ó
Õ™xTc           @   s~   d  d l  m Z d  d l m Z d  d l m Z m Z d  d l m Z d „  Z	 d „  Z
 e d k rz e
 ƒ  e	 ƒ  d GHn  d	 S(
   iÿÿÿÿ(   t   division(   t   Exception_expected(   t   null_outt   Sorry(   t   easy_runc             sG  d d l  m }  d d l m } d d l m } d d l m } d d l m ‰  d d  l	 ‰ d: } d } d } d } t
 d d ƒ j | | ƒ d } t
 d d ƒ j | ƒ t j d ƒ j ƒ  j d k sÎ t ‚ | j d ƒ }	 |	 j j d }
 |
 j ƒ  j d | j d ƒ ƒ } |
 j d | ƒ }
 ˆ j d ƒ |
 j d d ƒ } |
 j d d ƒ } | j | d d ƒ| j ƒ  j d ƒ | j d ƒ } | j j } | j j ƒ  } | j ƒ  j  } | j ƒ  j d  | j! d; ƒ ƒ } | j" ƒ  } | j# ƒ  } | ˆ  j$ | j% ƒ  d< ƒ 7} | j& | ƒ | j' ƒ  } | j( | ƒ t
 d( d ƒ j | j) d | ƒ ƒ | d) ƒ } | j* | ƒ } | j* | ƒ } t
 d* d ƒ j | j) d | ƒ ƒ | j ƒ  j d | j d+ ƒ ƒ } t
 d, d ƒ j | j) d | ƒ ƒ d- ‡  ‡ f d. † } | j ƒ  } | j+ d/ d0 | ƒ| j, ƒ  | j' ƒ  } | j( | ƒ t
 d1 d ƒ j | j) d | ƒ ƒ t
 d2 d ƒ j | j) ƒ  ƒ |  j- j. ƒ  } t/ | _0 d( d* d, d1 d2 g } |  j1 d3 | d4 d  d5 |
 d6 | d7 | d8 t3 d9 t4 ƒ  ƒ } | j5 d1 k sìt ‚ t3 | _0 |  j1 d3 | d4 d  d5 |
 d6 | d7 | d8 t3 d9 t4 ƒ  ƒ } | j5 d( k sCt ‚ d  S(=   Niÿÿÿÿ(   t   select_best_starting_model(   t   file_reader(   t   uctbx(   t   sgtbx(   t   flexgZd;ßï8@g¬Zd»!@g'1¬z9@g     €V@g…ëQ¸ÅZ@t   P21s!  CRYST1   24.937    8.866   25.477  90.00 107.08  90.00 P 1 21 1
SCALE1      0.040101  0.000000  0.012321        0.00000
SCALE2      0.000000  0.112790  0.000000        0.00000
SCALE3      0.000000  0.000000  0.041062        0.00000
ATOM      1  N   GLY A   1       8.992   0.474  -6.096  1.00 16.23           N
ATOM      2  CA  GLY A   1       9.033   0.047  -4.707  1.00 16.20           C
ATOM      3  C   GLY A   1       7.998  -1.029  -4.448  1.00 15.91           C
ATOM      4  O   GLY A   1       7.548  -1.689  -5.385  1.00 16.11           O
ATOM      5  N   ASN A   2       7.625  -1.218  -3.185  1.00 15.02           N
ATOM      6  CA  ASN A   2       6.523  -2.113  -2.848  1.00 13.92           C
ATOM      7  C   ASN A   2       5.220  -1.618  -3.428  1.00 12.24           C
ATOM      8  O   ASN A   2       4.955  -0.418  -3.432  1.00 11.42           O
ATOM      9  CB  ASN A   2       6.376  -2.261  -1.340  1.00 14.42           C
ATOM     10  CG  ASN A   2       7.620  -2.786  -0.697  1.00 13.92           C
ATOM     11  OD1 ASN A   2       8.042  -3.915  -0.978  1.00 14.39           O
ATOM     12  ND2 ASN A   2       8.232  -1.975   0.168  1.00 12.78           N
ATOM     13  N   ASN A   3       4.406  -2.553  -3.904  1.00 12.20           N
ATOM     14  CA  ASN A   3       3.164  -2.226  -4.594  1.00 11.81           C
ATOM     15  C   ASN A   3       1.925  -2.790  -3.910  1.00 10.59           C
ATOM     16  O   ASN A   3       1.838  -3.991  -3.653  1.00 10.32           O
ATOM     17  CB  ASN A   3       3.231  -2.727  -6.046  1.00 12.51           C
ATOM     18  CG  ASN A   3       1.973  -2.405  -6.848  1.00 12.59           C
ATOM     19  OD1 ASN A   3       1.662  -1.239  -7.106  1.00 13.64           O
ATOM     20  ND2 ASN A   3       1.260  -3.443  -7.268  1.00 12.39           N
