ó
¾™xTc           @   sØ   d  d l  m Z d  d l m Z d  d l Z d  d l m Z d  d l Z d  d l m	 Z	 d  d l
 Z d  d l m Z d  d l m Z d  d l m Z d  d l Z d	 „  Z d
 „  Z e d k rÔ e ƒ  e ƒ  d GHn  d S(   iÿÿÿÿ(   t   division(   t   real_space_correlationN(   t   file_reader(   t   flex(   t   approx_equal(   t   null_out(   t
   group_argsc       	   C   s’  t  j j d d d t j j ƒ }  t  j j d d d t j j ƒ } d  |  | g k r] d GHt St j	 |  ƒ } | j
 j } | j ƒ  j ƒ  | j
 j ƒ  } t j	 | ƒ } | j j d } | j j d } | j d | j ƒ  d k ƒ } t j j d	 | d
 | d | g d d ƒ } t j d | d | ƒ }	 t |	 j d d d ƒsDt ‚ | j ƒ  }
 |
 j d ƒ } | j d d ƒ j ƒ  j ƒ  } |
 j d ƒ } | j d d ƒ j ƒ  j ƒ  } | j  } t j! d t" j# | j$ ƒ  j% ƒ  t& ƒ d | d | d | ƒ } t | j |	 j d ƒ st ‚ t j' d | d | d t( ƒ  ƒ } t) | t* ƒ sCt ‚ t) | d t+ ƒ s\t ‚ | d j, d k sut ‚ | d j- d k sŽt ‚ t& S(   Nt   relative_paths    phenix_regression/pdb/1yjp_h.pdbt   tests+   phenix_regression/reflection_files/1yjp.mtzs*   phenix_regression not found, skipping testi    i   t   datat   f_obst   r_free_flagst   xray_structurest   scattering_tablet
   n_gaussiant   fragmentt   fmodelg¸…ëQ¸î?t   epsg{®Gáz„?s   2mFo-DFct   resolution_factorg      Ð?t   Fmodelt   atom_selectiont   map1t   map2t   xray_structuret   pdb_hierarchyt   logs    A   GLY    1    N  (.   t   libtbxt   envt   find_in_repositoriest   ost   patht   isfilet   Nonet   FalseR   t   any_filet   file_objectt	   hierarchyt   atomst   reset_i_seqt   xray_structure_simplet   file_servert   miller_arrayst   customized_copyR	   t   mmtbxt   utilst   fmodel_simpleR   t   map_statistics_for_fragmentR   t   cct   AssertionErrort   electron_density_mapt   map_coefficientst   fft_mapt   apply_sigma_scalingt   real_mapR   t!   map_statistics_for_atom_selectionR   t   boolt
   sites_cartt   sizet   Truet   simpleR   t
   isinstancet   listR   t   n_atomst   id_str(   t   pdb_filet   mtz_filet   pdb_inR$   t   xrst   mtz_inR
   t   r_freeR   t	   map_statst   edmt   map1_coeffsR   t   map2_coeffsR   R   t
   map_stats2t   results(    (    sY   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/regression/tst_real_space_correlation.pyt
   exercise_1   sb    										c       	   C   s†  d }  t  j j j d |  ƒ } | j j ƒ  } t | j d d ƒ j ƒ  ƒ } | j ƒ  } t	 j
 | j ƒ  d ƒ | j ƒ  d } | j d | ƒ } | j d d	 d
 d ƒ } | j d t ƒ } t j j d | d | d | g d d ƒ } | j d  k	 sø t ‚ t j d | d | j j ƒ  d | ƒ } | j j ƒ  }	 |	 j d ƒ }
 t j d | d | j j ƒ  d | d |
 ƒ } t j d |
 d | ƒ } d  S(   NsE  CRYST1   12.000    8.000   12.000  90.02  89.96  90.05 P 1           1
ATOM     39  N   ASN A   6       5.514   2.664   4.856  1.00 11.99           N
ATOM     40  CA  ASN A   6       6.831   2.310   4.318  1.00 12.30           C
ATOM     41  C   ASN A   6       7.854   2.761   5.324  1.00 13.40           C
ATOM     42  O   ASN A   6       8.219   3.943   5.374  1.00 13.92           O
ATOM     43  CB  ASN A   6       7.065   3.016   2.993  1.00 12.13           C
ATOM     44  CG  ASN A   6       5.961   2.735   2.003  1.00 12.77           C
ATOM     45  OD1 ASN A   6       5.798   1.604   1.551  1.00 14.27           O
ATOM     46  ND2 ASN A   6       5.195   3.747   1.679  1.00 10.07           N
ATOM     47  N   TYR A   7       8.292   1.817   6.147  1.00 14.70           N
ATOM     48  CA  TYR A   7       9.159   2.144   7.299  1.00 15.18           C
ATOM     49  C   TYR A   7      10.603   2.331   6.885  1.00 15.91           C
ATOM     50  O   TYR A   7      11.041   1.811   5.855  1.00 15.76           O
