from __future__ import absolute_import, division, print_function import iotbx.pdb from libtbx.test_utils import approx_equal from scitbx.array_family import flex import mmtbx.utils pdb_str = """\ ATOM 1 N TYR A 58 8.659 20.073 11.185 1.00 7.73 N ATOM 2 CA TYR A 58 9.250 19.144 10.233 1.00 8.65 C ATOM 3 C TYR A 58 9.039 17.721 10.706 1.00 9.84 C ATOM 4 O TYR A 58 9.023 17.464 11.919 1.00 8.58 O ATOM 5 CB TYR A 58 10.740 19.429 10.045 1.00 20.00 C ATOM 6 CG TYR A 58 11.155 20.825 10.457 1.00 20.00 C ATOM 7 CD1 TYR A 58 10.204 21.809 10.700 1.00 20.00 C ATOM 8 CD2 TYR A 58 12.494 21.155 10.603 1.00 20.00 C ATOM 9 CE1 TYR A 58 10.579 23.084 11.076 1.00 20.00 C ATOM 10 CE2 TYR A 58 12.879 22.429 10.980 1.00 20.00 C ATOM 11 CZ TYR A 58 11.918 23.388 11.215 1.00 20.00 C ATOM 12 OH TYR A 58 12.294 24.659 11.588 1.00 20.00 O ATOM 21 N SER A 59 8.887 16.797 9.756 1.00 9.65 N ATOM 22 CA SER A 59 8.720 15.382 10.080 1.00 5.80 C ATOM 23 C SER A 59 9.606 14.539 9.169 1.00 10.35 C ATOM 24 O SER A 59 9.972 14.972 8.075 1.00 10.56 O ATOM 25 CB SER A 59 7.257 14.957 9.943 1.00 20.00 C ATOM 26 OG SER A 59 6.811 15.089 8.604 1.00 20.00 O ATOM 32 N ILE A 60 9.964 13.344 9.625 1.00 9.39 N ATOM 33 CA ILE A 60 11.067 12.594 9.017 1.00 11.89 C ATOM 34 C ILE A 60 10.635 11.189 8.608 1.00 9.81 C ATOM 35 O ILE A 60 10.120 10.434 9.430 1.00 8.97 O ATOM 36 CB ILE A 60 12.262 12.515 9.987 1.00 20.00 C ATOM 37 CG1 ILE A 60 12.852 13.907 10.220 1.00 20.00 C ATOM 38 CG2 ILE A 60 13.321 11.565 9.451 1.00 20.00 C ATOM 39 CD1 ILE A 60 13.852 13.963 11.353 1.00 20.00 C ATOM 51 N VAL A 61 10.858 10.832 7.348 1.00 7.72 N ATOM 52 CA VAL A 61 10.510 9.497 6.870 1.00 9.11 C ATOM 53 C VAL A 61 11.692 8.812 6.178 1.00 10.61 C ATOM 54 O VAL A 61 11.963 9.081 5.006 1.00 11.05 O ATOM 55 CB VAL A 61 9.349 9.563 5.856 1.00 10.49 C ATOM 56 CG1 VAL A 61 9.023 8.166 5.330 1.00 8.40 C ATOM 57 CG2 VAL A 61 8.127 10.228 6.485 1.00 9.13 C ATOM 67 N VAL A 62 12.408 7.927 6.895 1.00 10.62 N ATOM 68 CA VAL A 62 13.520 7.240 6.220 1.00 7.26 C ATOM 69 C VAL A 62 13.019 6.486 5.000 1.00 10.75 C ATOM 70 O VAL A 62 11.946 5.890 5.048 1.00 11.44 O ATOM 71 CB VAL A 62 14.239 6.259 7.164 1.00 20.00 C ATOM 72 CG1 VAL A 62 15.297 5.470 6.407 1.00 20.00 C ATOM 73 CG2 VAL A 62 14.857 7.004 8.337 1.00 20.00 C """ max_distant = """\ ATOM 1 N TYR A 58 8.659 20.073 11.185 1.00 7.73 N ATOM 2 CA TYR A 58 9.250 19.144 10.233 1.00 8.65 C ATOM 3 C TYR A 58 9.039 17.721 10.706 1.00 9.84 C ATOM 4 O TYR A 58 9.023 17.464 11.919 1.00 8.58 O ATOM 5 CB TYR A 58 10.740 19.429 10.045 1.00 20.00 C ATOM 6 CG TYR A 58 11.415 18.526 9.036 1.00 20.00 C ATOM 7 CD1 TYR A 58 11.229 