from __future__ import absolute_import, division, print_function import iotbx.pdb import mmtbx.model from mmtbx.building.cablam_idealization import cablam_idealization, master_phil import sys import libtbx.load_env pdb_str = """\ CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 ATOM 3486 N ASP B 60 -68.331 -5.725 16.616 1.00356.89 N ATOM 3487 CA ASP B 60 -67.541 -4.918 17.544 1.00354.36 C ATOM 3488 C ASP B 60 -68.367 -3.945 18.382 1.00349.38 C ATOM 3489 O ASP B 60 -67.818 -3.097 19.085 1.00353.38 O ATOM 3490 CB ASP B 60 -66.380 -4.208 16.838 1.00364.04 C ATOM 3491 CG ASP B 60 -66.848 -3.072 15.947 1.00374.37 C ATOM 3492 OD1 ASP B 60 -67.274 -3.347 14.807 1.00380.37 O ATOM 3493 OD2 ASP B 60 -66.790 -1.905 16.390 1.00373.73 O ATOM 3494 N ARG B 61 -69.688 -4.069 18.299 1.00217.95 N ATOM 3495 CA ARG B 61 -70.579 -3.330 19.184 1.00218.28 C ATOM 3496 C ARG B 61 -70.384 -3.821 20.612 1.00234.70 C ATOM 3497 O ARG B 61 -70.597 -3.079 21.571 1.00234.95 O ATOM 3498 CB ARG B 61 -72.036 -3.522 18.760 1.00222.27 C ATOM 3499 CG ARG B 61 -72.308 -3.208 17.298 1.00232.42 C ATOM 3500 CD ARG B 61 -73.800 -3.126 17.017 1.00227.11 C ATOM 3501 NE ARG B 61 -74.437 -4.441 17.033 1.00220.57 N ATOM 3502 CZ ARG B 61 -75.224 -4.877 18.010 1.00214.60 C ATOM 3503 NH1 ARG B 61 -75.477 -4.104 19.058 1.00208.86 N ATOM 3504 NH2 ARG B 61 -75.765 -6.086 17.938 1.00218.17 N ATOM 3505 N PHE B 62 -69.981 -5.081 20.744 1.00313.84 N ATOM 3506 CA PHE B 62 -69.806 -5.705 22.048 1.00311.92 C ATOM 3507 C PHE B 62 -68.353 -5.573 22.485 1.00313.16 C ATOM 3508 O PHE B 62 -67.444 -5.948 21.745 1.00313.62 O ATOM 3509 CB PHE B 62 -70.185 -7.186 21.984 1.00309.55 C ATOM 3510 CG PHE B 62 -71.655 -7.434 21.800 1.00313.91 C ATOM 3511 CD1 PHE B 62 -72.220 -7.421 20.535 1.00321.28 C ATOM 3512 CD2 PHE B 62 -72.469 -7.693 22.889 1.00308.01 C ATOM 3513 CE1 PHE B 62 -73.571 -7.652 20.360 1.00337.52 C ATOM 3514 CE2 PHE B 62 -73.821 -7.926 22.722 1.00309.58 C ATOM 3515 CZ PHE B 62 -74.372 -7.906 21.456 1.00318.15 C ATOM 3516 N SER B 63 -68.130 -5.040 23.680 1.00111.87 N ATOM 3517 CA SER B 63 -66.767 -4.860 24.171 1.00114.06 C ATOM 3518 C SER B 63 -66.702 -5.129 25.666 1.00112.84 C ATOM 3519 O SER B 63 -67.647 -4.846 26.389 1.00114.81 O ATOM 3520 CB SER B 63 -66.285 -3.437 23.889 1.00122.19 C ATOM 3521 OG SER B 63 -66.964 -2.499 24.704 1.00128.65 O ATOM 3522 N GLY B 64 -65.590 -5.684 26.131 1.00202.30 N ATOM 3523 CA GLY B 64 -65.434 -5.946 27.550 1.00201.80 C ATOM 3524 C GLY B 64 -64.380 -5.070 28.196 1.00202.46 C ATOM 3525 O GLY B 64 -63.430 -4.645 27.540 1.00204.01 O ATOM 3526 N SER B 65 -64.546 -4.798 29.486 1.00415.58 N ATOM 3527 CA SER B 65 -63.617 -3.931 30.195 1.00415.64 C ATOM 3528 C SER B 65 -62.343 -4.708 30.511 1.00426.21 C ATOM 3529 O SER B 65 -62.412 -5.875 30.896 1.00421.89 O ATOM 3530 CB SER B 65 -64.248 -3.425 31.492 1.00419.11 C ATOM 3531 OG SER B 65 -64.591 -4.500 32.348 1.00420.16 O ATOM 3532 N PRO B 66 -61.178 -4.066 30.331 1.00169.68 N ATOM 3533 CA PRO B 66 -59.871 -4.722 30.477 1.00191.83 C ATOM 3534 C PRO B 66 -59.702 -5.422 31.823 1.00193.95 C ATOM 3535 O PRO B 66 -60.275 -4.979 32.818 1.00192.66 O ATOM 3536 CB PRO B 66 -58.865 -3.568 30.331 1.00194.66 C ATOM 3537 CG PRO B 66 -59.667 -2.310 30.440 1.00190.47 C ATOM 3538 CD PRO B 66 -61.046 -2.643 29.980 1.00169.32 C ATOM 3539 N GLY B 67 -58.925 -6.502 31.851 1.00 80.00 N ATOM 3540 CA GLY B 67 -58.642 -7.188 33.095 1.00 80.51 C ATOM 3541 C GLY B 67 -57.514 -6.497 33.837 1.00 81.49 C ATOM 3542 O GLY B 67 -56.425 -7.051 33.989 1.00 83.70 O ATOM 3543 N SER B 67A -57.783 -5.282 34.300 1.00199.92 N ATOM 3544 CA SER B 67A -56.736 -4.282 34.475 1.00200.79 C ATOM 3545 C SER B 67A -56.694 -3.694 35.881 1.00199.95 C ATOM 3546 O SER B 67A -56.174 -4.312 36.811 1.00200.95 O ATOM 3547 CB SER B 67A -56.901 -3.160 33.447 1.00200.17 C ATOM 3548 OG SER B 67A -58.231 -2.670 33.441 1.00197.80 O ATOM 3549 N THR B 67B -57.237 -2.486 36.012 1.00276.34 N ATOM 3550 CA THR B 67B -57.204 -1.728 37.262 1.00275.38 C ATOM 3551 C THR B 67B -57.762 -2.498 38.458 1.00273.67 C ATOM 3552 O THR B 67B -58.921 -2.912 38.460 1.00271.08 O ATOM 3553 CB THR B 67B -57.973 -0.398 37.122 1.00273.24 C ATOM 3554 OG1 THR B 67B -57.301 0.452 36.184 1.00275.35 O ATOM 3555 CG2 THR B 67B -58.069 0.309 38.467 1.00272.11 C ATOM 3556 N PHE B 67C -56.915 -2.687 39.465 1.00301.79 N ATOM 3557 CA PHE B 67C -57.241 -3.518 40.619 1.00297.93 C ATOM 3558 C PHE B 67C -58.413 -2.938 41.408 1.00293.60 C ATOM 3559 O PHE B 67C -58.542 -1.721 41.540 1.00292.18 O ATOM 3560 CB PHE B 67C -56.020 -3.669 41.525 1.00287.21 C ATOM 3561 CG PHE B 67C -54.845 -4.321 40.852 1.00291.30 C ATOM 3562 CD1 PHE B 67C -54.930 -5.621 40.385 1.00295.88 C ATOM 3563 CD2 PHE B 67C -53.656 -3.631 40.686 1.00295.09 C ATOM 3564 CE1 PHE B 67C -53.850 -6.220 39.762 1.00300.88 C ATOM 3565 CE2 PHE B 67C -52.573 -4.224 40.066 1.00296.89 C ATOM 3566 CZ PHE B 67C -52.670 -5.519 39.602 1.00298.84 C ATOM 3567 N GLY B 68 -59.262 -3.816 41.930 1.00112.35 N ATOM 3568 CA GLY B 68 -60.367 -3.398 42.774 1.00110.56 C ATOM 3569 C GLY B 68 -61.552 -2.863 41.995 1.00108.59 C ATOM 3570 O GLY B 68 -62.376 -2.123 42.534 1.00107.14 O ATOM 3571 N THR B 69 -61.637 -3.237 40.723 1.00183.07 N ATOM 3572 CA THR B 69 -62.745 -2.814 39.874 1.00181.38 C ATOM 3573 C THR B 69 -63.545 -4.003 39.353 1.00181.09 C ATOM 3574 O THR B 69 -63.091 -5.146 39.424 1.00182.43 O ATOM 3575 CB THR B 69 -62.277 -1.928 38.702 1.00181.62 C ATOM 3576 OG1 THR B 69 -61.373 -2.667 37.871 1.00183.42 O ATOM 3577 CG2 THR B 69 -61.575 -0.682 39.223 1.00181.84 C ATOM 3578 N THR B 70 -64.733 -3.732 38.825 1.00278.18 N ATOM 3579 CA THR B 70 -65.621 -4.789 38.364 