from __future__ import absolute_import, division, print_function from mmtbx.command_line import molprobity import iotbx.pdb from scitbx.array_family import flex from libtbx.test_utils import approx_equal from libtbx.utils import null_out from six.moves import cStringIO as StringIO from six.moves import zip # derivative of 1yjp, with alternate conformation Asn3 in different rotamer, # plus Asn2/Gln4 split. the unit cell 'b' edge has been increased to 6A to # compensate. pdb_raw_0 = """\ CRYST1 21.937 6.000 23.477 90.00 107.08 90.00 P 1 21 1 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.166667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 ATOM 1 N GLY A 1 -9.047 4.634 6.066 1.00 16.37 N ATOM 2 CA GLY A 1 -9.040 4.191 4.677 1.00 16.17 C ATOM 3 C GLY A 1 -7.991 3.118 4.432 1.00 15.46 C ATOM 4 O GLY A 1 -7.507 2.493 5.371 1.00 16.71 O ATOM 5 H1 GLY A 1 -9.744 5.171 6.203 1.00 16.37 H ATOM 6 H2 GLY A 1 -9.108 3.927 6.603 1.00 16.37 H ATOM 7 H3 GLY A 1 -8.294 5.075 6.240 1.00 16.37 H ATOM 8 HA2 GLY A 1 -9.911 3.831 4.446 1.00 16.17 H ATOM 9 HA3 GLY A 1 -8.853 4.945 4.096 1.00 16.17 H ATOM 10 N AASN A 2 -7.663 2.878 3.168 0.60 14.94 N ATOM 11 CA AASN A 2 -6.533 2.012 2.845 0.60 14.28 C ATOM 12 C AASN A 2 -5.242 2.518 3.452 0.60 12.87 C ATOM 13 O AASN A 2 -5.000 3.723 3.505 0.60 12.55 O ATOM 14 CB AASN A 2 -6.356 1.880 1.341 0.60 15.48 C ATOM 15 CG AASN A 2 -7.500 1.158 0.693 0.60 13.90 C ATOM 16 OD1AASN A 2 -8.052 1.622 -0.304 0.60 17.99 O ATOM 17 ND2AASN A 2 -7.867 0.008 1.252 0.60 11.61 N ATOM 18 H AASN A 2 -8.073 3.200 2.484 0.60 15.11 H ATOM 19 HA AASN A 2 -6.701 1.129 3.209 0.60 13.97 H ATOM 20 HB2AASN A 2 -6.298 2.766 0.949 0.60 15.07 H ATOM 21 HB3AASN A 2 -5.544 1.382 1.160 0.60 15.07 H ATOM 22 HD21AASN A 2 -8.569 -0.402 0.970 0.60 11.52 H ATOM 23 HD22AASN A 2 -7.404 -0.326 1.894 0.60 11.52 H ATOM 24 N BASN A 2 -7.626 2.899 3.175 0.40 15.11 N ATOM 25 CA BASN A 2 -6.447 2.085 2.893 0.40 13.97 C ATOM 26 C BASN A 2 -5.209 2.731 3.488 0.40 13.04 C ATOM 27 O BASN A 2 -5.077 3.953 3.479 0.40 11.55 O ATOM 28 CB BASN A 2 -6.250 1.906 1.394 0.40 15.07 C ATOM 29 CG BASN A 2 -7.412 1.207 0.741 0.40 13.81 C ATOM 30 OD1BASN A 2 -7.953 1.683 -0.257 0.40 17.17 O ATOM 31 ND2BASN A 2 -7.805 0.067 1.298 0.40 11.52 N ATOM 32 H BASN A 2 -8.032 3.202 2.480 0.40 15.11 H ATOM 33 HA BASN A 2 -6.556 1.209 3.295 0.40 13.97 H ATOM 34 HB2BASN A 2 -6.153 2.778 0.981 0.40 15.07 H ATOM 35 HB3BASN A 2 -5.454 