ATOM     51  CB  TYR A   7       9.061   1.065   8.369  1.00 15.35           C
ATOM     52  CG  TYR A   7       7.665   0.929   8.902  1.00 14.45           C
ATOM     53  CD1 TYR A   7       6.771   0.021   8.327  1.00 15.68           C
ATOM     54  CD2 TYR A   7       7.210   1.756   9.920  1.00 14.80           C
ATOM     55  CE1 TYR A   7       5.480  -0.094   8.796  1.00 13.46           C
ATOM     56  CE2 TYR A   7       5.904   1.649  10.416  1.00 14.33           C
ATOM     57  CZ  TYR A   7       5.047   0.729   9.831  1.00 15.09           C
ATOM     58  OH  TYR A   7       3.766   0.589  10.291  1.00 14.39           O
ATOM     59  OXT TYR A   7      11.358   2.999   7.612  1.00 17.49           O
TER
ATOM      1  N   ASN B   6       1.414   5.113   6.019  1.00 12.99           N
ATOM      2  CA  ASN B   6       2.720   4.776   5.445  1.00 13.30           C
ATOM      3  C   ASN B   6       3.763   5.209   6.438  1.00 14.40           C
ATOM      4  O   ASN B   6       4.125   6.391   6.507  1.00 14.92           O
ATOM      5  CB  ASN B   6       2.922   5.513   4.131  1.00 13.13           C
ATOM      6  CG  ASN B   6       1.798   5.250   3.160  1.00 13.77           C
ATOM      7  OD1 ASN B   6       1.629   4.129   2.686  1.00 15.27           O
ATOM      8  ND2 ASN B   6       1.022   6.266   2.875  1.00 11.07           N
ATOM      9  N   TYR B   7       4.222   4.248   7.230  1.00 15.70           N
ATOM     10  CA  TYR B   7       5.113   4.552   8.370  1.00 16.18           C
ATOM     11  C   TYR B   7       6.547   4.754   7.929  1.00 16.91           C
ATOM     12  O   TYR B   7       6.964   4.259   6.878  1.00 16.76           O
ATOM     13  CB  TYR B   7       5.042   3.449   9.417  1.00 16.35           C
ATOM     14  CG  TYR B   7       3.659   3.296   9.977  1.00 15.45           C
ATOM     15  CD1 TYR B   7       2.756   2.398   9.402  1.00 16.68           C
ATOM     16  CD2 TYR B   7       3.224   4.098  11.023  1.00 15.80           C
ATOM     17  CE1 TYR B   7       1.476   2.267   9.896  1.00 14.46           C
ATOM     18  CE2 TYR B   7       1.929   3.975  11.545  1.00 15.33           C
ATOM     19  CZ  TYR B   7       1.063   3.065  10.959  1.00 16.09           C
ATOM     20  OH  TYR B   7      -0.207   2.910  11.443  1.00 15.39           O
ATOM     21  OXT TYR B   7       7.316   5.408   8.654  1.00 18.49           O
END
t
   pdb_stringt   d_ming      ø?gš™™™™™¹?g¸…ëQ¸ž?t   sigmast   twin_laws   -l,-k,-ht   alphagš™™™™™Ù?t   use_lattice_symmetryR
   R   R   R   R   R   t	   pdb_atomsR   s   chain Bt	   selectionR   (   t   iotbxt   pdbR$   t   inputR'   t   abst   structure_factorst   f_calct#   set_observation_type_xray_amplitudeR   t   doubleR9   R	   R*   t	   twin_datat   generate_r_free_flagsR:   R+   R,   R-   RP   R    R0   R   t"   extract_map_stats_for_single_atomsR%   t   atom_selection_cacheRT   R6   (   t   pdb_strRB   RC   t   fct   sigft   fc_twint   flagsR   RF   t	   sel_cachet   selt   map_stats_2t   map_stats_3(    (    sY   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/regression/tst_real_space_correlation.pyt
   exercise_2D   s:    /&							t   __main__t   OK(   t
   __future__R    R+   R   t   mmtbx.utilsRU   R   t   iotbx.pdb.hierarchyt   scitbx.array_familyR   t   libtbx.load_envR   t   libtbx.test_utilsR   t   libtbx.utilsR   R   R   RL   Rj   t   __name__(    (    (    sY   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/regression/tst_real_space_correlation.pyt   <module>   s    	6	N