from __future__ import absolute_import, division, print_function import sys from libtbx import easy_run gnp = ''' HETATM 2435 PG GNP A 201 -5.193 14.551 -21.840 1.00 9.31 P HETATM 2436 O1G GNP A 201 -6.728 14.452 -21.462 1.00 12.25 O HETATM 2437 O2G GNP A 201 -5.090 14.640 -23.230 1.00 18.00 O HETATM 2438 O3G GNP A 201 -4.278 15.571 -21.150 1.00 15.01 O HETATM 2439 N3B GNP A 201 -4.611 12.945 -21.512 1.00 13.32 N HETATM 2440 PB GNP A 201 -3.816 12.564 -20.004 1.00 5.89 P HETATM 2441 O1B GNP A 201 -2.466 13.219 -20.064 1.00 12.14 O HETATM 2442 O2B GNP A 201 -4.929 13.094 -19.079 1.00 11.92 O HETATM 2443 O3A GNP A 201 -3.652 11.002 -20.112 1.00 6.88 O HETATM 2444 PA GNP A 201 -4.825 9.898 -19.654 1.00 9.13 P HETATM 2445 O1A GNP A 201 -4.707 9.944 -18.092 1.00 9.97 O HETATM 2446 O2A GNP A 201 -6.090 10.319 -20.321 1.00 6.24 O HETATM 2447 O5' GNP A 201 -4.205 8.569 -20.187 1.00 11.53 O HETATM 2448 C5' GNP A 201 -3.543 8.298 -21.351 1.00 6.70 C HETATM 2449 C4' GNP A 201 -3.319 6.842 -21.597 1.00 9.27 C HETATM 2450 O4' GNP A 201 -2.180 6.257 -20.945 1.00 11.15 O HETATM 2451 C3' GNP A 201 -4.555 5.972 -21.280 1.00 5.98 C HETATM 2452 O3' GNP A 201 -4.838 5.178 -22.402 1.00 20.95 O HETATM 2453 C2' GNP A 201 -4.170 5.413 -19.954 1.00 12.11 C HETATM 2454 O2' GNP A 201 -4.838 4.350 -19.264 1.00 16.85 O HETATM 2455 C1' GNP A 201 -2.581 5.457 -19.941 1.00 10.49 C HETATM 2456 N9 GNP A 201 -1.773 5.496 -18.743 1.00 14.77 N HETATM 2457 C8 GNP A 201 -1.890 6.470 -17.880 1.00 11.82 C HETATM 2458 N7 GNP A 201 -1.084 6.312 -16.856 1.00 14.77 N HETATM 2459 C5 GNP A 201 -0.458 5.227 -17.093 1.00 13.86 C HETATM 2460 C6 GNP A 201 0.560 4.449 -16.442 1.00 16.13 C HETATM 2461 O6 GNP A 201 0.924 4.910 -15.409 1.00 13.44 O HETATM 2462 N1 GNP A 201 1.054 3.385 -16.896 1.00 14.95 N HETATM 2463 C2 GNP A 201 0.591 2.888 -18.089 1.00 12.85 C HETATM 2464 N2 GNP A 201 1.104 1.752 -18.562 1.00 17.51 N HETATM 2465 N3 GNP A 201 -0.378 3.514 -18.819 1.00 12.28 N HETATM 2466 C4 GNP A 201 -0.911 4.657 -18.367 1.00 18.03 C HETATM 2467 DOG2 GNP A 201 -4.220 14.350 -23.480 1.00 21.60 D HETATM 2468 DNB3 GNP A 201 -4.638 12.314 -22.176 1.00 15.99 D HETATM 2469 H5'2 GNP A 201 -4.064 8.664 -22.100 1.00 8.04 H HETATM 2470 H5'1 GNP A 201 -2.670 8.749 -21.327 1.00 8.04 H HETATM 2471 H4' GNP A 201 -3.158 6.751 -22.563 1.00 11.13 H HETATM 2472 H3' GNP A 201 -5.321 6.570 -21.140 1.00 7.17 H HETATM 2473 DO3' GNP A 201 -5.612 5.410 -22.779 1.00 25.14 D HETATM 2474 H2' GNP A 201 -4.391 6.162 -19.360 1.00 14.54 H HETATM 2475 DO2' GNP A 201 -5.490 4.672 -18.757 1.00 20.22 D HETATM 2476 H1' GNP A 201 -2.361 4.562 -20.283 1.00 12.59 H HETATM 2477 H8 GNP A 201 -2.520 7.220 -17.970 1.00 14.18 H HETATM 2478 DN1 GNP A 201 1.698 2.933 -16.423 1.00 17.94 D HETATM 2479 DN21 GNP A 201 1.566 1.190 -18.004 1.00 21.01 D HETATM 2480 DN22 GNP A 201 0.995 1.532 -19.446 1.00 21.01 D ''' llp_neutron = ''' REMARK CRYST1 55.532 124.986 130.444 90.00 90.00 90.00 P 21 21 21 HETATM 1 N LLP B 258 -0.447 -10.941 14.499 1.00 15.19 N HETATM 2 CA LLP B 258 -0.166 -10.435 13.173 1.00 16.94 C HETATM 3 C LLP B 258 1.020 -9.463 13.270 1.00 16.29 C HETATM 4 O LLP B 258 1.880 -9.487 12.435 1.00 16.55 O HETATM 5 CB LLP B 258 -1.413 -9.787 12.490 1.00 19.72 C HETATM 6 CG LLP B 258 -2.474 -10.860 12.217 1.00 22.40 C HETATM 7 CD LLP B 258 -3.792 -10.723 13.002 1.00 23.55 