ó
Û™xTc           @   s¸   d  d l  m Z d  d l m Z d  d l 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 Z d Z d „  Z d „  Z e d	 k r´ e e j d
 ƒ n  d S(   iÿÿÿÿ(   t   division(   t   flexN(   t   miller(   t   maptbxsR  

REMARK iotbx.pdb.box_around_molecule --buffer-layer=2 "m.pdb"
REMARK Date 2013-12-16 Time 13:47:17 PST -0800 (1387230437.01 s)
CRYST1   12.380   14.615   11.502  90.00  90.00  90.00 P 1
ATOM      1  CB  PHE A   1       4.641   4.458   4.502  1.00 10.00           C
ATOM      2  CG  PHE A   1       3.809   3.637   5.453  1.00 10.00           C
ATOM      3  CD1 PHE A   1       2.792   2.781   4.971  1.00 10.00           C
ATOM      4  CD2 PHE A   1       4.035   3.712   6.843  1.00 10.00           C
ATOM      5  CE1 PHE A   1       2.000   2.000   5.869  1.00 10.00           C
ATOM      6  CE2 PHE A   1       3.256   2.941   7.761  1.00 10.00           C
ATOM      7  CZ  PHE A   1       2.234   2.081   7.270  1.00 10.00           C
ATOM      8  C   PHE A   1       4.830   6.416   2.964  1.00 10.00           C
ATOM      9  O   PHE A   1       5.380   5.842   2.000  1.00 10.00           O
ATOM     10  OXT PHE A   1       5.017   7.615   3.259  1.00 10.00           O
ATOM     11  N   PHE A   1       2.749   5.066   3.014  1.00 10.00           N
ATOM     12  CA  PHE A   1       3.874   5.605   3.831  1.00 10.00           C
ATOM     13  CB  PHE A   2       9.641   9.458   9.502  1.00 10.00           C
ATOM     14  C   PHE A   2       9.830  11.416   7.964  1.00 10.00           C
ATOM     15  O   PHE A   2      10.380  10.842   7.000  1.00 10.00           O
ATOM     16  OXT PHE A   2      10.017  12.615   8.259  1.00 10.00           O
ATOM     17  N   PHE A   2       7.749  10.066   8.014  1.00 10.00           N
ATOM     18  CA  PHE A   2       8.874  10.605   8.831  1.00 10.00           C
TER
END
c   
      C   sŠ  |  j  d |  j ƒ  d t j d d ƒ } t j d | d |  ƒ } | j ƒ  | j ƒ  } t j d | d | ƒ } | j ƒ  | j ƒ  } | j ƒ  | j ƒ  k s¡ t	 ‚ | j
 ƒ  | j
 ƒ  k s¿ t	 ‚ t j d |  j ƒ  d | j ƒ  d	 | j
 ƒ  d
 t j | j ƒ  ƒ d t j d g | j ƒ  j ƒ  ƒ ƒ } t j d | j | ƒ d | j | ƒ ƒ j ƒ  } d „  }	 | |	 d | d | ƒ |	 d | d | ƒ f S(   Nt   d_mint   symmetry_flagst   resolution_factorg      Ð?t   crystal_griddingt   fourier_coefficientst	   unit_cellt
   fft_n_realt
   fft_m_realt
   sites_cartt
   site_radiig      ø?t   xt   yc         S   sF   t  j ƒ  } x* | j ƒ  D] } | j |  j | ƒ ƒ q Wt  j | ƒ S(   N(   R   t   doublet
   sites_fract   appendt   eight_point_interpolationt   mean(   t   mt   xrst   rt   sf(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/maps/tst_composite_omit_map_2.pyt   md>   s    R   R   (   R   R   R   t   use_space_group_symmetryR   t   fft_mapt   apply_sigma_scalingt   real_map_unpaddedt   focust   AssertionErrort   allt   grid_indices_around_sitesR	   R   t   vec3_doubleR   R   t
   scattererst   sizet   linear_correlationt   selectt   coefficient(
   t   mc1t   mc2R   R   R   t   m1t   m2t   selt   ccR   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/maps/tst_composite_omit_map_2.pyt   get_cc&   s2    					
		
	%0	c         C   s:  t  j j d d  d t ƒ } | j ƒ  } | j ƒ  } | j ƒ  j d ƒ } | j	 | ƒ } | j	 | ƒ } | j
 d d ƒ j ƒ  } | j
 d d ƒ j ƒ  } | j d | ƒ }	 t | ƒ j d d ƒ }
 |
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 |
 j d	 | d d ƒ |
 j d	 |	 d d ƒ t j j d t | ƒ d | ƒ } | j ƒ  j d d d t d t ƒ } t d | d | d | ƒ Gt d | d | d | ƒ GHt d | d | d | ƒ Gt d | d | d | ƒ GHt d | d |	 d | ƒ Gt d | d |	 d | ƒ GHH| j ƒ  j d | j ƒ  j ƒ  d t j d d ƒ } x¢ d g D]— } | d k rnd } n  t j j  j! d d d | d  t d! | j" ƒ  d" | d# d$ ƒ } | j } | Gt d | d | d | ƒ Gt d | d | d | ƒ GHqSW|
 j d	 | d d% ƒ |
 j d	 | d d& ƒ |
 j ƒ  } | j d d' ƒ d  S((   Nt   source_infot   liness   resseq 1R   g      ø?t   phase_sourcet   column_root_labels   F-obst   miller_arrays   R-free-flagst	   file_names   data.mtzt   ft   FBt   FCt   f_obst   xray_structuret   map_typet   Fot
   isotropizet   fill_missingR(   R)   R   R   R   g      Ð?i   i    i   R   t   full_resolution_mapt   fmodelt   n_debias_cyclest   box_size_as_fractiong{®Gáz„?t   Ot   mcs   m.mtz(#   t   iotbxt   pdbt   inputt   Nonet   pdb_strt   construct_hierarchyt   xray_structure_simplet   atom_selection_cachet	   selectionR&   t   structure_factorst   f_calct   phase_transfert   abst   as_mtz_datasett   add_miller_arrayt   generate_r_free_flagst
   mtz_objectt   writet   mmtbxt   f_modelt   managert   electron_density_mapt   map_coefficientst   FalseR.   R8   R   R   R   R   t   mapst   composite_omit_mapt   runt	   deep_copy(   t   argst   pdb_inpt   phR   R,   t   xrs1t   xrs2t   FR6   R7   t   mtz_datasetRT   R?   RC   R   t   it   oot   mco(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/maps/tst_composite_omit_map_2.pyR^   E   s^    !	333		 			t   __main__i   (   t
   __future__R    t   cctbx.array_familyR   t	   iotbx.pdbRD   t   mmtbx.f_modelRV   t   cctbxR   t
   mmtbx.mapsR   t   mmtbx.maps.composite_omit_mapt   sysRH   R.   R^   t   __name__t   argv(    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/maps/tst_composite_omit_map_2.pyt   <module>   s   		9