ó
Ð™xTc           @   sñ   d  d l  m Z d  d l Z d  d l Z d  d l Z d  d l m Z d  d l j	 j
 Z d  d l Z d  d l Z d  d l Z d  d l Z d  d l Z d Z d Z d Z d d d	 „ Z e d
 k rí e j ƒ  Z e ƒ  d e j ƒ  e GHd GHn  d S(   iÿÿÿÿ(   t   divisionN(   t   flexsÆ  CRYST1   26.628   30.419   28.493  90.00  90.00  90.00 P 1
ATOM      1  N   THR A   1      15.638  20.419  12.645  1.00 10.00           N
ATOM      2  CA  THR A   1      15.527  19.061  12.125  1.00 10.00           C
ATOM      3  C   THR A   1      15.602  18.033  13.249  1.00 10.00           C
ATOM      4  O   THR A   1      16.417  18.157  14.163  1.00 10.00           O
ATOM      5  CB  THR A   1      16.628  18.760  11.092  1.00 10.00           C
ATOM      6  OG1 THR A   1      16.528  19.682  10.000  1.00 10.00           O
ATOM      7  CG2 THR A   1      16.491  17.340  10.565  1.00 10.00           C
TER
ATOM      1  N   THR B   1      10.624  17.093  17.237  1.00 10.00           N
ATOM      2  CA  THR B   1      11.140  16.654  15.945  1.00 10.00           C
ATOM      3  C   THR B   1      12.494  15.968  16.097  1.00 10.00           C
ATOM      4  O   THR B   1      13.351  16.426  16.852  1.00 10.00           O
ATOM      5  CB  THR B   1      11.279  17.832  14.963  1.00 10.00           C
ATOM      6  OG1 THR B   1      10.000  18.446  14.765  1.00 10.00           O
ATOM      7  CG2 THR B   1      11.818  17.350  13.625  1.00 10.00           C
TER
ATOM      1  N   THR C   1      12.949  10.000  18.493  1.00 10.00           N
ATOM      2  CA  THR C   1      12.735  10.702  17.233  1.00 10.00           C
ATOM      3  C   THR C   1      13.937  11.570  16.875  1.00 10.00           C
ATOM      4  O   THR C   1      14.508  12.241  17.734  1.00 10.00           O
ATOM      5  CB  THR C   1      11.474  11.584  17.284  1.00 10.00           C
ATOM      6  OG1 THR C   1      10.328  10.770  17.559  1.00 10.00           O
ATOM      7  CG2 THR C   1      11.273  12.305  15.960  1.00 10.00           C
TER
END
s  CRYST1   26.628   30.419   28.493  90.00  90.00  90.00 P 1
ATOM      1  N   THR A   1      15.886  19.796  13.070  1.00 10.00           N
ATOM      2  CA  THR A   1      15.489  18.833  12.050  1.00 10.00           C
ATOM      3  C   THR A   1      15.086  17.502  12.676  1.00 10.00           C
ATOM      4  O   THR A   1      15.739  17.017  13.600  1.00 10.00           O
ATOM      5  CB  THR A   1      16.619  18.590  11.033  1.00 10.00           C
ATOM      6  OG1 THR A   1      16.963  19.824  10.392  1.00 10.00           O
ATOM      7  CG2 THR A   1      16.182  17.583   9.980  1.00 10.00           C
TER       8      THR A   1
ATOM      1  N   THR B   1      10.028  17.193  16.617  1.00 10.00           N
ATOM      2  CA  THR B   1      11.046  16.727  15.681  1.00 10.00           C
ATOM      3  C   THR B   1      12.336  16.360  16.407  1.00 10.00           C
ATOM      4  O   THR B   1      12.772  17.068  17.313  1.00 10.00           O
ATOM      5  CB  THR B   1      11.356  17.789  14.609  1.00 10.00           C
ATOM      6  OG1 THR B   1      10.163  18.098  13.879  1.00 10.00           O
ATOM      7  CG2 THR B   1      12.418  17.281  13.646  1.00 10.00           C
TER      16      THR B   1
ATOM      1  N   THR C   1      12.121   9.329  18.086  1.00 10.00           N
ATOM      2  CA  THR C   1      12.245  10.284  16.991  1.00 10.00           C
ATOM      3  C   THR C   1      13.707  10.622  16.718  1.00 10.00           C
ATOM      4  O   THR C   1      14.493  10.814  17.645  1.00 10.00           O
ATOM      5  CB  THR C   1      11.474  11.584  17.284  1.00 10.00           C
ATOM      6  OG1 THR C   1      10.087  11.287  17.482  1.00 10.00           O
ATOM      7  CG2 THR C   1      11.619  12.563  16.129  1.00 10.00           C
TER      24      THR C   1
END
s  CRYST1   26.628   30.419   28.493  90.00  90.00  90.00 P 1
ATOM      1  N   THR A   1      15.886  19.796  13.070  1.00 10.00           N
ATOM      2  CA  THR A   1      15.489  18.833  12.050  1.00 10.00           C
