET A 248 -6.312 3.045 3.834 1.00 29.73 C ANISOU 3774 CA MET A 248 4299 3326 3672 1807 -547 -895 C ATOM 3775 C MET A 248 -6.646 4.429 4.362 1.00 22.08 C ANISOU 3775 C MET A 248 2714 3083 2591 972 4 -548 C ATOM 3776 O MET A 248 -6.681 4.689 5.562 1.00 23.02 O ANISOU 3776 O MET A 248 2580 3509 2656 793 -164 -592 O ATOM 3777 CB MET A 248 -7.221 1.978 4.379 1.00 38.11 C ANISOU 3777 CB MET A 248 6459 2679 5343 1548 339 -712 C ATOM 3778 CG MET A 248 -8.639 2.239 3.852 1.00 37.85 C ANISOU 3778 CG MET A 248 5001 2965 6417 1094 1857 -137 C ATOM 3779 SD MET A 248 -9.147 0.888 2.822 1.00 67.88 S ANISOU 3779 SD MET A 248 6928 8620 10245 2450 -1345 -4912 S ATOM 3780 CE MET A 248 -10.423 1.544 1.799 1.00 43.00 C ANISOU 3780 CE MET A 248 2904 3094 10341 226 1769 -2687 C ATOM 3781 H MET A 248 -4.854 2.669 5.067 1.00 55.93 H ATOM 3782 HA MET A 248 -6.394 3.055 2.858 1.00 35.68 H ATOM 3783 HB2 MET A 248 -6.916 1.103 4.093 1.00 45.73 H ATOM 3784 HB3 MET A 248 -7.217 2.002 5.349 1.00 45.73 H ATOM 3785 HG2 MET A 248 -9.254 2.333 4.597 1.00 45.43 H ATOM 3786 HG3 MET A 248 -8.653 3.064 3.342 1.00 45.43 H ATOM 3787 HE1 MET A 248 -10.778 0.847 1.243 1.00 64.50 H ATOM 3788 HE2 MET A 248 -10.063 2.241 1.246 1.00 64.50 H ATOM 3789 HE3 MET A 248 -11.123 1.902 2.350 1.00 64.50 H ATOM 3790 N TYR A 249 -6.873 5.325 3.430 1.00 23.25 N ANISOU 3790 N TYR A 249 3069 3108 2656 966 246 -485 N ATOM 3791 CA TYR A 249 -7.274 6.698 3.737 1.00 18.90 C ANISOU 3791 CA TYR A 249 2230 2821 2129 457 210 -277 C ATOM 3792 C TYR A 249 -8.737 6.893 3.412 1.00 17.18 C ANISOU 3792 C TYR A 249 2093 2781 1655 300 595 -381 C ATOM 3793 O TYR A 249 -9.313 6.090 2.683 1.00 18.40 O ANISOU 3793 O TYR A 249 2539 2576 1875 710 -34 -404 O ATOM 3794 CB TYR A 249 -6.416 7.700 3.006 1.00 21.83 C ANISOU 3794 CB TYR A 249 2065 3491 2738 254 552 -213 C ATOM 3795 CG TYR A 249 -4.945 7.586 3.391 1.00 25.15 C ANISOU 3795 CG TYR A 249 2122 3868 3564 414 384 -59 C ATOM 3796 CD1 TYR A 249 -4.512 8.033 4.635 1.00 26.16 C ANISOU 3796 CD1 TYR A 249 2080 3879 3980 77 0 -249 C ATOM 3797 CD2 TYR A 249 -4.004 7.042 2.531 1.00 29.90 C ANISOU 3797 CD2 TYR A 249 2219 5321 3821 827 539 -47 C ATOM 3798 CE1 TYR A 249 -3.183 7.961 5.050 1.00 32.64 C ANISOU 3798 CE1 TYR A 249 2177 5761 4465 273 -135 238 C ATOM 3799 CE2 TYR A 249 -2.692 6.979 2.957 1.00 34.37 C ANISOU 3799 CE2 TYR A 249 2181 6039 4837 861 452 149 C ATOM 3800 CZ TYR A 249 -2.256 7.417 4.181 1.00 33.76 C ANISOU 3800 CZ TYR A 249 1872 6491 4465 115 348 890 C ATOM 3801 OH TYR A 249 -0.922 7.324 4.553 1.00 40.76 O ANISOU 3801 OH TYR A 249 2151 7364 5972 698 -186 837 O ATOM 3802 H TYR A 249 -6.782 5.095 2.606 1.00 27.90 H ATOM 3803 HA TYR A 249 -7.156 6.841 4.699 1.00 22.68 H ATOM 3804 HB2 TYR A 249 -6.506 7.560 2.050 1.00 26.19 H ATOM 3805 HB3 TYR A 249 -6.730 8.595 3.207 1.00 26.19 H ATOM 3806 HD1 TYR A 249 -5.139 8.397 5.217 1.00 31.39 H ATOM 3807 HD2 TYR A 249 -4.250 6.728 1.690 1.00 35.88 H ATOM 3808 HE1 TYR A 249 -2.927 8.272 5.888 1.00 39.17 H ATOM 3809 HE2 TYR A 249 -2.064 6.616 2.375 1.00 41.24 H ATOM 3810 N VAL A 250 -9.305 7.956 3.940 1.00 16.60 N ANISOU 3810 N VAL A 250 2001 2588 1717 329 174 -331 N ATOM 3811 CA VAL A 250 -10.743 8.196 3.704 1.00 15.87 C ANISOU 3811 CA VAL A 250 1947 2389 1694 136 378 -319 C ATOM 3812 C VAL A 250 -11.034 8.242 2.203 1.00 15.66 C ANISOU 3812 C VAL A 250 1868 2293 1788 198 160 -398 C ATOM 3813 O VAL A 250 -12.137 7.787 1.818 1.00 16.36 O ANISOU 3813 O VAL A 250 1879 2196 2141 111 228 -521 O ATOM 3814 CB VAL A 250 -11.175 9.432 4.486 1.00 15.79 C ANISOU 3814 CB VAL A 250 1847 2325 1827 26 310 -356 C ATOM 3815 CG1 VAL A 250 -10.724 10.733 3.874 1.00 16.17 C ANISOU 3815 CG1 VAL A 250 1843 2333 1968 167 382 -264 C ATOM 3816 CG2 VAL A 250 -12.687 9.349 4.713 1.00 22.92 C ANISOU 3816 CG2 VAL A 250 2179 2341 4190 35 1319 -560 C ATOM 3817 H VAL A 250 -8.844 8.505 4.417 1.00 19.91 H ATOM 3818 HA VAL A 250 -11.231 7.430 4.074 1.00 19.05 H ATOM 3819 HB VAL A 250 -10.752 9.372 5.368 1.00 18.95 H ATOM 3820 HG11 VAL A 250 -9.773 10.712 3.742 1.00 24.25 H ATOM 3821 HG12 VAL A 250 -10.949 11.459 4.461 1.00 24.25 H ATOM 3822 HG13 VAL A 250 -11.162 10.858 3.029 1.00 24.25 H ATOM 3823 HG21 VAL A 250 -12.906 8.496 5.097 1.00 34.39 H ATOM 3824 HG22 VAL A 250 -13.143 9.448 3.874 1.00 34.39 H ATOM 3825 HG23 VAL A 250 -12.960 10.048 5.311 1.00 34.39 H END """, "cdl_test_3.pdb" : """CRYST1 78.400 78.400 36.970 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012755 