from __future__ import absolute_import, division, print_function from scitbx.array_family import flex from libtbx import easy_run import libtbx.load_env # import dependency import os from six.moves import zip pdb_str = """ CRYST1 34.896 15.928 22.972 90.00 90.00 90.00 P 1 SCALE1 0.028657 0.000000 0.000000 0.00000 SCALE2 0.000000 0.062783 0.000000 0.00000 SCALE3 0.000000 0.000000 0.043531 0.00000 ATOM 1 N GLY A 1 7.241 10.342 12.931 1.00 16.37 N ATOM 2 CA GLY A 1 7.248 9.899 11.542 1.00 16.17 C ATOM 3 C GLY A 1 8.297 8.826 11.297 1.00 15.46 C ATOM 4 O GLY A 1 8.781 8.201 12.236 1.00 16.71 O ATOM 5 H1 GLY A 1 6.544 10.879 13.068 1.00 16.37 H ATOM 6 H2 GLY A 1 7.180 9.635 13.468 1.00 16.37 H ATOM 7 H3 GLY A 1 7.994 10.783 13.105 1.00 16.37 H ATOM 8 HA2 GLY A 1 6.377 9.539 11.311 1.00 16.17 H ATOM 9 HA3 GLY A 1 7.435 10.653 10.961 1.00 16.17 H ATOM 10 N AASN A 2 8.625 8.586 10.033 0.60 14.94 N ATOM 11 CA AASN A 2 9.755 7.720 9.710 0.60 14.28 C ATOM 12 C AASN A 2 11.046 8.226 10.317 0.60 12.87 C ATOM 13 O AASN A 2 11.288 9.431 10.370 0.60 12.55 O ATOM 14 CB AASN A 2 9.932 7.588 8.206 0.60 15.48 C ATOM 15 CG AASN A 2 8.788 6.866 7.558 0.60 13.90 C ATOM 16 OD1AASN A 2 8.236 7.330 6.561 0.60 17.99 O ATOM 17 ND2AASN A 2 8.421 5.716 8.117 0.60 11.61 N ATOM 18 H AASN A 2 8.215 8.908 9.349 0.60 15.11 H ATOM 19 HA AASN A 2 9.587 6.837 10.074 0.60 13.97 H ATOM 20 HB2AASN A 2 9.990 8.474 7.814 0.60 15.07 H ATOM 21 HB3AASN A 2 10.744 7.090 8.025 0.60 15.07 H ATOM 22 HD21AASN A 2 7.719 5.306 7.835 0.60 11.52 H ATOM 23 HD22AASN A 2 8.884 5.382 8.759 0.60 11.52 H ATOM 24 N BASN A 2 8.662 8.607 10.040 0.40 15.11 N ATOM 25 CA BASN A 2 9.841 7.793 9.758 0.40 13.97 C ATOM 26 C BASN A 2 11.079 8.439 10.353 0.40 13.04 C ATOM 27 O BASN A 2 11.211 9.661 10.344 0.40 11.55 O ATOM 28 CB BASN A 2 10.038 7.614 8.259 0.40 15.07 C ATOM 29 CG BASN A 2 8.876 6.915 7.606 0.40 13.81 C ATOM 30 OD1BASN A 2 8.335 7.391 6.608 0.40 17.17 O ATOM 31 ND2BASN A 2 8.483 5.775 8.163 0.40 11.52 N ATOM 32 H BASN A 2 8.256 8.910 9.345 0.40 15.11 H ATOM 33 HA BASN A 2 9.732 6.917 10.160 0.40 13.97 H ATOM 34 HB2BASN A 2 10.135 8.486 7.846 0.40 15.07 H ATOM 35 HB3BASN A 2 10.834 7.082 8.105 0.40 15.07 H ATOM 36 HD21BASN A 2 7.804 5.353 7.845 0.40 11.52 H ATOM 37 HD22BASN A 2 8.907 5.459 8.841 0.40 11.52 H ATOM 38 N AASN A 3 11.874 7.290 10.763 0.60 12.35 N ATOM 39 CA AASN A 3 13.106 7.616 11.464 0.60 11.68 C ATOM 40 C AASN A 3 14.355 7.054 10.788 0.60 11.09 C ATOM 41 O AASN A 3 14.430 5.850 10.518 0.60 10.18 O ATOM 42 CB AASN A 3 13.029 7.115 12.915 0.60 11.62 C ATOM 43 CG AASN A 3 14.277 7.454 13.717 0.60 13.00 C ATOM 44 OD1AASN A 3 14.584 8.629 13.935 0.60 15.44 O ATOM 45 ND2AASN A 3 15.001 6.428 14.160 0.60 12.87 N ATOM 46 H AASN A 3 11.741 6.445 10.670 0.60 12.00 H ATOM 47 HA AASN A 3 13.210 8.579 11.499 0.60 11.53 H ATOM 48 HB2AASN A 3 