18.716 7.671 1.00 20.00 C ATOM 8 CD2 TYR A 58 12.237 17.488 9.448 1.00 20.00 C ATOM 9 CE1 TYR A 58 11.844 17.894 6.747 1.00 20.00 C ATOM 10 CE2 TYR A 58 12.857 16.660 8.530 1.00 20.00 C ATOM 11 CZ TYR A 58 12.657 16.868 7.183 1.00 20.00 C ATOM 12 OH TYR A 58 13.270 16.046 6.263 1.00 20.00 O ATOM 21 N SER A 59 8.887 16.797 9.756 1.00 9.65 N ATOM 22 CA SER A 59 8.720 15.382 10.080 1.00 5.80 C ATOM 23 C SER A 59 9.606 14.539 9.169 1.00 10.35 C ATOM 24 O SER A 59 9.972 14.972 8.075 1.00 10.56 O ATOM 25 CB SER A 59 7.257 14.957 9.943 1.00 20.00 C ATOM 26 OG SER A 59 6.438 15.638 10.879 1.00 20.00 O ATOM 32 N ILE A 60 9.964 13.344 9.625 1.00 9.39 N ATOM 33 CA ILE A 60 11.067 12.594 9.017 1.00 11.89 C ATOM 34 C ILE A 60 10.635 11.189 8.608 1.00 9.81 C ATOM 35 O ILE A 60 10.120 10.434 9.430 1.00 8.97 O ATOM 36 CB ILE A 60 12.262 12.515 9.987 1.00 20.00 C ATOM 37 CG1 ILE A 60 11.838 11.859 11.302 1.00 20.00 C ATOM 38 CG2 ILE A 60 12.836 13.900 10.238 1.00 20.00 C ATOM 39 CD1 ILE A 60 11.874 10.347 11.268 1.00 20.00 C ATOM 51 N VAL A 61 10.858 10.832 7.348 1.00 7.72 N ATOM 52 CA VAL A 61 10.510 9.497 6.870 1.00 9.11 C ATOM 53 C VAL A 61 11.692 8.812 6.178 1.00 10.61 C ATOM 54 O VAL A 61 11.963 9.081 5.006 1.00 11.05 O ATOM 55 CB VAL A 61 9.349 9.563 5.856 1.00 10.49 C ATOM 56 CG1 VAL A 61 8.097 10.135 6.519 1.00 8.40 C ATOM 57 CG2 VAL A 61 9.757 10.373 4.628 1.00 9.13 C ATOM 67 N VAL A 62 12.408 7.927 6.895 1.00 10.62 N ATOM 68 CA VAL A 62 13.520 7.240 6.220 1.00 7.26 C ATOM 69 C VAL A 62 13.019 6.486 5.000 1.00 10.75 C ATOM 70 O VAL A 62 11.946 5.890 5.048 1.00 11.44 O ATOM 71 CB VAL A 62 14.239 6.259 7.164 1.00 20.00 C ATOM 72 CG1 VAL A 62 14.849 7.004 8.342 1.00 20.00 C ATOM 73 CG2 VAL A 62 13.279 5.181 7.645 1.00 20.00 C """ min_distant="""\ ATOM 1 N TYR A 58 8.659 20.073 11.185 1.00 7.73 N ATOM 2 CA TYR A 58 9.250 19.144 10.233 1.00 8.65 C ATOM 3 C TYR A 58 9.039 17.721 10.706 1.00 9.84 C ATOM 4 O TYR A 58 9.023 17.464 11.919 1.00 8.58 O ATOM 5 CB TYR A 58 10.740 19.429 10.045 1.00 20.00 C ATOM 6 CG TYR A 58 11.032 20.755 9.375 1.00 20.00 C ATOM 7 CD1 TYR A 58 10.946 20.890 7.995 1.00 20.00 C ATOM 8 CD2 TYR A 58 11.391 21.866 10.124 1.00 20.00 C ATOM 9 CE1 TYR A 58 11.212 22.098 7.381 1.00 20.00 C ATOM 10 CE2 TYR A 58 11.658 23.080 9.517 1.00 20.00 C ATOM 11 CZ TYR A 58 11.567 23.190 8.147 1.00 20.00 C ATOM 12 OH TYR A 58 11.834 24.395 7.536 1.00 20.00 O ATOM 21 N SER A 59 8.887 16.797 9.756 1.00 9.65 N ATOM 22 CA SER A 59 8.720 15.382 10.080 1.00 5.80 C ATOM 23 C SER A 59 9.606 14.539 9.169 1.00 10.35 C ATOM 24 O SER A 59 9.972 14.972 8.075 1.00 10.56 O ATOM 25 CB SER A 59 7.257 14.957 9.943 