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012755 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027049 0.00000 ATOM 546 N GLY A 67 11.101 9.366 29.637 1.00 17.94 N ATOM 547 CA GLY A 67 12.163 8.693 30.425 1.00 18.26 C ATOM 548 C GLY A 67 13.507 9.365 30.392 1.00 19.97 C ATOM 549 O GLY A 67 14.488 8.801 30.951 1.00 20.09 O ATOM 550 N ARG A 68 13.628 10.523 29.748 1.00 17.72 N ATOM 551 CA ARG A 68 14.872 11.244 29.716 1.00 18.14 C ATOM 552 C ARG A 68 14.750 12.732 29.989 1.00 19.27 C ATOM 553 O ARG A 68 15.634 13.524 29.582 1.00 22.09 O ATOM 554 CB ARG A 68 15.628 10.987 28.386 1.00 18.05 C ATOM 555 CG ARG A 68 14.914 11.505 27.179 1.00 18.41 C ATOM 556 CD ARG A 68 15.883 11.529 26.010 1.00 19.08 C ATOM 557 NE ARG A 68 15.421 12.521 25.048 1.00 20.73 N ATOM 558 CZ ARG A 68 15.821 12.542 23.764 1.00 19.88 C ATOM 559 NH1 ARG A 68 16.664 11.596 23.351 1.00 20.06 N ATOM 560 NH2 ARG A 68 15.366 13.499 22.857 1.00 13.89 N ATOM 561 N THR A 69 13.695 13.162 30.686 1.00 17.50 N ATOM 562 CA THR A 69 13.549 14.569 30.983 1.00 17.41 C ATOM 563 C THR A 69 13.478 14.721 32.518 1.00 18.58 C ATOM 564 O THR A 69 12.424 14.701 33.115 1.00 18.15 O ATOM 565 CB THR A 69 12.285 15.177 30.327 1.00 17.98 C ATOM 566 OG1 THR A 69 12.307 14.794 28.923 1.00 18.45 O ATOM 567 CG2 THR A 69 12.311 16.761 30.405 1.00 16.00 C ATOM 568 N PRO A 70 14.637 14.873 33.132 1.00 20.91 N ATOM 569 CA PRO A 70 14.653 14.921 34.608 1.00 23.45 C ATOM 570 C PRO A 70 13.712 15.941 35.188 1.00 25.34 C ATOM 571 O PRO A 70 13.679 17.131 34.760 1.00 26.21 O ATOM 572 CB PRO A 70 16.109 15.285 34.922 1.00 24.93 C ATOM 573 CG PRO A 70 16.878 14.476 33.781 1.00 23.80 C ATOM 574 CD PRO A 70 15.990 14.884 32.557 1.00 22.05 C ATOM 575 N GLY A 71 12.919 15.489 36.148 1.00 25.17 N ATOM 576 CA GLY A 71 12.229 16.459 36.975 1.00 27.28 C ATOM 577 C GLY A 71 10.881 16.750 36.364 1.00 28.56 C ATOM 578 O GLY A 71 10.095 17.549 36.877 1.00 31.19 O ATOM 579 N SER A 72 10.591 16.091 35.253 1.00 28.46 N ATOM 580 CA SER A 72 9.414 16.396 34.499 1.00 28.52 C ATOM 581 C SER A 72 8.164 15.668 35.014 1.00 28.41 C ATOM 582 O SER A 72 8.207 14.680 35.763 1.00 26.59 O ATOM 583 CB SER A 72 9.671 16.096 33.019 1.00 27.53 C ATOM 584 OG SER A 72 9.706 14.690 32.833 1.00 26.85 O END """, "cdl_test_4.pdb" : """CRYST1 78.400 78.400 36.970 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012755 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012755 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027049 0.00000 ATOM 618 N ASN A 77 -0.512 11.604 31.096 1.00 20.93 N ATOM 619 C ASN A 77 -0.196 9.268 30.198 1.00 21.38 C ATOM 620 O ASN A 77 -0.881 8.283 30.000 1.00 21.80 O ATOM 621 CA AASN A 77 -0.387 10.160 31.412 0.50 20.46 C ATOM 622 CB AASN A 77 -1.589 9.725 32.281 0.50 21.87 C ATOM 623 CG AASN A 77 -1.756 10.639 33.481 0.50 20.45 C ATOM 624 OD1AASN A 77 -0.876 10.720 34.313 0.50 25.10 O ATOM 625 ND2AASN A 77 -2.869 11.346 33.553 0.50 23.32 N ATOM 626 CA BASN A 77 -0.453 10.150 31.410 0.50 21.90 C ATOM 627 CB BASN A 77 -1.758 9.718 32.170 0.50 23.71 C ATOM 628 CG BASN A 77 -2.305 8.359 31.743 0.50 29.20 C ATOM 629 OD1BASN A 77 -2.088 7.354 32.431 0.50 37.16 O ATOM 630 ND2BASN A 77 -3.077 8.325 30.635 0.50 33.49 N ATOM 631 N ILE A 78 0.793 9.619 29.363 1.00 19.09 N ATOM 632 CA ILE A 78 1.050 8.859 28.168 1.00 19.18 C ATOM 633 C ILE A 78 2.555 8.868 27.903 1.00 18.54 C ATOM 634 O ILE A 78 3.248 9.866 28.220 1.00 17.60 O ATOM 635 CB ILE A 78 0.445 9.543 26.881 1.00 19.36 C ATOM 636 CG1 ILE A 78 0.729 11.033 26.935 1.00 18.45 C ATOM 637 CG2 ILE A 78 -0.972 9.182 26.719 1.00 24.11 C ATOM 638 CD1 ILE A 78 0.487 11.784 25.606 1.00 24.47 C ATOM 639 N PRO A 79 3.060 7.785 27.288 1.00 18.41 N ATOM 640 CA PRO A 79 4.443 7.862 26.738 1.00 17.69 C ATOM 641 C PRO A 79 4.479 8.877 25.603 1.00 15.10 C ATOM 642 O PRO A 79 3.525 8.971 24.804 1.00 15.70 O ATOM 643 CB PRO A 79 4.692 6.482 26.182 1.00 17.34 C ATOM 644 CG PRO A 79 3.386 5.843 25.977 1.00 21.80 C ATOM 645 CD PRO A 79 2.344 6.567 26.831 1.00 19.64 C ATOM 646 N CYS A 80 5.548 9.649 25.518 1.00 15.91 N ATOM 647 CA CYS A 80 5.607 10.641 24.479 1.00 13.93 C ATOM 648 C CYS A 80 5.499 9.982 23.089 1.00 14.20 C ATOM 649 O CYS A 80 5.019 10.606 22.155 1.00 14.20 O ATOM 650 CB CYS A 80 6.936 11.394 24.588 1.00 13.89 C ATOM 651 SG CYS A 80 7.072 12.387 26.105 1.00 13.81 S END """, "cdl_test_5.pdb" : """CRYST1 78.400 78.400 36.970 