1.374 1.240 0.40 15.07 H ATOM 36 HD21BASN A 2 -8.484 -0.355 0.980 0.40 11.52 H ATOM 37 HD22BASN A 2 -7.381 -0.249 1.976 0.40 11.52 H ATOM 38 N AASN A 3 -4.414 1.582 3.898 0.60 12.35 N ATOM 39 CA AASN A 3 -3.182 1.908 4.599 0.60 11.68 C ATOM 40 C AASN A 3 -1.933 1.346 3.923 0.60 11.09 C ATOM 41 O AASN A 3 -1.858 0.142 3.653 0.60 10.18 O ATOM 42 CB AASN A 3 -3.259 1.407 6.050 0.60 11.62 C ATOM 43 CG AASN A 3 -2.011 1.746 6.852 0.60 13.00 C ATOM 44 OD1AASN A 3 -1.704 2.921 7.070 0.60 15.44 O ATOM 45 ND2AASN A 3 -1.287 0.720 7.295 0.60 12.87 N ATOM 46 H AASN A 3 -4.547 0.737 3.805 0.60 12.00 H ATOM 47 HA AASN A 3 -3.078 2.871 4.634 0.60 11.53 H ATOM 48 HB2AASN A 3 -4.019 1.821 6.488 0.60 12.90 H ATOM 49 HB3AASN A 3 -3.362 0.442 6.047 0.60 12.90 H ATOM 50 HD21AASN A 3 -0.573 0.863 7.753 0.60 12.97 H ATOM 51 HD22AASN A 3 -1.533 -0.086 7.123 0.60 12.97 H ATOM 52 N BASN A 3 -4.310 1.908 4.015 0.40 12.00 N ATOM 53 CA BASN A 3 -3.078 2.406 4.614 0.40 11.53 C ATOM 54 C BASN A 3 -1.844 1.661 4.111 0.40 11.70 C ATOM 55 O BASN A 3 -1.810 0.428 4.100 0.40 10.95 O ATOM 56 CB BASN A 3 -3.152 2.335 6.142 0.40 12.90 C ATOM 57 CG BASN A 3 -4.074 3.380 6.732 0.40 13.32 C ATOM 58 OD1BASN A 3 -4.367 4.398 6.099 0.40 15.04 O ATOM 59 ND2BASN A 3 -4.528 3.143 7.958 0.40 12.97 N ATOM 60 H BASN A 3 -4.390 1.052 4.038 0.40 12.00 H ATOM 61 HA BASN A 3 -2.956 3.336 4.370 0.40 11.53 H ATOM 62 HB2BASN A 3 -3.483 1.461 6.402 0.40 12.90 H ATOM 63 HB3BASN A 3 -2.265 2.476 6.508 0.40 12.90 H ATOM 64 HD21BASN A 3 -5.055 3.706 8.338 0.40 12.97 H ATOM 65 HD22BASN A 3 -4.295 2.426 8.372 0.40 12.97 H ATOM 66 N AGLN A 4 -0.970 2.230 3.649 0.60 10.54 N ATOM 67 CA AGLN A 4 0.385 1.832 3.248 0.60 10.42 C ATOM 68 C AGLN A 4 1.438 2.482 4.154 0.60 11.71 C ATOM 69 O AGLN A 4 1.592 3.742 4.128 0.60 8.92 O ATOM 70 CB AGLN A 4 0.671 2.161 1.771 0.60 9.88 C ATOM 71 CG AGLN A 4 1.921 1.446 1.228 0.60 10.02 C ATOM 72 CD AGLN A 4 2.481 2.048 -0.057 0.60 12.86 C ATOM 73 OE1AGLN A 4 2.716 3.260 -0.143 0.60 14.16 O ATOM 74 NE2AGLN A 4 2.719 1.195 -1.059 0.60 9.04 N ATOM 75 H AGLN A 4 -1.078 3.082 3.689 0.60 10.83 H ATOM 76 HA AGLN A 4 0.472 0.872 3.352 0.60 10.25 H ATOM 77 HB2AGLN A 4 -0.088 1.885 1.234 0.60 9.74 H ATOM 78 HB3AGLN A 4 0.810 3.117 1.682 0.60 9.74 H ATOM 79 HG2AGLN A 4 2.620 1.485 1.899 0.60 10.05 H ATOM 80 HG3AGLN A 4 1.694 0.521 1.045 0.60 10.05 H ATOM 81 HE21AGLN A 4 2.557 0.357 -0.958 0.60 8.91 H ATOM 82 HE22AGLN A 4 3.034 1.485 -1.805 0.60 8.91 H ATOM 83 N BGLN A 4 -0.835 2.425 3.699 0.40 10.83 N ATOM 84 CA BGLN A 4 0.428 1.863 3.233 0.40 10.25 C ATOM 85 C BGLN A 4 1.600 2.421 4.037 0.40 10.29 C ATOM 86 O BGLN A 4 2.033 3.551 3.826 0.40 10.50 O ATOM 87 CB BGLN A 4 0.633 2.137 1.738 0.40 9.74 C ATOM 88 CG BGLN A 4 1.808 1.376 1.129 0.40 10.05 C ATOM 89 CD BGLN A 4 2.359 2.037 -0.120 0.40 12.79 C ATOM 90 OE1BGLN A 4 2.503 3.262 -0.175 0.40 15.08 O ATOM 91 NE2BGLN A 4 2.674 1.228 -1.135 0.40 8.91 N ATOM 92 H BGLN A 4 -0.859 3.284 3.680 0.40 10.83 H ATOM 93 HA BGLN A 4 0.422 0.902 3.357 0.40 10.25 H ATOM 94 HB2BGLN A 4 -0.169 1.873 1.260 0.40 9.74 H ATOM 95 HB3BGLN A 4 0.791 3.086 1.615 0.40 9.74 H ATOM 96 HG2BGLN A 4 2.526 1.323 1.778 0.40 10.05 H ATOM 97 HG3BGLN A 4 1.513 0.484 0.889 0.40 10.05 H ATOM 98 HE21BGLN A 4 2.561 0.379 -1.059 0.40 8.91 H ATOM 99 HE22BGLN A 4 2.990 1.556 -1.865 0.40 8.91 H ATOM 100 N AGLN A 5 2.125 1.651 4.991 0.60 10.59 N ATOM 101 CA AGLN A 5 3.274 2.224 5.659 0.60 11.43 C ATOM 102 C AGLN A 5 4.582 1.732 5.073 0.60 11.24 C ATOM 103 O AGLN A 5 4.749 0.545 4.827 0.60 11.99 O ATOM 104 CB AGLN A 5 3.229 2.076 7.170 0.60 12.07 C ATOM 105 CG AGLN A 5 2.235 3.000 7.859 0.60 10.78 C ATOM 106 CD AGLN A 5 1.562 2.322 9.034 0.60 12.94 C ATOM 107 OE1AGLN A 5 1.005 1.233 8.899 0.60 10.72 O ATOM 108 NE2AGLN A 5 1.621 2.959 10.197 0.60 12.32 N ATOM 109 H AGLN A 5 1.948 0.827 5.163 0.60 10.59 H ATOM 110 HA AGLN A 5 3.279 3.179 5.509 0.60 11.43 H ATOM 111 HB2AGLN A 5 2.987 1.162 7.384 0.60 12.07 H ATOM 112 HB3AGLN A 5 4.109 2.273 7.527 0.60 12.07 H ATOM 113 HG2AGLN A 5 2.702 3.784 8.188 0.60 10.78 H ATOM 114 HG3AGLN A 5 1.548 3.260 7.225 0.60 10.78 H ATOM 115 HE21AGLN A 5 2.025 3.716 10.253 0.60 12.32 H ATOM 116 HE22AGLN A 5 1.255 2.615 10.895 0.60 12.32 H ATOM 117 N BGLN A 5 2.125 1.651 4.991 0.40 10.59 N ATOM 118 CA BGLN A 5 3.274 2.224 5.659 0.40 11.43 C ATOM 119 C BGLN A 5 4.582 1.732 5.073 0.40 11.24 C ATOM 120 O BGLN A 5 4.749 0.545 4.827 0.40 11.99 O ATOM 121 CB BGLN A 5 3.229 2.076 7.170 0.40 12.07 C ATOM 122 CG BGLN A 5 2.235 3.000 7.859 0.40 10.78 C ATOM 123 CD BGLN A 5 1.562 2.322 9.034 0.40 12.94 C ATOM 124 OE1BGLN A 5 1.005 1.233 8.899 0.40 10.72 O ATOM 125 NE2BGLN A 5 1.621 2.959 10.197 0.40 12.32 N ATOM 126 H BGLN A 5 1.863 0.873 5.246 0.40 10.59 H ATOM 127 HA BGLN A 5 3.288 3.182 5.538 0.40 11.43 H ATOM 128 HB2BGLN A 5 2.987 1.162 7.384 0.40 12.07 H ATOM 129 HB3BGLN A 5 4.109 2.273 7.527 0.40 