ó º™xTc @ sAddlmZddlZddlmZddlmZddlZ dZ dZ dZ dZ d ZdZd „Zd d „Zd d„Zedkr=eddde ddddgddddgƒeddde ddddgddddgƒeddde ddddgddddgƒeƒeƒndS(iÿÿÿÿ(tdivisionN(t approx_equal(tflexsX 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 sX 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 11.445 18.441 9.140 1.00 20.00 C ATOM 7 CD1 TYR A 58 11.302 18.512 7.759 1.00 20.00 C ATOM 8 CD2 TYR A 58 12.251 17.443 9.667 1.00 20.00 C ATOM 9 CE1 TYR A 58 11.944 17.612 6.931 1.00 20.00 C ATOM 10 CE2 TYR A 58 12.898 16.539 8.845 1.00 20.00 C ATOM 11 CZ TYR A 58 12.741 16.628 7.479 1.00 20.00 C ATOM 12 OH TYR A 58 13.380 15.729 6.655 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 6.442 15.621 10.894 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 11.865 11.768 11.262 1.00 20.00 C ATOM 38 CG2 ILE A 60 12.773 13.908 10.317 1.00 20.00 C ATOM 39 CD1 ILE A 60 12.314 10.324 11.286 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 8.083 10.087 6.532 1.00 8.40 C ATOM 57 CG2 VAL A 61 9.739 10.416 4.651 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 14.893 7.010 8.315 1.00 20.00 C ATOM 73 CG2 VAL A 62 13.267 5.212 7.685 1.00 20.00 C sX 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 11.034 20.783 9.437 1.00 20.00 C ATOM 7 CD1 TYR A 58 10.273 21.271 8.381 1.00 20.00 C ATOM 8 CD2 TYR A 58 12.069 21.570 9.919 1.00 20.00 C ATOM 9 CE1 TYR A 58 10.539 22.507 7.823 1.00 20.00 C ATOM 10 CE2 TYR A 58 12.342 22.809 9.367 1.00 20.00 C ATOM 11 CZ TYR A 58 11.574 23.271 8.321 1.00 20.00 C ATOM 12 OH TYR A 58 11.842 24.502 7.765 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 7.100 13.574 10.213 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 12.839 13.910 10.236 1.00 20.00 C ATOM 38 CG2 ILE A 60 13.330 11.580 9.441 1.00 20.00 C ATOM 39 CD1 ILE A 60 12.388 14.532 11.538 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 9.769 10.355 4.619 1.00 8.40 C ATOM 57 CG2 VAL A 61 8.876 8.157 5.492 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 13.291 5.155 7.608 1.00 20.00 C ATOM 73 CG2 VAL A 62 15.470 5.675 6.489 1.00 20.00 C sX 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 11.034 20.783 9.437 1.00 20.00 C ATOM 7 CD1 TYR A 58 10.273 21.271 8.381 1.00 20.00 C ATOM 8 CD2 TYR A 58 12.069 21.570 9.919 1.00 20.00 C ATOM 9 CE1 TYR A 58 10.539 22.507 7.823 1.00 20.00 C ATOM 10 CE2 TYR A 58 12.342 22.809 9.367 1.00 20.00 C ATOM 11 CZ TYR A 58 11.574 23.271 8.321 1.00 20.00 C ATOM 12 OH TYR A 58 11.842 24.502 7.765 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 6.816 15.072 8.601 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 12.855 13.906 10.216 1.00 20.00 C ATOM 38 