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012755 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012755 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027049 0.00000 HETATM 1 N ALA A 1 -5.418 -5.235 -2.694 1.00 20.00 A N HETATM 2 H ALA A 1 -5.559 -6.106 -2.484 1.00 20.00 A H HETATM 3 HN3 ALA A 1 -5.929 -5.009 -3.421 1.00 20.00 A H HETATM 4 CA ALA A 1 -5.784 -4.397 -1.564 1.00 20.00 A C HETATM 5 HA ALA A 1 -6.172 -3.588 -1.967 1.00 20.00 A H HETATM 6 CB ALA A 1 -6.892 -4.972 -0.715 1.00 20.00 A C HETATM 7 HB1 ALA A 1 -6.754 -5.931 -0.607 1.00 20.00 A H HETATM 8 HB2 ALA A 1 -7.755 -4.812 -1.151 1.00 20.00 A H HETATM 9 HB3 ALA A 1 -6.887 -4.539 0.166 1.00 20.00 A H HETATM 10 C ALA A 1 -4.606 -3.903 -0.772 1.00 20.00 A C HETATM 11 O ALA A 1 -4.275 -4.481 0.265 1.00 20.00 A O HETATM 12 N GLY A 2 -3.867 -2.761 -1.226 1.00 20.00 A N HETATM 13 H GLY A 2 -4.075 -2.373 -2.018 1.00 20.00 A H HETATM 14 CA GLY A 2 -2.829 -2.202 -0.405 1.00 20.00 A C HETATM 15 HA GLY A 2 -3.258 -1.801 0.387 1.00 20.00 A H HETATM 16 HB3 GLY A 2 -2.271 -2.927 -0.103 1.00 20.00 A H HETATM 17 C GLY A 2 -1.899 -1.119 -1.037 1.00 20.00 A C HETATM 18 O GLY A 2 -0.710 -1.366 -1.232 1.00 20.00 A O HETATM 19 N PRO A 3 -2.416 0.186 -1.325 1.00 20.00 A N HETATM 20 CA PRO A 3 -1.669 1.290 -1.839 1.00 20.00 A C HETATM 21 HA PRO A 3 -1.800 1.035 -2.770 1.00 20.00 A H HETATM 22 CB PRO A 3 -2.365 2.519 -1.353 1.00 20.00 A C HETATM 23 HB2 PRO A 3 -2.454 3.164 -2.086 1.00 20.00 A H HETATM 24 HB3 PRO A 3 -1.867 2.909 -0.614 1.00 20.00 A H HETATM 25 CG PRO A 3 -3.710 2.073 -0.886 1.00 20.00 A C HETATM 26 HG2 PRO A 3 -3.810 2.252 0.068 1.00 20.00 A H HETATM 27 HG3 PRO A 3 -4.401 2.526 -1.380 1.00 20.00 A H HETATM 28 CD PRO A 3 -3.772 0.612 -1.149 1.00 20.00 A C HETATM 29 HD2 PRO A 3 -4.172 0.149 -0.396 1.00 20.00 A H HETATM 30 HD3 PRO A 3 -4.283 0.444 -1.955 1.00 20.00 A H HETATM 31 C PRO A 3 -0.259 1.253 -1.277 1.00 20.00 A C HETATM 32 O PRO A 3 0.004 0.517 -0.341 1.00 20.00 A O HETATM 33 N PRO A 4 0.814 2.066 -1.908 1.00 20.00 A N HETATM 34 CA PRO A 4 2.197 2.085 -1.522 1.00 20.00 A C HETATM 35 HA PRO A 4 2.824 1.474 -1.952 1.00 20.00 A H HETATM 36 CB PRO A 4 2.709 3.438 -1.892 1.00 20.00 A C HETATM 37 HB2 PRO A 4 3.574 3.366 -2.305 1.00 20.00 A H HETATM 38 HB3 PRO A 4 2.762 3.997 -1.110 1.00 20.00 A H HETATM 39 CG PRO A 4 1.724 4.001 -2.857 1.00 20.00 A C HETATM 40 HG2 PRO A 4 2.154 4.166 -3.710 1.00 20.00 A H HETATM 41 HG3 PRO A 4 1.348 4.828 -2.503 1.00 20.00 A H HETATM 42 CD PRO A 4 0.649 2.963 -3.004 1.00 20.00 A C HETATM 43 HD2 PRO A 4 0.751 2.481 -3.845 1.00 20.00 A H HETATM 44 HD3 PRO A 4 -0.231 3.381 -2.960 1.00 20.00 A H HETATM 45 C PRO A 4 2.306 1.897 -0.025 1.00 20.00 A C HETATM 46 O PRO A 4 1.359 2.199 0.702 1.00 20.00 A O HETATM 47 N GLY A 5 3.573 1.428 0.572 1.00 20.00 A N HETATM 48 H GLY A 5 4.256 1.155 0.038 1.00 20.00 A H HETATM 49 CA GLY A 5 3.710 1.365 2.030 1.00 20.00 A C HETATM 50 HA GLY A 5 3.594 2.257 2.371 1.00 20.00 A H HETATM 51 HB3 GLY A 5 2.987 0.824 2.368 1.00 20.00 A H HETATM 52 C GLY A 5 5.001 0.817 2.608 1.00 20.00 A C HETATM 53 O GLY A 5 6.063 0.961 1.994 1.00 20.00 A O HETATM 54 N ALA A 6 5.011 0.259 3.975 1.00 20.00 A N HETATM 55 H ALA A 6 4.237 0.198 4.445 1.00 20.00 A H HETATM 56 CA ALA A 6 6.225 -0.222 4.540 1.00 20.00 A C HETATM 57 HA ALA A 6 6.839 -0.292 3.788 1.00 20.00 A H HETATM 58 CB ALA A 6 6.126 -1.610 5.086 1.00 20.00 A C HETATM 59 HB1 ALA A 6 5.470 -1.627 5.822 1.00 20.00 A H HETATM 60 HB2 ALA A 6 5.839 -2.218 4.380 1.00 20.00 A H HETATM 61 HB3 ALA A 6 6.995 -1.888 5.420 1.00 20.00 A H HETATM 62 C ALA A 6 6.883 0.752 5.486 1.00 20.00 A C HETATM 63 HC1 ALA A 6 7.560 1.373 5.156 1.00 20.00 A H HETATM 64 O ALA A 6 6.608 0.723 6.689 1.00 20.00 A O END """, "cdl_test_7.pdb" : """CRYST1 63.800 30.630 34.420 90.00 105.80 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015674 0.000000 0.004435 0.00000 SCALE2 0.000000 0.032648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030194 0.00000 ATOM 357 N LYS A 42 18.395 26.865 -5.091 1.00 15.63 N ANISOU 357 N LYS A 42 1174 2885 1878 -53 -141 932 N ATOM 358 CA LYS A 42 17.614 27.899 -4.447 1.00 15.69 C ANISOU 358 CA LYS A 42 1179 2887 1896 93 -160 1130 C ATOM 359 C LYS A 42 18.410 28.797 -3.504 1.00 15.56 C ANISOU 359 C LYS A 42 1130 2638 2145 245 -71 964 C ATOM 360 O LYS A 42 17.910 29.831 -3.034 1.00 17.53 O ANISOU 360 O LYS A 42 1248 2412 2999 315 -138 1003 O ATOM 361 CB LYS A 42 16.407 27.296 -3.693 1.00 