12.07 H ATOM 130 HG2BGLN A 5 2.702 3.784 8.188 0.40 10.78 H ATOM 131 HG3BGLN A 5 1.548 3.260 7.225 0.40 10.78 H ATOM 132 HE21BGLN A 5 2.025 3.716 10.253 0.40 12.32 H ATOM 133 HE22BGLN A 5 1.255 2.615 10.895 0.40 12.32 H ATOM 134 N ASN A 6 5.508 2.663 4.851 1.00 11.72 N ATOM 135 CA ASN A 6 6.825 2.322 4.325 1.00 12.12 C ATOM 136 C ASN A 6 7.854 2.763 5.330 1.00 13.15 C ATOM 137 O ASN A 6 8.221 3.937 5.380 1.00 13.93 O ATOM 138 CB ASN A 6 7.061 3.013 2.994 1.00 11.96 C ATOM 139 CG ASN A 6 5.963 2.732 2.005 1.00 12.58 C ATOM 140 OD1 ASN A 6 5.799 1.604 1.549 1.00 14.01 O ATOM 141 ND2 ASN A 6 5.192 3.751 1.679 1.00 9.96 N ATOM 142 HA ASN A 6 6.919 1.367 4.193 1.00 12.12 H ATOM 143 HB2 ASN A 6 7.099 3.972 3.133 1.00 11.96 H ATOM 144 HB3 ASN A 6 7.896 2.697 2.615 1.00 11.96 H ATOM 145 HD21 ASN A 6 4.551 3.642 1.116 1.00 9.96 H ATOM 146 HD22 ASN A 6 5.330 4.524 2.029 1.00 9.96 H ATOM 147 H AASN A 6 5.396 3.503 4.998 0.60 11.72 H ATOM 148 H BASN A 6 5.396 3.503 4.998 0.40 11.72 H ATOM 149 N TYR A 7 8.297 1.822 6.155 1.00 14.62 N ATOM 150 CA TYR A 7 9.162 2.146 7.291 1.00 15.04 C ATOM 151 C TYR A 7 10.611 2.329 6.888 1.00 15.56 C ATOM 152 O TYR A 7 11.046 1.810 5.854 1.00 15.52 O ATOM 153 CB TYR A 7 9.056 1.072 8.370 1.00 14.86 C ATOM 154 CG TYR A 7 7.657 0.941 8.898 1.00 14.38 C ATOM 155 CD1 TYR A 7 6.767 0.030 8.334 1.00 15.46 C ATOM 156 CD2 TYR A 7 7.206 1.753 9.930 1.00 14.37 C ATOM 157 CE1 TYR A 7 5.476 -0.089 8.802 1.00 13.24 C ATOM 158 CE2 TYR A 7 5.905 1.644 10.409 1.00 13.84 C ATOM 159 CZ TYR A 7 5.049 0.722 9.836 1.00 14.98 C ATOM 160 OH TYR A 7 3.767 0.593 10.299 1.00 14.28 O ATOM 161 OXT TYR A 7 11.361 3.003 7.603 1.00 17.34 O ATOM 162 H TYR A 7 8.113 0.985 6.081 1.00 14.62 H ATOM 163 HA TYR A 7 8.860 2.981 7.681 1.00 15.04 H ATOM 164 HB2 TYR A 7 9.319 0.217 7.995 1.00 14.86 H ATOM 165 HB3 TYR A 7 9.638 1.306 9.110 1.00 14.86 H ATOM 166 HD1 TYR A 7 7.053 -0.517 7.638 1.00 15.46 H ATOM 167 HD2 TYR A 7 7.785 2.372 10.313 1.00 14.37 H ATOM 168 HE1 TYR A 7 4.895 -0.708 8.422 1.00 13.24 H ATOM 169 HE2 TYR A 7 5.614 2.185 11.107 1.00 13.84 H ATOM 170 HH TYR A 7 3.563 1.261 10.764 1.00 14.28 H TER HETATM 171 O HOH S 8 -6.473 5.220 7.122 1.00 22.61 O HETATM 172 O HOH S 9 10.427 1.864 3.212 1.00 19.32 O HETATM 173 O HOH S 10 -11.288 1.762 -1.464 1.00 16.97 O HETATM 174 O HOH S 11 11.803 4.188 9.965 1.00 23.89 O HETATM 175 O HOH S 12 13.608 1.315 9.196 1.00 26.08 O HETATM 176 O HOH S 13 -2.736 