1.00281.57 C ATOM 3580 C THR B 70 -65.624 -4.886 36.844 1.00285.93 C ATOM 3581 O THR B 70 -65.496 -3.878 36.148 1.00285.87 O ATOM 3582 CB THR B 70 -67.068 -4.575 38.851 1.00284.48 C ATOM 3583 OG1 THR B 70 -67.548 -3.307 38.386 1.00289.32 O ATOM 3584 CG2 THR B 70 -67.132 -4.608 40.367 1.00284.89 C ATOM 3585 N ALA B 71 -65.768 -6.105 36.336 1.00205.02 N ATOM 3586 CA ALA B 71 -65.795 -6.328 34.898 1.00205.75 C ATOM 3587 C ALA B 71 -67.103 -5.798 34.328 1.00203.15 C ATOM 3588 O ALA B 71 -68.160 -5.945 34.941 1.00200.88 O ATOM 3589 CB ALA B 71 -65.641 -7.806 34.587 1.00207.09 C ATOM 3590 N THR B 72 -67.030 -5.179 33.155 1.00197.86 N ATOM 3591 CA THR B 72 -68.216 -4.610 32.533 1.00196.26 C ATOM 3592 C THR B 72 -68.291 -4.959 31.050 1.00196.89 C ATOM 3593 O THR B 72 -67.278 -4.957 30.351 1.00198.50 O ATOM 3594 CB THR B 72 -68.256 -3.075 32.716 1.00195.44 C ATOM 3595 OG1 THR B 72 -68.046 -2.749 34.094 1.00195.12 O ATOM 3596 CG2 THR B 72 -69.592 -2.507 32.261 1.00193.77 C ATOM 3597 N LEU B 73 -69.496 -5.259 30.579 1.00101.29 N ATOM 3598 CA LEU B 73 -69.729 -5.469 29.161 1.00 88.83 C ATOM 3599 C LEU B 73 -70.496 -4.274 28.618 1.00 88.26 C ATOM 3600 O LEU B 73 -71.556 -3.918 29.130 1.00 87.52 O ATOM 3601 CB LEU B 73 -70.547 -6.740 28.948 1.00103.60 C ATOM 3602 CG LEU B 73 -71.101 -6.977 27.540 1.00104.89 C ATOM 3603 CD1 LEU B 73 -69.973 -7.253 26.559 1.00 92.28 C ATOM 3604 CD2 LEU B 73 -72.103 -8.120 27.544 1.00 91.89 C ATOM 3605 N THR B 74 -69.957 -3.662 27.572 1.00223.92 N ATOM 3606 CA THR B 74 -70.593 -2.524 26.929 1.00224.10 C ATOM 3607 C THR B 74 -71.120 -2.933 25.561 1.00227.31 C ATOM 3608 O THR B 74 -70.407 -3.554 24.766 1.00233.82 O ATOM 3609 CB THR B 74 -69.602 -1.357 26.762 1.00233.24 C ATOM 3610 OG1 THR B 74 -69.143 -0.930 28.051 1.00232.54 O ATOM 3611 CG2 THR B 74 -70.260 -0.188 26.050 1.00232.76 C ATOM 3612 N ILE B 75 -72.374 -2.583 25.294 1.00280.73 N ATOM 3613 CA ILE B 75 -72.965 -2.786 23.980 1.00278.29 C ATOM 3614 C ILE B 75 -73.403 -1.447 23.399 1.00281.31 C ATOM 3615 O ILE B 75 -74.302 -0.797 23.926 1.00294.58 O ATOM 3616 CB ILE B 75 -74.174 -3.739 24.042 1.00293.28 C ATOM 3617 CG1 ILE B 75 -73.824 -4.996 24.844 1.00285.07 C ATOM 3618 CG2 ILE B 75 -74.636 -4.103 22.640 1.00278.12 C ATOM 3619 CD1 ILE B 75 -75.031 -5.760 25.342 1.00287.98 C """ def exercise_insertions(prefix="tst_cablam_insertions"): pdb_inp = iotbx.pdb.input(lines=pdb_str.split('\n'), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp) with open("%s_start.pdb" % prefix, 'w') as f: f.write(model.model_as_pdb()) ci = cablam_idealization(model = model, params=master_phil.extract().cablam_idealization, log=sys.stdout) pdb_txt = model.model_as_pdb() if __name__ == '__main__': if (not libtbx.env.has_module(name="probe")): print("Skipping: probe not configured") else: exercise_insertions()