17.00 C ANISOU 361 CB LYS A 42 1291 2893 2277 -3 5 1082 C ATOM 362 CG LYS A 42 15.344 26.658 -4.544 1.00 18.44 C ANISOU 362 CG LYS A 42 1165 3253 2588 -3 -31 920 C ATOM 363 CD LYS A 42 14.532 27.707 -5.300 1.00 21.35 C ANISOU 363 CD LYS A 42 1425 3532 3157 -298 -502 1293 C ATOM 364 CE LYS A 42 13.510 27.042 -6.206 1.00 22.84 C ANISOU 364 CE LYS A 42 1794 3767 3117 -83 -619 845 C ATOM 365 NZ LYS A 42 12.571 28.017 -6.821 1.00 23.31 N ANISOU 365 NZ LYS A 42 1834 4551 2470 -20 -515 1255 N ATOM 366 N PHE A 43 19.628 28.411 -3.168 1.00 13.55 N ANISOU 366 N PHE A 43 1111 2289 1750 176 -19 692 N ATOM 367 CA PHE A 43 20.491 29.155 -2.266 1.00 12.82 C ANISOU 367 CA PHE A 43 1228 2079 1563 378 136 395 C ATOM 368 C PHE A 43 21.588 29.873 -3.018 1.00 13.05 C ANISOU 368 C PHE A 43 1271 1872 1817 207 -52 489 C ATOM 369 O PHE A 43 22.623 29.246 -3.287 1.00 12.13 O ANISOU 369 O PHE A 43 1072 1840 1695 -36 -99 400 O ATOM 370 CB APHE A 43 21.138 28.326 -1.148 0.54 13.33 C ANISOU 370 CB APHE A 43 1095 2283 1688 229 6 504 C ATOM 371 CB BPHE A 43 21.107 28.204 -1.235 0.46 12.43 C ANISOU 371 CB BPHE A 43 1285 1918 1520 308 29 285 C ATOM 372 CG APHE A 43 20.164 27.778 -0.102 0.54 11.73 C ANISOU 372 CG APHE A 43 932 2235 1291 262 -176 359 C ATOM 373 CG BPHE A 43 20.126 27.442 -0.348 0.46 10.59 C ANISOU 373 CG BPHE A 43 1177 1391 1456 379 -31 65 C ATOM 374 CD1APHE A 43 19.528 26.591 -0.346 0.54 12.33 C ANISOU 374 CD1APHE A 43 1096 2169 1419 270 268 116 C ATOM 375 CD1BPHE A 43 19.524 26.263 -0.766 0.46 10.91 C ANISOU 375 CD1BPHE A 43 1269 1490 1385 435 21 -132 C ATOM 376 CD2APHE A 43 19.963 28.454 1.063 0.54 13.16 C ANISOU 376 CD2APHE A 43 1322 2021 1658 260 -39 163 C ATOM 377 CD2BPHE A 43 19.884 27.949 0.902 0.46 11.05 C ANISOU 377 CD2BPHE A 43 1067 1744 1386 -211 -145 -95 C ATOM 378 CE1APHE A 43 18.682 26.025 0.592 0.54 12.53 C ANISOU 378 CE1APHE A 43 1037 2084 1639 456 489 94 C ATOM 379 CE1BPHE A 43 18.684 25.566 0.121 0.46 13.29 C ANISOU 379 CE1BPHE A 43 1461 1859 1731 -7 -7 -36 C ATOM 380 CE2APHE A 43 19.094 27.900 2.007 0.54 13.14 C ANISOU 380 CE2APHE A 43 1211 2508 1274 314 -144 87 C ATOM 381 CE2BPHE A 43 19.044 27.272 1.787 0.46 10.84 C ANISOU 381 CE2BPHE A 43 897 1694 1530 93 -84 168 C ATOM 382 CZ APHE A 43 18.455 26.706 1.748 0.54 12.26 C ANISOU 382 CZ APHE A 43 714 2323 1622 485 393 113 C ATOM 383 CZ BPHE A 43 18.461 26.093 1.368 0.46 11.15 C ANISOU 383 CZ BPHE A 43 1072 1528 1635 94 148 168 C ATOM 384 N ASP A 44 21.437 31.147 -3.318 1.00 15.77 N ANISOU 384 N ASP A 44 1567 2043 2384 322 75 783 N ATOM 385 CA ASP A 44 22.544 31.869 -3.932 1.00 16.47 C ANISOU 385 CA ASP A 44 1672 1969 2616 180 163 714 C ATOM 386 C AASP A 44 23.758 31.742 -3.013 0.62 18.30 C ANISOU 386 C AASP A 44 1864 2132 2956 -265 -85 975 C ATOM 387 C BASP A 44 23.871 31.755 -3.195 0.38 18.75 C ANISOU 387 C BASP A 44 2012 1899 3212 -390 -423 792 C ATOM 388 O AASP A 44 24.926 31.718 -3.371 0.62 21.31 O ANISOU 388 O AASP A 44 1788 2706 3601 -153 -12 1547 O ATOM 389 O BASP A 44 24.888 31.692 -3.888 0.38 17.70 O ANISOU 389 O BASP A 44 1658 2205 2862 -512 -760 1253 O ATOM 390 CB ASP A 44 22.143 33.330 -4.128 1.00 22.20 C ANISOU 390 CB ASP A 44 2754 1991 3691 126 -200 1068 C ATOM 391 CG ASP A 44 21.166 33.573 -5.248 1.00 27.77 C ANISOU 391 CG ASP A 44 3558 2501 4490 214 -877 1628 C ATOM 392 OD1 ASP A 44 20.889 32.667 -6.057 1.00 28.61 O ANISOU 392 OD1 ASP A 44 3727 3698 3446 899 -782 1151 O ATOM 393 OD2 ASP A 44 20.767 34.754 -5.305 1.00 35.69 O ANISOU 393 OD2 ASP A 44 4278 2879 6403 845 -1295 1598 O ATOM 394 N AARG A 45 23.412 31.660 -1.733 0.62 16.64 N ANISOU 394 N AARG A 45 2103 1404 2815 37 -219 380 N ATOM 395 N BARG A 45 23.874 31.742 -1.873 0.38 16.77 N ANISOU 395 N BARG A 45 1635 1512 3224 -71 -469 -81 N ATOM 396 CA AARG A 45 24.341 31.598 -0.631 0.62 15.97 C ANISOU 396 CA AARG A 45 1881 1308 2880 -541 -157 244 C ATOM 397 CA BARG A 45 25.113 31.653 -1.116 0.38 17.04 C ANISOU 397 CA BARG A 45 1579 1508 3388 -550 -546 -59 C ATOM 398 C AARG A 45 25.232 30.357 -0.688 0.62 15.73 C ANISOU 398 C AARG A 45 1583 1486 2906 -501 -473 431 C ATOM 399 C BARG A 45 25.789 30.293 -1.141 0.38 14.13 C ANISOU 399 C BARG A 45 1024 1600 2744 -595 -60 600 C ATOM 400 O AARG A 45 26.356 30.433 -0.147 0.62 17.06 O ANISOU 400 O AARG A 45 1646 2177 2660 -660 -440 558 O ATOM 401 O BARG A 45 26.976 30.147 -0.823 0.38 17.78 O ANISOU 401 O BARG A 45 1530 1736 3489 -694 -1102 550 O ATOM 402 CB AARG A 45 23.578 31.610 0.690 