ATOM     21  N   GLN A   4       0.973  -1.913  -3.608  1.00 10.34           N
ATOM     22  CA  GLN A   4      -0.366  -2.335  -3.208  1.00 10.00           C
ATOM     23  C   GLN A   4      -1.402  -1.637  -4.085  1.00 10.21           C
ATOM     24  O   GLN A   4      -1.514  -0.414  -4.070  1.00  8.99           O
ATOM     25  CB  GLN A   4      -0.656  -2.027  -1.736  1.00 10.00           C
ATOM     26  CG  GLN A   4      -1.927  -2.705  -1.229  1.00 10.50           C
ATOM     27  CD  GLN A   4      -2.482  -2.102   0.060  1.00 11.36           C
ATOM     28  OE1 GLN A   4      -2.744  -0.900   0.151  1.00 12.29           O
ATOM     29  NE2 GLN A   4      -2.684  -2.951   1.055  1.00 10.43           N
ATOM     30  N   GLN A   5      -2.154  -2.406  -4.857  1.00 10.48           N
ATOM     31  CA  GLN A   5      -3.247  -1.829  -5.630  1.00 11.24           C
ATOM     32  C   GLN A   5      -4.591  -2.382  -5.178  1.00 11.40           C
ATOM     33  O   GLN A   5      -4.789  -3.599  -5.092  1.00 11.94           O
ATOM     34  CB  GLN A   5      -3.024  -2.023  -7.129  1.00 11.14           C
ATOM     35  CG  GLN A   5      -1.852  -1.222  -7.653  1.00 10.65           C
ATOM     36  CD  GLN A   5      -1.338  -1.748  -8.965  1.00 10.73           C
ATOM     37  OE1 GLN A   5      -0.794  -2.845  -9.028  1.00 10.14           O
ATOM     38  NE2 GLN A   5      -1.511  -0.968 -10.027  1.00 11.31           N
ATOM     39  N   ASN A   6      -5.504  -1.471  -4.872  1.00 11.56           N
ATOM     40  CA  ASN A   6      -6.809  -1.838  -4.359  1.00 12.07           C
ATOM     41  C   ASN A   6      -7.856  -1.407  -5.353  1.00 13.18           C
ATOM     42  O   ASN A   6      -8.257  -0.251  -5.362  1.00 13.64           O
ATOM     43  CB  ASN A   6      -7.053  -1.149  -3.017  1.00 12.12           C
ATOM     44  CG  ASN A   6      -5.966  -1.446  -1.998  1.00 12.31           C
ATOM     45  OD1 ASN A   6      -5.833  -2.579  -1.517  1.00 13.43           O
ATOM     46  ND2 ASN A   6      -5.198  -0.423  -1.645  1.00 11.88           N
ATOM     47  N   TYR A   7      -8.298  -2.332  -6.193  1.00 14.34           N
ATOM     48  CA  TYR A   7      -9.162  -1.980  -7.317  1.00 15.00           C
ATOM     49  C   TYR A   7     -10.603  -1.792  -6.893  1.00 15.64           C
ATOM     50  O   TYR A   7     -11.013  -2.278  -5.838  1.00 15.68           O
ATOM     51  CB  TYR A   7      -9.064  -3.041  -8.412  1.00 15.31           C
ATOM     52  CG  TYR A   7      -7.657  -3.197  -8.931  1.00 15.06           C
ATOM     53  CD1 TYR A   7      -6.785  -4.118  -8.368  1.00 15.24           C
ATOM     54  CD2 TYR A   7      -7.193  -2.400  -9.960  1.00 14.96           C
ATOM     55  CE1 TYR A   7      -5.489  -4.253  -8.830  1.00 14.94           C
ATOM     56  CE2 TYR A   7      -5.905  -2.526 -10.429  1.00 15.13           C
ATOM     57  CZ  TYR A   7      -5.055  -3.451  -9.861  1.00 14.97           C
ATOM     58  OH  TYR A   7      -3.768  -3.572 -10.335  1.00 14.93           O