12.269 7.529 13.353 0.60 12.90 H ATOM 49 HB3AASN A 3 12.926 6.150 12.912 0.60 12.90 H ATOM 50 HD21AASN A 3 15.715 6.571 14.618 0.60 12.97 H ATOM 51 HD22AASN A 3 14.755 5.622 13.988 0.60 12.97 H ATOM 52 N BASN A 3 11.978 7.616 10.880 0.40 12.00 N ATOM 53 CA BASN A 3 13.210 8.114 11.479 0.40 11.53 C ATOM 54 C BASN A 3 14.444 7.369 10.976 0.40 11.70 C ATOM 55 O BASN A 3 14.478 6.136 10.965 0.40 10.95 O ATOM 56 CB BASN A 3 13.136 8.043 13.007 0.40 12.90 C ATOM 57 CG BASN A 3 12.214 9.088 13.597 0.40 13.32 C ATOM 58 OD1BASN A 3 11.921 10.106 12.964 0.40 15.04 O ATOM 59 ND2BASN A 3 11.760 8.851 14.823 0.40 12.97 N ATOM 60 H BASN A 3 11.898 6.760 10.903 0.40 12.00 H ATOM 61 HA BASN A 3 13.332 9.044 11.235 0.40 11.53 H ATOM 62 HB2BASN A 3 12.805 7.169 13.267 0.40 12.90 H ATOM 63 HB3BASN A 3 14.023 8.184 13.373 0.40 12.90 H ATOM 64 HD21BASN A 3 11.233 9.414 15.203 0.40 12.97 H ATOM 65 HD22BASN A 3 11.993 8.134 15.237 0.40 12.97 H ATOM 66 N AGLN A 4 15.318 7.938 10.514 0.60 10.54 N ATOM 67 CA AGLN A 4 16.673 7.540 10.113 0.60 10.42 C ATOM 68 C AGLN A 4 17.726 8.190 11.019 0.60 11.71 C ATOM 69 O AGLN A 4 17.880 9.450 10.993 0.60 8.92 O ATOM 70 CB AGLN A 4 16.959 7.869 8.636 0.60 9.88 C ATOM 71 CG AGLN A 4 18.209 7.154 8.093 0.60 10.02 C ATOM 72 CD AGLN A 4 18.769 7.756 6.808 0.60 12.86 C ATOM 73 OE1AGLN A 4 19.004 8.968 6.722 0.60 14.16 O ATOM 74 NE2AGLN A 4 19.007 6.903 5.806 0.60 9.04 N ATOM 75 H AGLN A 4 15.210 8.790 10.554 0.60 10.83 H ATOM 76 HA AGLN A 4 16.760 6.580 10.217 0.60 10.25 H ATOM 77 HB2AGLN A 4 16.200 7.593 8.099 0.60 9.74 H ATOM 78 HB3AGLN A 4 17.098 8.825 8.547 0.60 9.74 H ATOM 79 HG2AGLN A 4 18.908 7.193 8.764 0.60 10.05 H ATOM 80 HG3AGLN A 4 17.982 6.229 7.910 0.60 10.05 H ATOM 81 HE21AGLN A 4 18.845 6.065 5.907 0.60 8.91 H ATOM 82 HE22AGLN A 4 19.322 7.193 5.060 0.60 8.91 H ATOM 83 N BGLN A 4 15.453 8.133 10.564 0.40 10.83 N ATOM 84 CA BGLN A 4 16.716 7.571 10.098 0.40 10.25 C ATOM 85 C BGLN A 4 17.888 8.129 10.902 0.40 10.29 C ATOM 86 O BGLN A 4 18.321 9.259 10.691 0.40 10.50 O ATOM 87 CB BGLN A 4 16.921 7.845 8.603 0.40 9.74 C ATOM 88 CG BGLN A 4 18.096 7.084 7.994 0.40 10.05 C ATOM 89 CD BGLN A 4 18.647 7.745 6.745 0.40 12.79 C ATOM 90 OE1BGLN A 4 18.791 8.970 6.690 0.40 15.08 O ATOM 91 NE2BGLN A 4 18.962 6.936 5.730 0.40 8.91 N ATOM 92 H BGLN A 4 15.429 8.992 10.545 0.40 10.83 H ATOM 93 HA BGLN A 4 16.710 6.610 10.222 0.40 10.25 H ATOM 94 HB2BGLN A 4 16.119 7.581 8.125 0.40 9.74 H ATOM 95 HB3BGLN A 4 17.079 8.794 8.480 0.40 9.74 H ATOM 96 HG2BGLN A 4 18.814 7.031 8.643 0.40 10.05 H ATOM 97 HG3BGLN A 4 17.801 6.192 7.754 0.40 10.05 H ATOM 98 HE21BGLN A 4 18.849 6.087 5.806 0.40 8.91 H ATOM 99 HE22BGLN A 4 19.278 7.264 5.000 0.40 8.91 H ATOM 100 N AGLN A 5 18.413 7.359 11.856 0.60 10.59 N ATOM 101 CA AGLN A 5 19.562 7.932 12.524 0.60 11.43 C ATOM 102 C AGLN A 5 20.870 7.440 