3.452 10.015 1.00 38.68 O HETATM 177 O HOH S 14 -1.495 0.667 10.978 1.00 44.24 O TER END """ # test for corner cases (synthetic data okay) def exercise_synthetic(): pdb_in = iotbx.pdb.input(source_info=None, lines=pdb_raw_0) xrs = pdb_in.xray_structure_simple() fc = abs(xrs.structure_factors(d_min=1.5).f_calc()) flags = fc.resolution_filter(d_min=1.6).generate_r_free_flags() ls = fc.lone_set(other=flags) # case 1: no work set in high-res shell flags2 = ls.array(data=flex.bool(ls.size(), True)) flags_all = flags.concatenate(other=flags2) mtz_out = fc.as_mtz_dataset(column_root_label="F") mtz_out.add_miller_array(flags_all, column_root_label="FreeR_flag") mtz_out.mtz_object().write("tst_molprobity_1.mtz") open("tst_molprobity_1.pdb", "w").write(pdb_raw_0) args = [ "tst_molprobity_1.pdb", "tst_molprobity_1.mtz", "--kinemage", "--maps", "flags.clashscore=False", "flags.xtriage=True", ] result = molprobity.run(args=args, ignore_missing_modules=True, out=null_out()).validation out = StringIO() result.show(out=out) # case 2: no test set in high-res shell flags2 = ls.array(data=flex.bool(ls.size(), False)) flags_all = flags.concatenate(other=flags2) mtz_out = fc.as_mtz_dataset(column_root_label="F") mtz_out.add_miller_array(flags_all, column_root_label="FreeR_flag") result = molprobity.run(args=args, ignore_missing_modules=True, out=null_out()).validation out = StringIO() result.show(out=out) # case 3: multi-MODEL structure # XXX This is not a very sophisticated test - it only ensures that the # program does not crash. We need a test for expected output... hierarchy = pdb_in.construct_hierarchy() model2 = hierarchy.only_model().detached_copy() hierarchy.append_model(model2) hierarchy.models()[0].id = "1" hierarchy.models()[1].id = "2" open("tst_molprobity_multi_model.pdb", "w").write(hierarchy.as_pdb_string()) args = [ "tst_molprobity_multi_model.pdb", "tst_molprobity_1.mtz", "--kinemage", "--maps", ] result = molprobity.run(args=args, ignore_missing_modules=True, out=null_out()).validation out = StringIO() result.show(out=out) # test rotamer distributions open("tst_molprobity_misc1.pdb", "w").write(pdb_raw_0) args = [ "tst_molprobity_1.pdb", "rotamer_library=8000", ] out = StringIO() result = molprobity.run(args=args, ignore_missing_modules=True, out=null_out()).validation result.show(outliers_only=False, out=out) def exercise_cdl(): pdb_raw = """ ATOM 1270 N LEU A 199 6.903 55.119 -0.416 1.00 25.48 