1.00 20.00 C ATOM 26 OG SER A 59 7.098 13.577 10.226 1.00 20.00 O ATOM 32 N ILE A 60 9.964 13.344 9.625 1.00 9.39 N ATOM 33 CA ILE A 60 11.067 12.594 9.017 1.00 11.89 C ATOM 34 C ILE A 60 10.635 11.189 8.608 1.00 9.81 C ATOM 35 O ILE A 60 10.120 10.434 9.430 1.00 8.97 O ATOM 36 CB ILE A 60 12.262 12.515 9.987 1.00 20.00 C ATOM 37 CG1 ILE A 60 12.803 13.915 10.280 1.00 20.00 C ATOM 38 CG2 ILE A 60 13.354 11.625 9.415 1.00 20.00 C ATOM 39 CD1 ILE A 60 12.132 14.595 11.453 1.00 20.00 C ATOM 51 N VAL A 61 10.858 10.832 7.348 1.00 7.72 N ATOM 52 CA VAL A 61 10.510 9.497 6.870 1.00 9.11 C ATOM 53 C VAL A 61 11.692 8.812 6.178 1.00 10.61 C ATOM 54 O VAL A 61 11.963 9.081 5.006 1.00 11.05 O ATOM 55 CB VAL A 61 9.349 9.563 5.856 1.00 10.49 C ATOM 56 CG1 VAL A 61 9.784 10.315 4.599 1.00 8.40 C ATOM 57 CG2 VAL A 61 8.845 8.160 5.528 1.00 9.13 C ATOM 67 N VAL A 62 12.408 7.927 6.895 1.00 10.62 N ATOM 68 CA VAL A 62 13.520 7.240 6.220 1.00 7.26 C ATOM 69 C VAL A 62 13.019 6.486 5.000 1.00 10.75 C ATOM 70 O VAL A 62 11.946 5.890 5.048 1.00 11.44 O ATOM 71 CB VAL A 62 14.239 6.259 7.164 1.00 20.00 C ATOM 72 CG1 VAL A 62 13.305 5.129 7.570 1.00 20.00 C ATOM 73 CG2 VAL A 62 15.496 5.710 6.506 1.00 20.00 C """ exact_match="""\ ATOM 1 N TYR A 58 8.659 20.073 11.185 1.00 7.73 N ATOM 2 CA TYR A 58 9.250 19.144 10.233 1.00 8.65 C ATOM 3 C TYR A 58 9.039 17.721 10.706 1.00 9.84 C ATOM 4 O TYR A 58 9.023 17.464 11.919 1.00 8.58 O ATOM 5 CB TYR A 58 10.740 19.429 10.045 1.00 20.00 C ATOM 6 CG TYR A 58 11.032 20.755 9.375 1.00 20.00 C ATOM 7 CD1 TYR A 58 10.946 20.890 7.995 1.00 20.00 C ATOM 8 CD2 TYR A 58 11.391 21.866 10.124 1.00 20.00 C ATOM 9 CE1 TYR A 58 11.212 22.098 7.381 1.00 20.00 C ATOM 10 CE2 TYR A 58 11.658 23.080 9.517 1.00 20.00 C ATOM 11 CZ TYR A 58 11.567 23.190 8.147 1.00 20.00 C ATOM 12 OH TYR A 58 11.834 24.395 7.536 1.00 20.00 O ATOM 21 N SER A 59 8.887 16.797 9.756 1.00 9.65 N ATOM 22 CA SER A 59 8.720 15.382 10.080 1.00 5.80 C ATOM 23 C SER A 59 9.606 14.539 9.169 1.00 10.35 C ATOM 24 O SER A 59 9.972 14.972 8.075 1.00 10.56 O ATOM 25 CB SER A 59 7.257 14.957 9.943 1.00 20.00 C ATOM 26 OG SER A 59 6.829 15.030 8.594 1.00 20.00 O ATOM 32 N ILE A 60 9.964 13.344 9.625 1.00 9.39 N ATOM 33 CA ILE A 60 11.067 12.594 9.017 1.00 11.89 C ATOM 34 C ILE A 60 10.635 11.189 8.608 1.00 9.81 C ATOM 35 O ILE A 60 10.120 10.434 9.430 1.00 8.97 O ATOM 36 CB ILE A 60 12.262 12.515 9.987 1.00 20.00 C ATOM 37 CG1 ILE A 60 12.808 13.915 10.275 1.00 20.00 C ATOM 38 CG2 ILE A 60 13.351 11.619 9.419 1.00 20.00 C ATOM 39 CD1 ILE A 60 13.808 13.957 11.408 1.00 20.00 C ATOM 51 N VAL A 61 10.858 10.832 7.348 1.00 7.72 