ATOM     59  OXT TYR A   7     -11.378  -1.149  -7.601  1.00 15.89           O
TER
s@  HETATM   64  O   HOH S   1     -10.466  -2.347  -3.168  1.00 17.57           O
HETATM   65  O   HOH S   2       6.469   1.081  -7.070  1.00 21.27           O
HETATM   66  O   HOH S   3     -11.809   0.108  -9.956  1.00 27.52           O
HETATM   67  O   HOH S   4       1.580  -3.455 -11.035  1.00 44.76           O
END
s   tst_start_model_base.pdbt   wsÅ   
    high_resolution = 1.75
    add_sigmas = True
    pdb_file = tst_start_model_base.pdb
    output {
      label = F
      type = *real complex
      file_name = tst_start_model_base.mtz
    }
  s   tst_start_model_fmodel.effs(   phenix.fmodel tst_start_model_fmodel.effi    s   tst_start_model_base.mtzt   space_group_infot   P2t   crystal_symmetryi90  t   fractiongš™™™™™¹?t   column_root_labelt   Ft
   FreeR_flags   tst_start_model.mtzt	   unit_cellg;ßO�—î8@g;ßO�—®!@gÇK7‰A€9@g     àZ@g      ð?g        g      à?s   tst_start_model_1.pdbs2   (name N or name C or name O or name CA or name CB)s   tst_start_model_2.pdbt   P1s   tst_start_model_3.pdbi   c            s>   ˆ  j  ƒ  } x+ t |  ƒ D] } | j ˆ j ƒ  | ƒ q W| S(   N(   t   doublet   ranget   appendt   random(   t   sizet   factort   dt   x(   R	   R   (    s]   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_select_best_starting_model.pyt   random_double’   s    gš™™™™™É?R   s   tst_start_model_4.pdbs   tst_start_model_5.pdbt   model_namest
   model_datat   f_obst   r_free_flagst   paramst   skip_twin_detectiont   log(   gZd;ßï8@g¬Zd»!@g'1¬z9@g     €V@g…ëQ¸ÅZ@g     €V@(   g;ßO�—î8@g;ßO�—®!@gÇK7‰A€9@g     €V@g     àZ@g     €V@(   g      ð?g        g      à?(6   t   mmtbx.refinementR   t   iotbxR   t   cctbxR   R   t   scitbx.array_familyR	   R   t   opent   writeR   t   fully_bufferedt   raise_if_errorst   return_codet   AssertionErrort   any_filet   file_servert   miller_arraysR   t   customized_copyR   t   seedt   generate_r_free_flagst   as_mtz_datasett   add_miller_arrayt
   mtz_objectt   file_objectt	   hierarchyt   xray_structure_simplet   atom_selection_cachet	   selectionR   t   deep_copy_scattererst
   sites_cartt   vec3_doubleR   t   set_sites_cartt	   deep_copyt   adopt_xray_structuret   as_pdb_stringt   selectt   shake_sites_in_placet	   shake_adpt   master_philt   extractt   Falset   rigid_body_refinet   select_modelt   Nonet   TrueR   t   best_model_name(   R   R   R   R   R   t   space_groupt   pdb_baset   pdb_base_waterR"   t   mtz_inR    t   symmt   flagst   mtz_datat   pdb_int   hierarchy_int   xrs_inR<   t   symm2t   xrs_outR>   t   hierarchy_outt   mc_selet   symm3R   R   t   result(    (   R	   R   s]   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_select_best_starting_model.pyt   exercise_main   s¬    B
		
					c          C   sw  d d l  m }  d d l m } d d  l } d } d } t | d ƒ j | ƒ | j j j	 | ƒ } | j } | j	 j
 ƒ  } | j ƒ  } | j t ƒ d k s¢ t ‚ | j d | ƒ | j | ƒ |  j d	 | d
 | d d d t ƒ  ƒ \ }	 }
 | j ƒ  } | j t ƒ d k st ‚ |