11.938 0.60 11.24 C ATOM 103 O AGLN A 5 21.037 6.253 11.692 0.60 11.99 O ATOM 104 CB AGLN A 5 19.517 7.784 14.035 0.60 12.07 C ATOM 105 CG AGLN A 5 18.523 8.708 14.724 0.60 10.78 C ATOM 106 CD AGLN A 5 17.850 8.030 15.899 0.60 12.94 C ATOM 107 OE1AGLN A 5 17.293 6.941 15.764 0.60 10.72 O ATOM 108 NE2AGLN A 5 17.909 8.667 17.062 0.60 12.32 N ATOM 109 H AGLN A 5 18.236 6.535 12.028 0.60 10.59 H ATOM 110 HA AGLN A 5 19.567 8.887 12.374 0.60 11.43 H ATOM 111 HB2AGLN A 5 19.275 6.870 14.249 0.60 12.07 H ATOM 112 HB3AGLN A 5 20.397 7.981 14.392 0.60 12.07 H ATOM 113 HG2AGLN A 5 18.990 9.492 15.053 0.60 10.78 H ATOM 114 HG3AGLN A 5 17.836 8.968 14.090 0.60 10.78 H ATOM 115 HE21AGLN A 5 18.313 9.424 17.118 0.60 12.32 H ATOM 116 HE22AGLN A 5 17.543 8.323 17.760 0.60 12.32 H ATOM 117 N BGLN A 5 18.413 7.359 11.856 0.40 10.59 N ATOM 118 CA BGLN A 5 19.562 7.932 12.524 0.40 11.43 C ATOM 119 C BGLN A 5 20.870 7.440 11.938 0.40 11.24 C ATOM 120 O BGLN A 5 21.037 6.253 11.692 0.40 11.99 O ATOM 121 CB BGLN A 5 19.517 7.784 14.035 0.40 12.07 C ATOM 122 CG BGLN A 5 18.523 8.708 14.724 0.40 10.78 C ATOM 123 CD BGLN A 5 17.850 8.030 15.899 0.40 12.94 C ATOM 124 OE1BGLN A 5 17.293 6.941 15.764 0.40 10.72 O ATOM 125 NE2BGLN A 5 17.909 8.667 17.062 0.40 12.32 N ATOM 126 H BGLN A 5 18.151 6.581 12.111 0.40 10.59 H ATOM 127 HA BGLN A 5 19.576 8.890 12.403 0.40 11.43 H ATOM 128 HB2BGLN A 5 19.275 6.870 14.249 0.40 12.07 H ATOM 129 HB3BGLN A 5 20.397 7.981 14.392 0.40 12.07 H ATOM 130 HG2BGLN A 5 18.990 9.492 15.053 0.40 10.78 H ATOM 131 HG3BGLN A 5 17.836 8.968 14.090 0.40 10.78 H ATOM 132 HE21BGLN A 5 18.313 9.424 17.118 0.40 12.32 H ATOM 133 HE22BGLN A 5 17.543 8.323 17.760 0.40 12.32 H ATOM 134 N ASN A 6 21.796 8.371 11.716 1.00 11.72 N ATOM 135 CA ASN A 6 23.113 8.030 11.190 1.00 12.12 C ATOM 136 C ASN A 6 24.142 8.471 12.195 1.00 13.15 C ATOM 137 O ASN A 6 24.509 9.645 12.245 1.00 13.93 O ATOM 138 CB ASN A 6 23.349 8.721 9.859 1.00 11.96 C ATOM 139 CG ASN A 6 22.251 8.440 8.870 1.00 12.58 C ATOM 140 OD1 ASN A 6 22.087 7.312 8.414 1.00 14.01 O ATOM 141 ND2 ASN A 6 21.480 9.459 8.544 1.00 9.96 N ATOM 142 HA ASN A 6 23.207 7.075 11.058 1.00 12.12 H ATOM 143 HB2 ASN A 6 23.387 9.680 9.998 1.00 11.96 H ATOM 144 HB3 ASN A 6 24.184 8.405 9.480 1.00 11.96 H ATOM 145 HD21 ASN A 6 20.839 9.350 7.981 1.00 9.96 H ATOM 146 HD22 ASN A 6 21.618 10.232 8.894 1.00 9.96 H ATOM 147 H AASN A 6 21.684 9.211 11.863 0.60 11.72 H ATOM 148 H BASN A 6 21.684 9.211 11.863 0.40 11.72 H ATOM 149 N TYR A 7 24.585 7.530 13.020 1.00 14.62 N ATOM 150 CA TYR A 7 25.450 7.854 14.156 1.00 15.04 C ATOM 151 C TYR A 7 26.899 8.037 13.753 1.00 15.56 C ATOM 152 O TYR A 7 27.334 7.518 12.719 1.00 15.52 O ATOM 153 CB TYR A 7 25.344 6.780 15.235 1.00 14.86 C ATOM 154 CG TYR A 7 23.945 6.649 15.763 1.00 14.38 C ATOM 155 CD1 TYR A 7 23.055 5.738 15.199 