0.62 18.40 C ANISOU 402 CB AARG A 45 2253 1956 2783 -460 -76 261 C ATOM 403 CB BARG A 45 24.855 31.998 0.354 0.38 18.43 C ANISOU 403 CB BARG A 45 1840 1880 3281 -53 -630 81 C ATOM 404 CG AARG A 45 24.339 31.969 1.925 0.62 17.49 C ANISOU 404 CG AARG A 45 1380 2348 2917 -485 87 304 C ATOM 405 CG BARG A 45 23.918 31.058 1.078 0.38 16.97 C ANISOU 405 CG BARG A 45 1362 1968 3116 114 -792 174 C ATOM 406 CD AARG A 45 23.391 32.292 3.091 0.62 16.95 C ANISOU 406 CD AARG A 45 1802 1676 2962 129 -81 -41 C ATOM 407 CD BARG A 45 23.612 31.615 2.472 0.38 19.89 C ANISOU 407 CD BARG A 45 1973 2278 3308 313 -483 101 C ATOM 408 NE AARG A 45 24.080 32.172 4.360 0.62 17.21 N ANISOU 408 NE AARG A 45 1245 2257 3039 344 -54 -142 N ATOM 409 NE BARG A 45 23.115 32.990 2.347 0.38 23.31 N ANISOU 409 NE BARG A 45 2655 2715 3485 1121 -370 116 N ATOM 410 CZ AARG A 45 23.462 32.261 5.544 0.62 19.15 C ANISOU 410 CZ AARG A 45 1182 3107 2988 252 -140 -373 C ATOM 411 CZ BARG A 45 23.529 34.017 3.069 0.38 26.09 C ANISOU 411 CZ BARG A 45 3599 1963 4352 767 -806 637 C ATOM 412 NH1AARG A 45 22.177 32.489 5.690 0.62 25.59 N ANISOU 412 NH1AARG A 45 1495 4972 3256 1158 104 -193 N ATOM 413 NH1BARG A 45 24.459 33.809 3.991 0.38 24.55 N ANISOU 413 NH1BARG A 45 2276 2187 4867 571 -586 -56 N ATOM 414 NH2AARG A 45 24.195 32.127 6.654 0.62 27.38 N ANISOU 414 NH2AARG A 45 1130 6242 3030 99 -103 -53 N ATOM 415 NH2BARG A 45 23.040 35.233 2.906 0.38 29.85 N ANISOU 415 NH2BARG A 45 3533 2527 5281 1687 125 374 N ATOM 416 N APHE A 46 24.811 29.238 -1.314 0.62 14.05 N ANISOU 416 N APHE A 46 1534 1362 2443 -293 -128 408 N ATOM 417 N BPHE A 46 24.958 29.283 -1.457 0.38 13.32 N ANISOU 417 N BPHE A 46 1291 1374 2398 -322 -678 323 N ATOM 418 CA PHE A 46 25.500 27.952 -1.293 1.00 13.73 C ANISOU 418 CA PHE A 46 1094 1576 2548 -154 -60 502 C ATOM 419 C PHE A 46 25.742 27.338 -2.662 1.00 14.20 C ANISOU 419 C PHE A 46 1113 1648 2634 -60 -134 398 C ATOM 420 O PHE A 46 26.415 26.282 -2.756 1.00 15.60 O ANISOU 420 O PHE A 46 1145 1685 3097 -18 137 487 O ATOM 421 CB PHE A 46 24.719 26.983 -0.408 1.00 14.08 C ANISOU 421 CB PHE A 46 1094 1436 2820 -80 -100 584 C ATOM 422 CG PHE A 46 24.523 27.495 1.008 1.00 15.24 C ANISOU 422 CG PHE A 46 1140 2109 2540 -88 -166 918 C ATOM 423 CD1 PHE A 46 25.610 27.940 1.750 1.00 14.61 C ANISOU 423 CD1 PHE A 46 1167 1520 2865 -128 55 309 C ATOM 424 CD2 PHE A 46 23.285 27.487 1.615 1.00 17.37 C ANISOU 424 CD2 PHE A 46 1106 3182 2313 -41 -169 1247 C ATOM 425 CE1 PHE A 46 25.451 28.424 3.026 1.00 15.97 C ANISOU 425 CE1 PHE A 46 1588 1860 2620 -134 155 560 C ATOM 426 CE2 PHE A 46 23.164 27.975 2.897 1.00 18.23 C ANISOU 426 CE2 PHE A 46 1622 3096 2208 -177 -1 1381 C ATOM 427 CZ PHE A 46 24.207 28.434 3.646 1.00 16.95 C ANISOU 427 CZ PHE A 46 1580 2503 2357 121 92 996 C END """, "cdl_test_8.pdb" : """CRYST1 29.475 29.475 29.480 90.00 90.00 90.00 P 41 21 2 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.033927 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033927 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033921 0.00000 ATOM 25 N CYS A 4 -1.017 11.791 3.510 1.00 5.40 N ATOM 26 CA CYS A 4 -1.211 11.782 2.064 1.00 5.20 C ATOM 27 C CYS A 4 -2.703 11.983 1.729 1.00 5.50 C ATOM 28 O CYS A 4 -3.156 11.557 0.671 1.00 5.81 O ATOM 29 CB CYS A 4 -0.708 10.530 1.426 1.00 6.10 C ATOM 30 SG CYS A 4 -1.749 9.057 1.832 1.00 5.73 S ATOM 31 N TYR A 5 -3.441 12.684 2.609 1.00 5.06 N ATOM 32 CA TYR A 5 -4.882 12.770 2.375 1.00 5.21 C ATOM 33 C TYR A 5 -5.158 13.567 1.094 1.00 5.25 C ATOM 34 O TYR A 5 -4.616 14.713 0.914 1.00 5.88 O ATOM 35 CB TYR A 5 -5.568 13.494 3.574 1.00 5.48 C ATOM 36 CG TYR A 5 -7.029 13.724 3.329 1.00 5.59 C ATOM 37 CD1 TYR A 5 -7.488 14.961 2.861 1.00 6.24 C ATOM 38 CD2 TYR A 5 -7.947 12.712 3.571 1.00 6.54 C ATOM 39 CE1 TYR A 5 -8.844 15.156 2.644 1.00 7.21 C ATOM 40 CE2 TYR A 5 -9.290 12.938 3.330 1.00 7.81 C ATOM 41 CZ TYR A 5 -9.711 14.144 2.862 1.00 8.31 C ATOM 42 OH TYR A 5 -11.070 14.386 2.640 1.00 12.07 O ATOM 43 N PRO A 6 -6.046 13.065 0.236 1.00 5.32 N ATOM 44 CD PRO A 6 -6.525 13.878 -0.938 1.00 6.62 C ATOM 45 CG PRO A 6 -7.611 13.053 -1.435 1.00 12.66 C ATOM 46 CB PRO A 6 -7.933 11.914 -0.642 1.00 7.02 C ATOM 47 CA PRO A 6 -6.759 11.758 0.397 1.00 5.50 C ATOM 48 C PRO A 6 -5.935 10.619 0.104 1.00 5.60 C ATOM 49 OXT PRO A 6 -5.268 10.568 -1.166 1.00 6.37 O """, # added for test_omega,py "cdl_test_9.pdb" : """CRYST1 74.560 104.040 69.150 90.00 90.00 