 j ƒ  j t ƒ d k s5t ‚ |	 j ƒ  j } | d ƒ } | j t ƒ d k skt ‚ | d ƒ } | j t ƒ d k s’t ‚ | d ƒ } | j t ƒ d k s¹t ‚ | d ƒ } | j t ƒ d k sàt ‚ |
 j ƒ  j ƒ  } |	 j ƒ  j ƒ  } | j | ƒ r"| j d ƒ s(t ‚ |
 j ƒ  j t ƒ sCt ‚ | j ƒ  j t ƒ d k sdt ‚ |  j d	 | d
 | d t d t d d d t ƒ  ƒ \ }	 }
 |	 j ƒ  j } | d ƒ j t ƒ d k sÍt ‚ |
 j ƒ  j t ƒ d k sît ‚ | j ƒ  d j ƒ  } | j | ƒ y+ |  j d	 | d
 | d t ƒ  ƒ \ }	 }
 Wn t k
 rOn Xt  ‚ y1 |  j d	 | d
 | d | d t ƒ  ƒ \ }	 }
 Wn t k
 ršn Xt  ‚ |  j d | d t d d d t ƒ  ƒ \ }	 }
 | j j j	 d d ƒ } t! | j	 j" ƒ  ƒ d k st ‚ |  j d | d t d t d d d t ƒ  ƒ \ }	 }
 t d ƒ j# ƒ  } x$ | D] } | j$ d ƒ sSt ‚ qSWd  S(   Niÿÿÿÿ(   R   (   R   s\'  REMARK this is a remark record!
CRYST1   21.937    4.866   23.477  90.00 107.08  90.00 P 1 21 1
SCALE1      0.045585  0.000000  0.014006        0.00000
SCALE2      0.000000  0.205508  0.000000        0.00000
SCALE3      0.000000  0.000000  0.044560        0.00000
ATOM      1  N   GLY A   1      -9.009   4.612   6.102  0.00 16.77           N
ATOM      2  CA  GLY A   1      -9.052   4.207   4.651  0.00 16.57           C
ATOM      3  C   GLY A   1      -8.015   3.140   4.419  0.00 16.16           C
ATOM      4  O   GLY A   1      -7.523   2.521   5.381  0.00 16.78           O
ATOM      5  H1  GLY A   1      -9.802   4.938   6.343  0.00 16.77           H
ATOM      6  H2  GLY A   1      -8.816   3.902   6.603  0.00 16.77           H
ATOM      7  H3  GLY A   1      -8.385   5.236   6.218  0.00 16.77           H
ATOM      8  HA2 GLY A   1      -9.928   3.856   4.426  0.00 16.57           H
ATOM      9  HA3 GLY A   1      -8.858   4.970   4.084  0.00 16.57           H
ATOM     10  N   ASN A   2      -7.656   2.923   3.155  1.00 15.02           N
ATOM     11  CA  ASN A   2      -6.522   2.038   2.831  1.00 14.10           C
ATOM     12  C   ASN A   2      -5.241   2.537   3.427  1.00 13.13           C
ATOM     13  O   ASN A   2      -4.978   3.742   3.426  1.00 11.91           O
ATOM     14  CB  ASN A   2      -6.346   1.881   1.341  1.00 15.38           C
ATOM     15  CG  ASN A   2      -7.584   1.342   0.692  1.00 14.08           C
ATOM     16  OD1 ASN A   2      -8.025   0.227   1.016  1.00 17.46           O
ATOM     17  ND2 ASN A   2      -8.204   2.155  -0.169  1.00 11.72           N
ATOM     18  H   ASN A   2      -8.044   3.269   2.470  1.00 15.02           H
ATOM     19  HA  ASN A   2      -6.698   1.159   3.202  1.00 14.10           H
ATOM     20  HB2 ASN A   2      -6.150   2.746   0.949  1.00 15.38           H
ATOM     21  HB3 ASN A   2      -5.619   1.262   1.169  1.00 15.38           H
ATOM     22 HD21 ASN A   2      -8.919   1.893  -0.569  1.00 11.72           H
ATOM     23 HD22 ASN A   2      -7.888   2.940  -0.323  1.00 11.72           H
ATOM     24  N  AASN A   3      -4.438   1.590   3.905  0.50 12.26           N
ATOM     25  CA AASN A   3      -3.193   1.904   4.589  0.50 11.74           C
ATOM     26  C  AASN A   3      -1.955   1.332   3.895  0.50 11.10           C
ATOM     27  O  AASN A   3      -1.872   0.119   3.648  0.50 10.42           O