N ATOM 52 CA VAL A 61 10.510 9.497 6.870 1.00 9.11 C ATOM 53 C VAL A 61 11.692 8.812 6.178 1.00 10.61 C ATOM 54 O VAL A 61 11.963 9.081 5.006 1.00 11.05 O ATOM 55 CB VAL A 61 9.349 9.563 5.856 1.00 10.49 C ATOM 56 CG1 VAL A 61 9.064 8.175 5.283 1.00 8.40 C ATOM 57 CG2 VAL A 61 8.107 10.171 6.504 1.00 9.13 C ATOM 67 N VAL A 62 12.408 7.927 6.895 1.00 10.62 N ATOM 68 CA VAL A 62 13.520 7.240 6.220 1.00 7.26 C ATOM 69 C VAL A 62 13.019 6.486 5.000 1.00 10.75 C ATOM 70 O VAL A 62 11.946 5.890 5.048 1.00 11.44 O ATOM 71 CB VAL A 62 14.239 6.259 7.164 1.00 20.00 C ATOM 72 CG1 VAL A 62 15.313 5.487 6.412 1.00 20.00 C ATOM 73 CG2 VAL A 62 14.836 7.001 8.350 1.00 20.00 C """ fix_outliers="""\ ATOM 1 N TYR A 58 8.659 20.073 11.185 1.00 7.73 N ATOM 2 CA TYR A 58 9.250 19.144 10.233 1.00 8.65 C ATOM 3 C TYR A 58 9.039 17.721 10.706 1.00 9.84 C ATOM 4 O TYR A 58 9.023 17.464 11.919 1.00 8.58 O ATOM 5 CB TYR A 58 10.740 19.429 10.045 1.00 20.00 C ATOM 6 CG TYR A 58 11.032 20.755 9.375 1.00 20.00 C ATOM 7 CD1 TYR A 58 10.946 20.890 7.995 1.00 20.00 C ATOM 8 CD2 TYR A 58 11.391 21.866 10.124 1.00 20.00 C ATOM 9 CE1 TYR A 58 11.212 22.098 7.381 1.00 20.00 C ATOM 10 CE2 TYR A 58 11.658 23.080 9.517 1.00 20.00 C ATOM 11 CZ TYR A 58 11.567 23.190 8.147 1.00 20.00 C ATOM 12 OH TYR A 58 11.834 24.395 7.536 1.00 20.00 O ATOM 21 N SER A 59 8.887 16.797 9.756 1.00 9.65 N ATOM 22 CA SER A 59 8.720 15.382 10.080 1.00 5.80 C ATOM 23 C SER A 59 9.606 14.539 9.169 1.00 10.35 C ATOM 24 O SER A 59 9.972 14.972 8.075 1.00 10.56 O ATOM 25 CB SER A 59 7.257 14.957 9.943 1.00 20.00 C ATOM 26 OG SER A 59 6.811 15.089 8.604 1.00 20.00 O ATOM 32 N ILE A 60 9.964 13.344 9.625 1.00 9.39 N ATOM 33 CA ILE A 60 11.067 12.594 9.017 1.00 11.89 C ATOM 34 C ILE A 60 10.635 11.189 8.608 1.00 9.81 C ATOM 35 O ILE A 60 10.120 10.434 9.430 1.00 8.97 O ATOM 36 CB ILE A 60 12.262 12.515 9.987 1.00 20.00 C ATOM 37 CG1 ILE A 60 12.852 13.907 10.220 1.00 20.00 C ATOM 38 CG2 ILE A 60 13.321 11.565 9.451 1.00 20.00 C ATOM 39 CD1 ILE A 60 13.852 13.963 11.353 1.00 20.00 C ATOM 51 N VAL A 61 10.858 10.832 7.348 1.00 7.72 N ATOM 52 CA VAL A 61 10.510 9.497 6.870 1.00 9.11 C ATOM 53 C VAL A 61 11.692 8.812 6.178 1.00 10.61 C ATOM 54 O VAL A 61 11.963 9.081 5.006 1.00 11.05 O ATOM 55 CB VAL A 61 9.349 9.563 5.856 1.00 10.49 C ATOM 56 CG1 VAL A 61 9.023 8.166 5.330 1.00 8.40 C ATOM 57 CG2 VAL A 61 8.127 10.228 6.485 1.00 9.13 C ATOM 67 N VAL A 62 12.408 7.927 6.895 1.00 10.62 N ATOM 68 CA VAL A 62 13.520 7.240 6.220 1.00 7.26 C ATOM 69 C VAL A 62 13.019 6.486 5.000 1.00 10.75 C ATOM 70 O VAL A 62 11.946 5.890 5.048 1.00 11.44 O ATOM 71 CB VAL A 62 14.239 