CG2 ILE A 60 13.319 11.561 9.453 1.00 20.00 C ATOM 39 CD1 ILE A 60 13.856 13.963 11.349 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 9.076 8.178 5.270 1.00 8.40 C ATOM 57 CG2 VAL A 61 8.102 10.155 6.509 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 15.302 5.475 6.409 1.00 20.00 C ATOM 73 CG2 VAL A 62 14.851 7.003 8.341 1.00 20.00 C sX 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 11.034 20.783 9.437 1.00 20.00 C ATOM 7 CD1 TYR A 58 10.273 21.271 8.381 1.00 20.00 C ATOM 8 CD2 TYR A 58 12.069 21.570 9.919 1.00 20.00 C ATOM 9 CE1 TYR A 58 10.539 22.507 7.823 1.00 20.00 C ATOM 10 CE2 TYR A 58 12.342 22.809 9.367 1.00 20.00 C ATOM 11 CZ TYR A 58 11.574 23.271 8.321 1.00 20.00 C ATOM 12 OH TYR A 58 11.842 24.502 7.765 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 c C s7d|}tjjdddtƒjƒ}|jƒjƒ}|jdd|ƒt j j d|d|ƒ}|jdd|ƒtjjddd|ƒjƒjƒ}|jƒjƒ}t j ||jƒƒjƒjƒ} t| |d ƒsöt‚t j ||jƒƒjƒjƒ} t| |d ƒs3t‚dS( Ns exercise_%st source_infotlinest file_names %s_in.pdbt pdb_hierarchytmodes %s_out.pdbgü©ñÒMbP?gš™™™™™¹?(tiotbxtpdbtinputtNonetpdb_strtconstruct_hierarchytatomst extract_xyztwrite_pdb_filetmmtbxtutilstswitch_rotamersRtsqrttdott min_max_meantas_tupleRtAssertionError( Rtresulttt1tt2tprefixtphts0ts1ts2td((sM/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/tst_switch_rotamers.pytcore s !'%%texercise_fix_outlierscC sØtjjdddtƒjƒ}|jƒjddƒ}|jƒj ƒ}|j dd|ƒt j j d|dd ƒ}|j dd |ƒtjjdddtƒjƒj ƒ}|jƒj ƒ}tj|j|ƒ|j|ƒjƒƒjƒjƒ}t|d d d gƒst‚tj|j|ƒ|j|ƒjƒƒjƒjƒ}t|d d d gƒsut‚tj|j|ƒ|j|ƒjƒƒjƒjƒ}t|d d d gƒsÌt‚tj|j|ƒ|j|ƒjƒƒjƒjƒ}t|d d d gd ƒs$t‚tj|j|ƒ|j|ƒjƒƒjƒjƒ}t|d ddgdƒs|t‚tj|j|ƒ|j|ƒjƒƒjƒjƒ}t|d ddgdƒsÔt‚dS(NRRtstringsFresname TYR and not (name O or name CA or name N or name C or name CB)Rs %s_in.pdbRRt fix_outlierss %s_out.pdbigü©ñÒMbP?gÍÌÌÌÌÌì?gffffff@gffffff@gš™™™™™¹?(RR R R R R tatom_selection_cachet selectionRRRRRRR%RRtselectRRRRR(RRtselRRR R!((sM/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/tst_switch_rotamers.pyR#s*! '9997!7!7texercise_selectioncC sštjjdddtƒjƒ}|jƒjddƒ}|jƒj ƒ}|j dd|ƒt j j d|dd d |ƒ}|j dd |ƒtjjdddtƒjƒj ƒ}|jƒj ƒ}tj||jƒƒjƒjƒ}t|d d d gƒst‚tj||jƒƒjƒjƒ}t|d d d gƒsSt‚tj||jƒƒjƒjƒ}t|d d d gƒs–t‚dS( NRRR$snot resname TYRRs %s_in.pdbRRR%R's %s_out.pdbi(RR R R R R R&R'RRRRRRRRRRRRR(RRR)RRR R!((sM/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/tst_switch_rotamers.pyR*0s! '%%%t__main__Rt max_distantRRiRgffffff$@gø?t min_distantgffffff@gffffffæ?t exact_matchgš™™™™™Ù?(t __future__Rt iotbx.pdbRtlibtbx.test_utilsRtscitbx.array_familyRt mmtbx.utilsRR R,R-R.R%R'R"R#R*t__name__(((sM/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/utils/tst_switch_rotamers.pyts&  ++++++    111