C HETATM 8 CE LLP B 258 -4.807 -11.905 12.717 1.00 24.31 C HETATM 9 NZ LLP B 258 -6.088 -11.491 13.288 1.00 24.08 N HETATM 10 C2 LLP B 258 -9.937 -9.685 14.136 1.00 18.63 C HETATM 11 C2' LLP B 258 -10.748 -8.689 13.386 1.00 18.63 C HETATM 12 C3 LLP B 258 -8.817 -10.412 13.596 1.00 18.26 C HETATM 13 C4 LLP B 258 -8.134 -11.344 14.456 1.00 20.66 C HETATM 14 C4' LLP B 258 -7.015 -12.088 13.961 1.00 24.62 C HETATM 15 C5 LLP B 258 -8.637 -11.466 15.781 1.00 19.23 C HETATM 16 C5' LLP B 258 -7.977 -12.415 16.725 1.00 19.27 C HETATM 17 C6 LLP B 258 -9.708 -10.734 16.205 1.00 16.33 C HETATM 18 D LLP B 258 -0.978 -10.290 15.036 1.00 15.65 D HETATM 19 DB2 LLP B 258 -1.099 -9.339 11.539 1.00 19.84 D HETATM 20 DB3 LLP B 258 -1.817 -8.976 13.109 1.00 21.03 D HETATM 21 DD2 LLP B 258 -3.584 -10.689 14.078 1.00 25.88 D HETATM 22 DE2 LLP B 258 -4.436 -12.823 13.186 1.00 24.67 D HETATM 23 DE3 LLP B 258 -4.912 -12.073 11.641 1.00 23.22 D HETATM 24 DG2 LLP B 258 -2.076 -11.872 12.359 1.00 22.69 D HETATM 25 DG3 LLP B 258 -2.733 -10.803 11.151 1.00 21.60 D HETATM 26 N1 LLP B 258 -10.252 -9.936 15.386 1.00 16.38 N HETATM 27 O3 LLP B 258 -8.483 -10.155 12.287 1.00 22.39 O HETATM 28 OP1 LLP B 258 -5.476 -15.288 16.374 1.00 16.32 O HETATM 29 OP2 LLP B 258 -7.046 -14.828 18.431 1.00 13.48 O HETATM 30 OP3 LLP B 258 -4.890 -13.481 18.022 1.00 15.01 O HETATM 31 OP4 LLP B 258 -6.764 -13.026 16.528 1.00 20.08 O HETATM 32 P LLP B 258 -6.052 -14.262 17.370 1.00 13.48 P HETATM 33 H6 LLP B 258 -10.075 -10.811 17.219 1.00 17.86 H HETATM 34 H2'3 LLP B 258 -11.798 -9.003 13.358 1.00 19.77 H HETATM 35 H4'1 LLP B 258 -6.902 -13.121 14.273 1.00 23.11 H HETATM 36 H5'1 LLP B 258 -8.706 -13.215 16.912 1.00 19.90 H HETATM 37 H5'2 LLP B 258 -7.879 -11.891 17.686 1.00 18.49 H HETATM 38 D1ZALLP B 258 -11.031 -9.415 15.735 0.94 16.15 D HETATM 39 DA ALLP B 258 0.162 -11.264 12.527 0.90 17.45 D HETATM 40 DD3ALLP B 258 -4.256 -9.766 12.729 0.67 24.01 D HETATM 41 D2'1ALLP B 258 -10.434 -8.534 12.352 0.24 19.01 D HETATM 42 D2'2ALLP B 258 -10.701 -7.714 13.885 0.40 19.18 D HETATM 43 HA BLLP B 258 0.162 -11.264 12.527 0.10 17.45 H HETATM 44 HD3BLLP B 258 -4.256 -9.766 12.729 0.33 24.01 H HETATM 45 H1ZBLLP B 258 -11.031 -9.415 15.735 0.06 16.15 H HETATM 46 H2'1BLLP B 258 -10.434 -8.534 12.352 0.76 19.01 H HETATM 47 H2'2BLLP B 258 -10.701 -7.714 13.885 0.60 19.18 H ''' def run1(): f = open('tst_pH_gnp.pdb', 'w') f.write(gnp) f.close() cmd = 'phenix.geometry_minimization tst_pH_gnp.pdb' print(cmd) rc = easy_run.go(cmd) find = ['Changed 28 bond restraint(s), added 1 bond restraint(s)', 'Changed 43 angle restraint(s), added 1 angle restraint(s)', ] for f in find: for line in rc.stdout_lines: if line.find(f)>-1: print(line) break else: assert 0, 'line not found: %s' % f return rc def run2(): f = open('tst_LLP_neutron.pdb', 'w') f.write(llp_neutron) f.close() cmd = 'phenix.geometry_minimization tst_LLP_neutron.pdb' print(cmd) rc = easy_run.go(cmd) find = ['Changed 32 bond restraint(s), added 2 bond restraint(s)', 'Changed 52 angle restraint(s), added 4 angle restraint(s)', ] for f in find: for line in rc.stdout_lines: if line.find(f)>-1: print(line) break else: assert 0, 'line not found: %s' % f return rc if __name__=="__main__": args = sys.argv[1:] del sys.argv[1:] rc = run1() assert rc.return_code==0 rc = run2() assert rc.return_code==0