ATOM      3  C   THR A   1      15.086  17.502  12.676  1.00 10.00           C
ATOM      4  O   THR A   1      15.739  17.017  13.600  1.00 10.00           O
ATOM      5  CB  THR A   1      16.619  18.590  11.033  1.00 10.00           C
ATOM      6  OG1 THR A   1      16.963  19.824  10.392  1.00 10.00           O
ATOM      7  CG2 THR A   1      16.182  17.583   9.980  1.00 10.00           C
TER       8      THR A   1
t   tstg      ð?c   #      C   sr  d |  } t  | d ƒ } | t IJ| j ƒ  d |  } t  | d ƒ } | t IJ| j ƒ  t j j d | ƒ } | j ƒ  } | j ƒ  j	 ƒ  | j
 ƒ  } t j j d | ƒ } | j ƒ  }	 t j j j d t ƒ }
 |	 j ƒ  j	 ƒ  | j
 ƒ  } t j j d t ƒ j d t j ƒ  ƒ d } t j j d	 | j d
 t ƒ d | ƒ t j j d | j d t ƒ d t ƒ } | j d | ƒ j ƒ  } | j d d ƒ } | j ƒ  | j ƒ  } t j j d | d t ƒ } | j  d d d | j! ƒ  d d ƒ | j" } | j# } | d g } | d g } t j j d |
 d | d | ƒ } t$ j% d | ƒ } t$ j& d | d d t' j( d d  d! ƒ } t$ j) d | d | ƒ } t$ j* d | ƒ \ } } | | } | | } | | _" | | _# | j+ d" | j, j ƒ  j- ƒ  ƒ | j  d d# d | j! ƒ  d d ƒ t$ j. | | | ƒ } | j/ ƒ  } t0 j1 t2 | j3 ƒ ƒ } x#t2 d$ ƒ D]} d } xt t g t t g g D]ì } | \ } }  t j4 j5 j6 d% | d& | d' | d( | d) | d* d+ | d, | d- | d. |  ƒ 	}! t j4 j5 j7 d/ |! d& | d' | d( | d0 t d1 d2 d- | d. |  ƒ }" |! j } |	 j8 |! j ƒ t j j d |	 d t ƒ } t$ j* d' | ƒ \ } } qjWqEW|	 j  d d3 ƒ d4 S(5   s/   
  NCS constraints: xyz, adp, and operators.
  s   %s_answer.pdbt   ws   %s_poor.pdbt	   file_namet
   pdb_stringt   logt   raw_recordsi    t   x1t   show_summaryt   x2t   geometryt   show_energiest   normalizationt   d_mint   resolution_factorg      Ð?t   pdb_hierarchyt   add_identitys   asu.pdbt   crystal_symmetryt   modet   asut   pdb_hierarchy_inpt	   rotationst   translationst   transforms_objt   xt   shake_angles_sigmai   i´   t   shake_translation_sigmagš™™™™™¹?t   sites_cart_master_ncs_copys   asu2.pdbi   t   map_datat   xray_structuret   ncs_restraints_group_listt   refine_selectiont   real_space_gradients_deltai   t   restraints_managert   data_weightt   refine_sitest   refine_transformationst   target_and_grads_objectt   finite_grad_differences_testt   max_iterationsi<   s   refined.pdbN(9   t   opent   pdb_str_answert   closet   pdb_str_poort   iotbxt   pdbt   inputt   construct_hierarchyt   atomst   reset_i_seqt   xray_structure_simplet	   hierarchyt   pdb_str_poor2t   mmtbxt   utilst   process_pdb_file_srvt   Falset   process_pdb_filest
   splitlinest   assert_xray_structures_equalR   t
   restraintst   managert   geometry_restraints_managert   Truet   structure_factorst   f_calct   fft_mapt   apply_sigma_scalingt   real_map_unpaddedt   ncst   asu_ncs_convertert   write_pdb_fileR   t   back_rotation_matricest   back_translation_vectorst   nut   concatenate_rot_trant   shake_transformationst   matht   pit   update_rot_trant    get_rotation_translation_as_listt   update_sites_cartt   ph_first_chaint   extract_xyzt   update_transformst   get_ncs_restraints_group_listR   t   size_tt   xranget   total_asu_lengtht
   refinementt   minimization_ncs_constraintst$   target_function_and_grads_real_spacet   lbfgst   adopt_xray_structure(#   t   prefixR   t   pdb_file_name_answert   oft   pdb_file_name_poort   pdb_inp_answert	   ph_answert
   xrs_answert   pdb_inp_poort   ph_poort   ph_poor_objt   xrs_poort   ppfR"   t   fcRC   R   t   ncs_obj_poort   rmt   tvt   irt   itR   R   t   rm_t   tv_R   R    t   iR#   t   actionR$   R%   t   tfg_objt	   minimized(    (    sj   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/real_space/tst_minimization_ncs_constraints.pyt   runU   s²    





	
						

			

					t   __main__s   Time: %6.4ft   OK(   t
   __future__R    t   timet-   mmtbx.refinement.minimization_ncs_constraintsR6   t"   mmtbx.refinement.real_space.weightt   scitbx.array_familyR   t   mmtbx.ncs.ncs_utilsRF   t	   ncs_utilsRK   t   mmtbx.utilst	   iotbx.ncsR-   t	   iotbx.pdbt	   mmtbx.ncsRN   R*   R,   R5   Rw   t   __name__t   t0(    (    (    sj   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/real_space/tst_minimization_ncs_constraints.pyt   <module>   s&   y