6.259 7.164 1.00 20.00 C ATOM 72 CG1 VAL A 62 15.297 5.470 6.407 1.00 20.00 C ATOM 73 CG2 VAL A 62 14.857 7.004 8.337 1.00 20.00 C """ selection="""\ ATOM 1 N TYR A 58 8.659 20.073 11.185 1.00 7.73 N ATOM 2 CA TYR A 58 9.250 19.144 10.233 1.00 8.65 C ATOM 3 C TYR A 58 9.039 17.721 10.706 1.00 9.84 C ATOM 4 O TYR A 58 9.023 17.464 11.919 1.00 8.58 O ATOM 5 CB TYR A 58 10.740 19.429 10.045 1.00 20.00 C ATOM 6 CG TYR A 58 11.155 20.825 10.457 1.00 20.00 C ATOM 7 CD1 TYR A 58 10.204 21.809 10.700 1.00 20.00 C ATOM 8 CD2 TYR A 58 12.494 21.155 10.603 1.00 20.00 C ATOM 9 CE1 TYR A 58 10.579 23.084 11.076 1.00 20.00 C ATOM 10 CE2 TYR A 58 12.879 22.429 10.980 1.00 20.00 C ATOM 11 CZ TYR A 58 11.918 23.388 11.215 1.00 20.00 C ATOM 12 OH TYR A 58 12.294 24.659 11.588 1.00 20.00 O ATOM 21 N SER A 59 8.887 16.797 9.756 1.00 9.65 N ATOM 22 CA SER A 59 8.720 15.382 10.080 1.00 5.80 C ATOM 23 C SER A 59 9.606 14.539 9.169 1.00 10.35 C ATOM 24 O SER A 59 9.972 14.972 8.075 1.00 10.56 O ATOM 25 CB SER A 59 7.257 14.957 9.943 1.00 20.00 C ATOM 26 OG SER A 59 6.811 15.089 8.604 1.00 20.00 O ATOM 32 N ILE A 60 9.964 13.344 9.625 1.00 9.39 N ATOM 33 CA ILE A 60 11.067 12.594 9.017 1.00 11.89 C ATOM 34 C ILE A 60 10.635 11.189 8.608 1.00 9.81 C ATOM 35 O ILE A 60 10.120 10.434 9.430 1.00 8.97 O ATOM 36 CB ILE A 60 12.262 12.515 9.987 1.00 20.00 C ATOM 37 CG1 ILE A 60 12.852 13.907 10.220 1.00 20.00 C ATOM 38 CG2 ILE A 60 13.321 11.565 9.451 1.00 20.00 C ATOM 39 CD1 ILE A 60 13.852 13.963 11.353 1.00 20.00 C ATOM 51 N VAL A 61 10.858 10.832 7.348 1.00 7.72 N ATOM 52 CA VAL A 61 10.510 9.497 6.870 1.00 9.11 C ATOM 53 C VAL A 61 11.692 8.812 6.178 1.00 10.61 C ATOM 54 O VAL A 61 11.963 9.081 5.006 1.00 11.05 O ATOM 55 CB VAL A 61 9.349 9.563 5.856 1.00 10.49 C ATOM 56 CG1 VAL A 61 9.023 8.166 5.330 1.00 8.40 C ATOM 57 CG2 VAL A 61 8.127 10.228 6.485 1.00 9.13 C ATOM 67 N VAL A 62 12.408 7.927 6.895 1.00 10.62 N ATOM 68 CA VAL A 62 13.520 7.240 6.220 1.00 7.26 C ATOM 69 C VAL A 62 13.019 6.486 5.000 1.00 10.75 C ATOM 70 O VAL A 62 11.946 5.890 5.048 1.00 11.44 O ATOM 71 CB VAL A 62 14.239 6.259 7.164 1.00 20.00 C ATOM 72 CG1 VAL A 62 15.297 5.470 6.407 1.00 20.00 C ATOM 73 CG2 VAL A 62 14.857 7.004 8.337 1.00 20.00 C """ def core(mode, result, t1, t2): prefix = "exercise_%s"%mode ph = iotbx.pdb.input(source_info=None, lines=pdb_str).construct_hierarchy() s0 = ph.atoms().extract_xyz() ph.write_pdb_file(file_name="%s_in.pdb"%prefix) ph = mmtbx.utils.switch_rotamers(pdb_hierarchy=ph, mode=mode) ph.write_pdb_file(file_name="%s_out.pdb"%prefix) s1 = iotbx.pdb.input(source_info=None,lines=result).atoms().extract_xyz() s2 = ph.atoms().extract_xyz() d = flex.sqrt((s1 - s2).dot()).min_max_mean().as_tuple() assert approx_equal(d, t1, 1.e-3) d = flex.sqrt((s2 - s0).dot()).min_max_mean().as_tuple() assert approx_equal(d, t2, 0.1) def exercise_fix_outliers(prefix="exercise_fix_outliers"): ph = iotbx.pdb.input(source_info=None, lines=pdb_str).construct_hierarchy() sel = ph.atom_selection_cache().selection(string = "resname TYR and not (name O or name CA or name N or name C or name CB)") s0 = ph.atoms().extract_xyz() ph.write_pdb_file(file_name="%s_in.pdb"%prefix) ph = mmtbx.utils.switch_rotamers(pdb_hierarchy=ph, mode="fix_outliers") ph.write_pdb_file(file_name="%s_out.pdb"%prefix) s1 =iotbx.pdb.input(source_info=None,lines=fix_outliers).atoms().extract_xyz() s2 = ph.atoms().extract_xyz() # assert fixed do not move d = flex.sqrt((s1.select(~sel) - s2.select(~sel)).dot()).min_max_mean().as_tuple() assert approx_equal(d, [0,0,0]) d = flex.sqrt((s1.select(~sel) - s0.select(~sel)).dot()).min_max_mean().as_tuple() assert approx_equal(d, [0,0,0]) d = flex.sqrt((s2.select(~sel) - s0.select(~sel)).dot()).min_max_mean().as_tuple() assert approx_equal(d, [0,0,0]) # d = flex.sqrt((s1.select(sel)-s2.select(sel)).dot()).min_max_mean().as_tuple() assert approx_equal(d, [0,0,0], 1.e-3) d = flex.sqrt((s1.select(sel)-s0.select(sel)).dot()).min_max_mean().as_tuple() assert approx_equal(d, [1.1, 4.0, 2.6], 0.1) d = flex.sqrt((s2.select(sel)-s0.select(sel)).dot()).min_max_mean().as_tuple() assert approx_equal(d, [1.1, 4.0, 2.6], 0.1) def exercise_selection(prefix="exercise_selection"): ph = iotbx.pdb.input(source_info=None, lines=pdb_str).construct_hierarchy() sel = ph.atom_selection_cache().selection(string = "not resname TYR") s0 = ph.atoms().extract_xyz() ph.write_pdb_file(file_name="%s_in.pdb"%prefix) ph = mmtbx.utils.switch_rotamers(pdb_hierarchy=ph, mode="fix_outliers", selection = sel) ph.write_pdb_file(file_name="%s_out.pdb"%prefix) s1 =iotbx.pdb.input(source_info=None,lines=selection).atoms().extract_xyz() s2 = ph.atoms().extract_xyz() # assert fixed do not move d = flex.sqrt((s1 - s2).dot()).min_max_mean().as_tuple() assert approx_equal(d, [0,0,0]) d = flex.sqrt((s1 - s0).dot()).min_max_mean().as_tuple() assert approx_equal(d, [0,0,0]) d = flex.sqrt((s2 - s0).dot()).min_max_mean().as_tuple() assert approx_equal(d, [0,0,0]) if (__name__ == "__main__"): core(mode="max_distant", result=max_distant, t1=[0,0,0], t2=[0, 10.2, 1.5]) core(mode="min_distant", result=min_distant, t1=[0,0,0], t2=[0, 4.1, 0.8]) core(mode="exact_match", result=exact_match, t1=[0,0,0], t2=[0, 4.1, 0.4]) exercise_fix_outliers() exercise_selection()