ATOM     28  CB AASN A   3      -3.259   1.378   6.042  0.50 12.15           C
ATOM     29  CG AASN A   3      -2.006   1.739   6.861  0.50 12.82           C
ATOM     30  OD1AASN A   3      -1.702   2.925   7.072  0.50 15.05           O
ATOM     31  ND2AASN A   3      -1.271   0.715   7.306  0.50 13.48           N
ATOM     32  H  AASN A   3      -4.597   0.747   3.843  0.50 12.26           H
ATOM     33  HA AASN A   3      -3.083   2.866   4.633  0.50 11.74           H
ATOM     34  HB2AASN A   3      -4.029   1.767   6.485  0.50 12.15           H
ATOM     35  HB3AASN A   3      -3.339   0.411   6.025  0.50 12.15           H
ATOM     36 HD21AASN A   3      -0.560   0.864   7.766  0.50 13.48           H
ATOM     37 HD22AASN A   3      -1.509  -0.093   7.132  0.50 13.48           H
ATOM     38  N  BASN A   3      -4.338   1.590   3.905  0.50 12.26           N
ATOM     39  CA BASN A   3      -3.093   1.904   4.589  0.50 11.74           C
ATOM     40  C  BASN A   3      -1.855   1.332   3.895  0.50 11.10           C
ATOM     41  O  BASN A   3      -1.772   0.119   3.648  0.50 10.42           O
ATOM     42  CB BASN A   3      -3.159   1.378   6.042  0.50 12.15           C
ATOM     43  CG BASN A   3      -4.127   2.189   6.923  0.50 12.82           C
ATOM     44  OD1BASN A   3      -4.598   1.573   8.012  0.50 15.05           O
ATOM     45  ND2BASN A   3      -4.430   3.358   6.630  0.50 13.48           N
ATOM     46  H  BASN A   3      -4.464   0.743   3.823  0.50 12.26           H
ATOM     47  HA BASN A   3      -2.983   2.866   4.621  0.50 11.74           H
ATOM     48  HB2BASN A   3      -3.463   0.457   6.031  0.50 12.15           H
ATOM     49  HB3BASN A   3      -2.275   1.432   6.438  0.50 12.15           H
ATOM     50 HD21BASN A   3      -3.922   3.821   6.115  0.50 13.48           H
ATOM     51 HD22BASN A   3      -5.147   3.708   6.952  0.50 13.48           H
ATOM     52  N   GLN A   4      -1.005   2.228   3.598  1.00 10.29           N
ATOM     53  CA  GLN A   4       0.384   1.888   3.199  1.00 10.53           C
ATOM     54  C   GLN A   4       1.435   2.606   4.088  1.00 10.24           C
ATOM     55  O   GLN A   4       1.547   3.843   4.115  1.00  8.86           O
ATOM     56  CB  GLN A   4       0.656   2.148   1.711  1.00  9.80           C
ATOM     57  CG  GLN A   4       1.944   1.458   1.213  1.00 10.25           C
ATOM     58  CD  GLN A   4       2.504   2.044  -0.089  1.00 12.43           C
ATOM     59  OE1 GLN A   4       2.744   3.268  -0.190  1.00 14.62           O
ATOM     60  NE2 GLN A   4       2.750   1.161  -1.091  1.00  9.05           N
ATOM     61  HA  GLN A   4       0.509   0.941   3.335  1.00 10.53           H
ATOM     62  HB2 GLN A   4      -0.088   1.808   1.189  1.00  9.80           H
ATOM     63  HB3 GLN A   4       0.752   3.103   1.569  1.00  9.80           H
ATOM     64  HG2 GLN A   4       2.630   1.544   1.893  1.00 10.25           H
ATOM     65  HG3 GLN A   4       1.753   0.520   1.057  1.00 10.25           H