N ATOM 1271 CA LEU A 199 7.726 56.192 -0.941 1.00 25.93 C ATOM 1272 C LEU A 199 6.996 56.972 -2.047 1.00 26.39 C ATOM 1273 O LEU A 199 7.020 58.180 -2.064 1.00 25.38 O ATOM 1274 CB LEU A 199 9.033 55.633 -1.490 1.00 25.66 C ATOM 1278 N ARG A 200 6.361 56.258 -2.980 1.00 27.31 N ATOM 1279 CA ARG A 200 5.576 56.913 -3.993 1.00 28.53 C ATOM 1280 C ARG A 200 4.520 57.823 -3.397 1.00 27.54 C ATOM 1281 O ARG A 200 4.397 58.949 -3.851 1.00 27.50 O ATOM 1282 CB ARG A 200 4.933 55.879 -4.899 1.00 30.38 C ATOM 1289 N ALA A 201 3.790 57.365 -2.357 1.00 26.90 N ATOM 1290 CA ALA A 201 2.764 58.200 -1.713 1.00 26.49 C ATOM 1291 C ALA A 201 3.406 59.407 -1.045 1.00 26.59 C ATOM 1292 O ALA A 201 2.866 60.516 -1.082 1.00 26.58 O ATOM 1293 CB ALA A 201 1.959 57.412 -0.715 1.00 25.11 C ATOM 1294 N ARG A 202 4.566 59.205 -0.419 1.00 25.66 N ATOM 1295 CA ARG A 202 5.245 60.296 0.240 1.00 26.93 C ATOM 1296 C ARG A 202 5.676 61.346 -0.767 1.00 26.93 C ATOM 1297 O ARG A 202 5.555 62.541 -0.489 1.00 25.79 O ATOM 1298 CB ARG A 202 6.493 59.779 0.996 1.00 28.25 C ATOM 1305 N ILE A 203 6.154 60.912 -1.931 1.00 26.99 N ATOM 1306 CA ILE A 203 6.611 61.848 -2.965 1.00 27.49 C ATOM 1307 C ILE A 203 5.430 62.674 -3.480 1.00 28.29 C ATOM 1308 O ILE A 203 5.548 63.905 -3.624 1.00 27.82 O ATOM 1309 CB ILE A 203 7.322 61.125 -4.075 1.00 28.09 C ATOM 1313 N SER A 204 4.288 62.025 -3.678 1.00 27.96 N ATOM 1314 CA SER A 204 3.119 62.736 -4.184 1.00 28.04 C ATOM 1315 C SER A 204 2.683 63.793 -3.199 1.00 28.16 C ATOM 1316 O SER A 204 2.311 64.910 -3.605 1.00 28.25 O ATOM 1317 CB SER A 204 1.962 61.780 -4.504 1.00 27.64 C """ pdb_raw_2 = """\ REMARK 3 GEOSTD + MON.LIB. + CDL v1.2 """ + pdb_raw open("tst_molprobity_cdl_1.pdb", "w").write(pdb_raw) open("tst_molprobity_cdl_2.pdb", "w").write(pdb_raw_2) files = ["tst_molprobity_cdl_1.pdb","tst_molprobity_cdl_2.pdb"] rmsds = [0.9019, 0.8769] for file_name, rmsd, cdl_expected in zip(files, rmsds, [False, True]): result = molprobity.run(args=[file_name, "flags.clashscore=False"], ignore_missing_modules=True, out=null_out()).validation assert approx_equal(result.rms_angles(), rmsd, eps=0.001), rmsd if cdl_expected : out = StringIO() result.show(out=out) assert ("Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2" in out.getvalue()) else: out = StringIO() result.show(out=out) assert ("CDL" not in out.getvalue()) if (__name__ == "__main__"): exercise_cdl() exercise_synthetic() print("OK")