1.00 15.46 C ATOM 156 CD2 TYR A 7 23.494 7.461 16.795 1.00 14.37 C ATOM 157 CE1 TYR A 7 21.764 5.619 15.667 1.00 13.24 C ATOM 158 CE2 TYR A 7 22.193 7.352 17.274 1.00 13.84 C ATOM 159 CZ TYR A 7 21.337 6.430 16.701 1.00 14.98 C ATOM 160 OH TYR A 7 20.055 6.301 17.164 1.00 14.28 O ATOM 161 OXT TYR A 7 27.649 8.711 14.468 1.00 17.34 O ATOM 162 H TYR A 7 24.401 6.693 12.946 1.00 14.62 H ATOM 163 HA TYR A 7 25.148 8.689 14.546 1.00 15.04 H ATOM 164 HB2 TYR A 7 25.607 5.925 14.860 1.00 14.86 H ATOM 165 HB3 TYR A 7 25.926 7.014 15.975 1.00 14.86 H ATOM 166 HD1 TYR A 7 23.341 5.191 14.503 1.00 15.46 H ATOM 167 HD2 TYR A 7 24.073 8.080 17.178 1.00 14.37 H ATOM 168 HE1 TYR A 7 21.183 5.000 15.287 1.00 13.24 H ATOM 169 HE2 TYR A 7 21.902 7.893 17.972 1.00 13.84 H ATOM 170 HH TYR A 7 19.851 6.969 17.629 1.00 14.28 H TER HETATM 171 O HOH S 8 9.815 10.928 13.987 1.00 22.61 O HETATM 172 O HOH S 9 26.715 7.572 10.077 1.00 19.32 O HETATM 173 O HOH S 10 5.000 7.470 5.401 1.00 16.97 O HETATM 174 O HOH S 11 28.091 9.896 16.830 1.00 23.89 O HETATM 175 O HOH S 12 29.896 7.023 16.061 1.00 26.08 O HETATM 176 O HOH S 13 13.552 9.160 16.880 1.00 38.68 O HETATM 177 O HOH S 14 14.793 6.375 17.843 1.00 44.24 O TER END """ def exercise(): pdb_file = "tmp_ringer.pdb" f = open(pdb_file, "w") f.write(pdb_str) f.close() mtz_file = "tmp_ringer.mtz" cmd = " ".join([ "phenix.fmodel", pdb_file, "high_resolution=2.0", "type=real", "r_free_flags_fraction=0.1", "random_seed=12345", "label=F", "output.file_name=%s" % mtz_file, ]) print(cmd) easy_run.call(cmd) result = easy_run.fully_buffered( "phenix.maps \"%s\" \"%s\" output.prefix=tmp_ringer" % (pdb_file, mtz_file)).raise_if_errors() assert (result.return_code == 0) result = easy_run.fully_buffered( "mmtbx.ringer \"%s\" tmp_ringer_map_coeffs.mtz" % pdb_file).raise_if_errors() with open("tmp_ringer_ringer.csv") as f: _lines1 = f.read().splitlines() lines1 = [] for line in _lines1 : if ("2mFo-DFc" in line): lines1.append(line) os.remove("tmp_ringer_ringer.csv") assert (result.return_code == 0) # Now with ccp4 map as input result2 = easy_run.fully_buffered( "phenix.mtz2map tmp_ringer_map_coeffs.mtz") assert (result2.return_code == 0) result3 = easy_run.fully_buffered( "mmtbx.ringer \"%s\" tmp_ringer_map_coeffs_2mFo-DFc.ccp4" % pdb_file) assert (result3.return_code == 0) , "DL: crash is expected due to new sanity check. Will replace input map." with open("tmp_ringer_ringer.csv") as f: lines2 = f.read().splitlines() assert len(lines1) == len(lines2) for line1, line2 in zip(lines1, lines2): fields1 = line1.split(",") fields2 = line2.split(",") rho1 = flex.double([ float(x) for x in fields1[4:] ]) rho2 = flex.double([ float(x) for x in fields2[4:] ]) cc = flex.linear_correlation(x=rho1, y=rho2).coefficient() assert (cc >= 0.99), cc if (__name__ == "__main__"): exercise() print("OK")