90.00 C 2 2 21 SCALE1 0.013412 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014461 0.00000 ATOM 3586 N LEU A 265 12.362 20.789 -0.224 1.00 39.28 N ATOM 3587 CA LEU A 265 10.958 21.100 -0.450 1.00 25.81 C ATOM 3588 C LEU A 265 10.613 21.342 -1.914 1.00 29.00 C ATOM 3589 O LEU A 265 9.427 21.349 -2.256 1.00 24.23 O ATOM 3590 CB LEU A 265 10.562 22.339 0.362 1.00 29.70 C ATOM 3591 CG LEU A 265 10.712 22.246 1.881 1.00 42.25 C ATOM 3592 CD1 LEU A 265 10.529 23.620 2.508 0.84 29.47 C ATOM 3593 CD2 LEU A 265 9.719 21.250 2.465 0.86 30.85 C ATOM 3594 H LEU A 265 12.873 21.481 -0.221 1.00 47.14 H ATOM 3595 HA LEU A 265 10.420 20.356 -0.137 1.00 30.97 H ATOM 3596 HB2 LEU A 265 11.109 23.083 0.065 1.00 35.64 H ATOM 3597 HB3 LEU A 265 9.630 22.535 0.178 1.00 35.64 H ATOM 3598 HG LEU A 265 11.607 21.937 2.092 1.00 50.69 H ATOM 3599 HD11 LEU A 265 10.627 23.544 3.470 0.46 35.36 H ATOM 3600 HD12 LEU A 265 11.202 24.222 2.153 0.63 35.36 H ATOM 3601 HD13 LEU A 265 9.643 23.950 2.291 0.53 35.36 H ATOM 3602 HD21 LEU A 265 9.838 21.213 3.427 0.54 37.02 H ATOM 3603 HD22 LEU A 265 8.818 21.543 2.254 0.45 37.02 H ATOM 3604 HD23 LEU A 265 9.883 20.377 2.077 0.60 37.02 H ATOM 3605 N ILE A 266 11.598 21.541 -2.783 1.00 25.15 N ATOM 3606 CA ILE A 266 11.300 21.894 -4.165 1.00 17.45 C ATOM 3607 C ILE A 266 11.066 20.627 -4.979 1.00 26.65 C ATOM 3608 O ILE A 266 10.493 20.675 -6.067 1.00 44.84 O ATOM 3609 CB ILE A 266 12.416 22.771 -4.786 1.00 21.23 C ATOM 3610 CG1 ILE A 266 13.593 21.922 -5.287 1.00 25.40 C ATOM 3611 CG2 ILE A 266 12.898 23.814 -3.770 1.00 25.56 C ATOM 3612 CD1 ILE A 266 14.606 22.711 -6.073 1.00 38.72 C ATOM 3613 H ILE A 266 12.437 21.479 -2.601 1.00 30.18 H ATOM 3614 HA ILE A 266 10.478 22.410 -4.182 1.00 20.94 H ATOM 3615 HB ILE A 266 12.041 23.242 -5.546 1.00 25.48 H ATOM 3616 HG12 ILE A 266 14.047 21.532 -4.524 1.00 30.47 H ATOM 3617 HG13 ILE A 266 13.251 21.220 -5.862 1.00 30.47 H ATOM 3618 HG21 ILE A 266 13.596 24.351 -4.177 1.00 30.67 H ATOM 3619 HG22 ILE A 266 12.150 24.377 -3.518 1.00 30.67 H ATOM 3620 HG23 ILE A 266 13.246 23.356 -2.989 1.00 30.67 H ATOM 3621 HD11 ILE A 266 15.318 22.117 -6.357 1.00 46.46 H ATOM 3622 HD12 ILE A 266 14.171 23.101 -6.847 1.00 46.46 H ATOM 3623 HD13 ILE A 266 14.967 23.413 -5.508 1.00 46.46 H ATOM 3624 N SER A 267 11.505 19.495 -4.440 1.00 41.57 N """, } def test_res_type(hierarchy, filename, restraints_manager, ): for i, threes in enumerate(cdl.generate_protein_threes( hierarchy, #restraints_manager=restraints_manager geometry=restraints_manager.geometry, cdl_class=True, ) ): print(threes.show(), end=' ') res_type_group = cdl_utils.get_res_type_group( threes[1].resname, threes[2].resname, ) assert res_type_group print(i, res_type_group, filenames[filename][0][i]) assert res_type_group == filenames[filename][0][i] def test_phi_psi_key(hierarchy, filename, restraints_manager, ): for i, threes in enumerate(cdl.generate_protein_threes( hierarchy, #restraints_manager=restraints_manager geometry=restraints_manager.geometry, cdl_class=True, ) ): key = threes.get_cdl_key() print(i,key,filenames[filename][1]) assert key == filenames[filename][1][i] def test_cdl_lookup(hierarchy, filename, restraints_manager, ): for i, threes in enumerate(cdl.generate_protein_threes( hierarchy, #restraints_manager=restraints_manager geometry=restraints_manager.geometry, cdl_class=True, ) ): res_type_group = cdl_utils.get_res_type_group( threes[1].resname, threes[2].resname, ) key = threes.get_cdl_key() print('key',key) if key is None: assert filenames[filename][2][i] is None continue restraint_values = cdl_database[res_type_group][key] print(restraint_values[:4]) assert restraint_values[:3] == filenames[filename][2][i] def test_cis_trans_peptide(hierarchy, filename, restraints_manager, ): for i, threes in enumerate(cdl.generate_protein_threes( hierarchy, geometry=restraints_manager.geometry, cdl_class=True, ) ): cis_peptide_bond = threes.cis_group() if cis_peptide_bond: print(cis_peptide_bond) assert cis_peptide_bond == filenames[filename][3][i] def test_average(hierarchy, filename, restraints_manager, ): for i, threes in enumerate(cdl.generate_protein_threes( hierarchy, geometry=restraints_manager.geometry, cdl_class=True, ) ): if threes.registry.n: for key in threes.registry.n.keys(): assert key in filenames[filename][3] def get_managers(filename, testing=False, verbose=False): mon_lib_srv = monomer_library.server.server() ener_lib = monomer_library.server.ener_lib() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = ener_lib, file_name = filename, raw_records = None, force_symmetry = True, ) ################ geometry = processed_pdb_file.geometry_restraints_manager( show_energies = False, plain_pairs_radius = 5.0) restraints_manager = mmtbx.restraints.manager(geometry = geometry, normalization = False) xray_structure = processed_pdb_file.xray_structure() selection = flex.bool(xray_structure.scatterers().size(), True) # Not used anywhere, incorrect creation. # mol = mmtbx.model.manager( # restraints_manager = restraints_manager, # xray_structure = xray_structure, # pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy) return processed_pdb_file, restraints_manager def run_apply(filename, testing=False, verbose=False): processed_pdb_file, restraints_manager = get_managers(filename) if testing: test_res_type(processed_pdb_file.all_chain_proxies.pdb_hierarchy, filename, restraints_manager, ) test_phi_psi_key(processed_pdb_file.all_chain_proxies.pdb_hierarchy, filename, restraints_manager, ) test_cdl_lookup(processed_pdb_file.all_chain_proxies.pdb_hierarchy, filename, restraints_manager, ) test_cis_trans_peptide(processed_pdb_file.all_chain_proxies.pdb_hierarchy, filename, restraints_manager, ) print("OK") sites_cart = processed_pdb_file.all_chain_proxies.sites_cart_exact() if True: lines = StringIO() restraints_manager.geometry.show_sorted(sites_cart=sites_cart, f=lines) f=open("%s_pre.geo" % os.path.basename(filename)[:-4], "w") f.write(lines.getvalue()) f.close() t0=time.time() cdl_proxies = cdl_setup.setup_restraints(restraints_manager.geometry, verbose=verbose, ) cdl.update_restraints(processed_pdb_file.all_chain_proxies.pdb_hierarchy, geometry=restraints_manager.geometry, cdl_proxies=cdl_proxies, verbose=verbose, ) if testing: test_average(processed_pdb_file.all_chain_proxies.pdb_hierarchy, filename, restraints_manager, ) print('OK') print('Time to update restraints %0.5fs' % (time.time()-t0)) if True: lines = StringIO() restraints_manager.geometry.show_sorted(sites_cart=sites_cart, f=lines) f=open("%s_post.geo" % os.path.basename(filename)[:-4], "w") f.write(lines.getvalue()) f.close() def convert_dict_to_excel(keys_number=4, column_number=6, ): key = sorted(cdl_database.keys())[keys_number] outl = " " phi_range = (0, 370, 10) psi_range = (0, 370, 10) phi_range = (180, -190, -10) psi_range = (-180, 190, 10) for i, psi in enumerate(range(*psi_range)): outl += ", %d" % psi outl += "\n" for i, phi in enumerate(range(*phi_range)): outl += "%3d" % phi if phi>=180: phi-=360 for j, psi in enumerate(range(*psi_range)): if psi>=180: psi-=360 print(phi, psi, cdl_database[key][(phi, psi)][column_number]) outl += ", %0.2f" % cdl_database[key][(phi, psi)][column_number] outl += "\n" outl += "\n" print(outl) return outl def convert_dict_to_gnuplot(keys_number=4, column_number=6, dales_format=False, ): key = sorted(cdl_database.keys())[keys_number] outl = " " if dales_format: header = """set terminal png size 1850,2000 linewidth 1 set output '%s.png' set border 4095 front linetype -1 linewidth 1.000 set title "CDL for (!Gly,!Pro,!Ile,!Val)-!Pro" set xlabel "phi" set ylabel "psi" #unset key #unset colorbar #set tic scale 0 set palette rgbformulae 33,13,10 # rainbow set cbrange [%s:%s] set ticslevel 60 set xtic 60 set xrange [-180:180] set ytic 60 set yrange [-180:180] set view map set samples 36, 36 set isosamples 36, 36 splot '-' matrix using (10*$2-180):(10*$1-180):3 with image """ outl = "" phi_range = (-180, 190, 10) psi_range = (-180, 190, 10) data = [] for i, phi in enumerate(range(*phi_range)): if phi>=180: kphi=phi-360 else: kphi=phi for j, psi in enumerate(range(*psi_range)): if psi>=180: kpsi=psi-360 else: kpsi=psi outl += " %7.3f" % (cdl_database[key][(kphi, kpsi)][column_number]) data.append(cdl_database[key][(kphi, kpsi)][column_number]) outl += "\n" outl = header % (key, min(data), max(data)) + outl else: phi_range = (0, 370, 10) psi_range = (0, 370, 10) for i, phi in enumerate(range(*phi_range)): if phi>=180: kphi=phi-360 else: kphi=phi for j, psi in enumerate(range(*psi_range)): if psi>=180: kpsi=psi-360 else: kpsi=psi outl += " %12.5f %12.5f %12.5f\n" % (phi, psi, cdl_database[key][(kphi, kpsi)][column_number]) return outl def convert_dict_to_scilab(keys_number=4, column_number=6, ): key = sorted(cdl_database.keys())[keys_number] phi_range = (0, 370, 10) psi_range = (0, 370, 10) #phi_range = (-180, 190, 10) #psi_range = (-180, 190, 10) outl = '' outl += "X = [\n" for i, phi in enumerate(range(*phi_range)): outl += " %12.5f" % phi outl += "];\n" outl += "Y = [\n" for i, psi in enumerate(range(*psi_range)): outl += " %12.5f" % psi outl += "];\n" outl += "Z = [" for i, phi in enumerate(range(*phi_range)): if phi>=180: kphi=phi-360 else: kphi=phi for j, psi in enumerate(range(*psi_range)): if psi>=180: kpsi=psi-360 else: kpsi=psi outl += " %12.5f" % (cdl_database[key][(kphi, kpsi)][column_number]-110) outl += "\n" outl += "];\n" outl += """ surf(X,Y,Z); """ #scf(10) #axfig10=gca(); #surf(axfig10,Z,'zdat',[100:119],'marker','d','markerfac','green','markeredg','yel') // draw onto the axe of figure 10 print(outl) return outl def convert_dict_to_kin2Dcont(keys_number=4, column_number=6, ): key = sorted(cdl_database.keys())[keys_number] outl = "PHI/PSI %s %s" % (key, column_number) outl = """# Table name/description: "motif.loose_threeten" # Number of dimensions: 2 # For each dimension, 1 to 2: lower_bound upper_bound number_of_bins wrapping # x1: -180.0 180.0 120 true # x2: -180.0 180.0 120 true # List of table coordinates and values. (Value is last number on each line.) """ phi_range = (0, 370, 10) psi_range = (0, 370, 10) #phi_range = (-180, 190, 10) #psi_range = (-180, 190, 10) for i, phi in enumerate(range(*phi_range)): if phi>=180: kphi=phi-360 else: kphi=phi for j, psi in enumerate(range(*psi_range)): if psi>=180: kpsi=psi-360 else: kpsi=psi outl += " %12.5f %12.5f %12.5f\n" % (phi, psi, cdl_database[key][(kphi, kpsi)][column_number]) print(outl) return outl def get_min_max_table(): from mmtbx.conformation_dependent_library import columns def anglise(s): outl = "" for c in s: if c in ["m", "s"]: continue if c=="A": outl += "%s-" % "CA" elif c=="B": outl += "%s-" % "CB" else: outl += "%s-" % c return outl[:-1] svl_data = [None, None, 121.7, 1.8, 110.4, 1.5, 111.2, 2.8, None, None, 120.8, 1.7, 116.2, 2.0, 123.0, 1.6, ] ## min_values = [1e9]*26 min_data = [None]*26 max_values = [-1e9]*26 max_data = [None]*26 for i, (residue_class, resdiue_data) in enumerate(cdl_database.items()): if residue_class.startswith("Gly"): continue if residue_class.startswith("Pro"): continue print(residue_class) for j, (phi_psi, data) in enumerate(sorted(resdiue_data.items())): for k, d in enumerate(data): if k<2: continue if dmax_values[k]: max_values[k]=d max_data[k]=(residue_class, phi_psi) print(min_values) print(max_values) print(min_data) print(max_data) outl = "Angle\tSVL\tmin(CDL)\tmax(CDL)\n" for i, c in enumerate(columns): if i<2: continue if i>15: continue if c.startswith("s"): continue print(i, c) outl += anglise(c) if svl_data[i] is None: outl += "\t-" else: outl += "\t%0.1f" % svl_data[i] outl += "\t%0.1f" % min_values[i] outl += "\t%0.1f" % max_values[i] #outl += "\t#%s %s" % min_data[i] #outl += "\t%s %s" % max_data[i] outl += "\n" print(outl) assert 0 def run(filename=None): if 0: print(get_min_max_table()) assert 0 if 0: for i, key in enumerate(sorted(cdl_database)): output = "n_ca_c_m_%s.dat" % key print(i+1,key,output) f=open(output, "w") f.write(convert_dict_to_gnuplot(keys_number=i, dales_format=True)) f.close() cmd = "gnuplot %s" % output os.system(cmd) assert 0 f=open("n_ca_c_e.dat", "w") f.write(convert_dict_to_gnuplot(column_number=7)) f.close() f=open("n_ca_c_m.csv", "w") f.write(convert_dict_to_excel()) f.close() f=open("n_ca_c_m.cse", "w") f.write(convert_dict_to_scilab()) f.close() assert 0 if filename: print('run CDL on',filename) run_apply(filename, #verbose=True, ) else: print('Running tests') for filename in output_filenames: print(filename) f=open(filename, "w") f.write(output_filenames[filename]) f.close() for filename in filenames: #if filename.find("_8")==-1: continue print(('%s ' % filename)*5) run_apply(filename, testing=True) def test_threes_methods(): import iotbx.pdb from mmtbx.conformation_dependent_library import generate_protein_threes tmp_hierarchy = iotbx.pdb.input( source_info=None, lines=flex.split_lines(output_filenames["cdl_test_8.pdb"])).\ construct_hierarchy() for three in generate_protein_threes( hierarchy=tmp_hierarchy, geometry=None): # there should be only one! assert three.get_resnames() == ["CYS", "TYR", "PRO"], '%s!=%s' % ( three.get_resnames(), ["CYS", "TYR", "PRO"]) if __name__=="__main__": args = sys.argv[1:] del sys.argv[1:] run(*tuple(args)) test_threes_methods()