ATOM     66 HE21 GLN A   4       2.592   0.324  -0.975  1.00  9.05           H
ATOM     67 HE22 GLN A   4       3.064   1.439  -1.842  1.00  9.05           H
ATOM     68  H  AGLN A   4      -1.142   3.077   3.620  0.50 10.29           H
ATOM     69  H  BGLN A   4      -1.168   3.072   3.606  0.50 10.29           H
ATOM     70  N   GLN A   5       2.154   1.821   4.871  1.00 10.38           N
ATOM     71  CA  GLN A   5       3.270   2.361   5.640  1.00 11.39           C
ATOM     72  C   GLN A   5       4.594   1.768   5.172  1.00 11.52           C
ATOM     73  O   GLN A   5       4.768   0.546   5.054  1.00 12.05           O
ATOM     74  CB  GLN A   5       3.056   2.183   7.147  1.00 11.96           C
ATOM     75  CG  GLN A   5       1.829   2.950   7.647  1.00 10.81           C
ATOM     76  CD  GLN A   5       1.344   2.414   8.954  1.00 13.10           C
ATOM     77  OE1 GLN A   5       0.774   1.325   9.002  1.00 10.65           O
ATOM     78  NE2 GLN A   5       1.549   3.187  10.039  1.00 12.30           N
ATOM     79  H   GLN A   5       2.021   0.978   4.977  1.00 10.38           H
ATOM     80  HA  GLN A   5       3.333   3.315   5.487  1.00 11.39           H
ATOM     81  HB2 GLN A   5       2.924   1.242   7.341  1.00 11.96           H
ATOM     82  HB3 GLN A   5       3.834   2.516   7.621  1.00 11.96           H
ATOM     83  HG2 GLN A   5       2.063   3.883   7.769  1.00 10.81           H
ATOM     84  HG3 GLN A   5       1.111   2.866   7.000  1.00 10.81           H
ATOM     85 HE21 GLN A   5       1.943   3.947   9.957  1.00 12.30           H
ATOM     86 HE22 GLN A   5       1.286   2.920  10.813  1.00 12.30           H
ATOM     87  N   ASN A   6       5.514   2.664   4.856  1.00 11.99           N
ATOM     88  CA  ASN A   6       6.831   2.310   4.318  1.00 12.30           C
ATOM     89  C   ASN A   6       7.854   2.761   5.324  1.00 13.40           C
ATOM     90  O   ASN A   6       8.219   3.943   5.374  1.00 13.92           O
ATOM     91  CB  ASN A   6       7.065   3.016   2.993  1.00 12.13           C
ATOM     92  CG  ASN A   6       5.961   2.735   2.003  1.00 12.77           C
ATOM     93  OD1 ASN A   6       5.798   1.604   1.551  1.00 14.27           O
ATOM     94  ND2 ASN A   6       5.195   3.747   1.679  1.00 10.07           N
ATOM     95  H   ASN A   6       5.401   3.512   4.945  1.00 11.99           H
ATOM     96  HA  ASN A   6       6.909   1.352   4.189  1.00 12.30           H
ATOM     97  HB2 ASN A   6       7.098   3.974   3.140  1.00 12.13           H
ATOM     98  HB3 ASN A   6       7.901   2.707   2.610  1.00 12.13           H
ATOM     99 HD21 ASN A   6       4.553   3.638   1.117  1.00 10.07           H
ATOM    100 HD22 ASN A   6       5.334   4.521   2.028  1.00 10.07           H
ATOM    101  N   MSE A   7       8.292   1.817   6.147  1.00 14.70           N
ATOM    102  CA  MSE A   7       9.159   2.144   7.299  1.00 15.18           C
ATOM    103  C   MSE A   7      10.603   2.331   6.885  1.00 15.91           C
ATOM    104  O   MSE A   7      11.041   1.811   5.855  1.00 15.76           O
ATOM    105  CB  MSE A   7       9.071   1.027   8.337  1.00 20.00           C
ATOM    106  CG  MSE A   7       7.703   0.904   8.987  1.00 20.00           C
ATOM    107 SE   MSE A   7       7.114   2.484   9.902  1.00 20.00          Se
ATOM    108  CE  MSE A   7       8.400   2.453  11.367  1.00 20.00           C
ATOM    109  H   MSE A   7       8.109   0.980   6.070  1.00 14.70           H
ATOM    110  HA  MSE A   7       8.841   2.961   7.708  1.00 15.18           H
ATOM    111  HB2 MSE A   7       9.270   0.186   7.900  1.00 20.00           H
ATOM    112  HB3 MSE A   7       9.724   1.195   9.033  1.00 20.00           H
ATOM    113  HG2 MSE A   7       7.042   0.539   8.377  1.00 20.00           H
ATOM    114  HG3 MSE A   7       8.123   0.264   9.563  1.00 20.00           H
ATOM    115  HE1 MSE A   7       8.976   3.219  11.304  1.00 20.00           H
ATOM    116  HE2 MSE A   7       8.333   2.133  12.198  1.00 20.00           H
ATOM    117  HE3 MSE A   7       9.010   1.805  10.983  1.00 20.00           H
TER
HETATM  118 CL    CL     1      -6.471   5.227   7.124  1.00 30.00          Cl
TER
HETATM  119  O   HOH A   9      10.431   1.858   3.216  1.00 19.71           O
HETATM  120  O   HOH A  10     -11.286   1.756  -1.468  1.00 17.08           O
HETATM  121  O   HOH A  11      11.808   4.179   9.970  1.00 23.99           O
HETATM  122  O   HOH A  12      13.605   1.327   9.198  1.00 26.17           O
HETATM  123  O   HOH A  13      -2.749   3.429  10.024  1.00 39.15           O
HETATM  124  O   HOH A  14      -1.500   0.682  10.967  1.00 43.49           O
TER
END
s   tst_start_model_misc.pdbR   i7   R<   t   pdb_hierarchyt   xray_structuret   output_files   tst_start_model_misc_new.pdbR$   i    s   resname MSEs   resname HOHs
   altloc 'B's
   element CLi   g      ð?t   remove_ligandst   remove_hydrogenss   tst_start_model_misc_new2.pdbs
   resname CLi0   t	   file_namet   preserve_remarkst   reset_hetatm_flagt   HETATM(%   R%   R   R&   R   t   iotbx.pdb.hierarchyR)   R*   t   pdbR9   t   inputR:   t   hd_selectiont   countRM   R.   t   convert_to_anisotropicRB   t   strip_modelR   R;   R<   t
   scattererst   extract_occupanciest   atomst   extract_occt   all_eqt   use_u_anisoRI   t   modelst   detached_copyt   append_modelR   R   t   lent   remark_sectiont	   readlinest
   startswith(   R   R   R&   t   pdb_strt   pdb_fileRV   R`   Ra   t   hd_selt   hierarchy_newt   xrs_newt   selt   mse_selt   hoh_selt   alt_selt   cl_selt   occ_xrst   occ_pdbt   model2t   pdb_newt   linest   line(    (    s]   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_select_best_starting_model.pyt   exercise_miscÀ   s     ‡		!$!	!!			!	t   __main__t   OKN(   t
   __future__R    t   libtbx.test_utilsR   t   libtbx.utilsR   R   t   libtbxR   R_   R�   t   __name__(    (    (    s]   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_select_best_starting_model.pyt   <module>   s   	¹	à