ó
Ñ™xTc           @   sm  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  d l m Z d Z d Z d Z d Z d	 d
 d „ Z e d k rie j ƒ  Z x• e e e e g ƒ D]~ \ Z Z xo e e g D]a Z xX e g D]M Z xD e e g D]6 Z e Ge Ge Ge GHe d e d e d e d e ƒ qWqú Wqê WqÑ Wd e j ƒ  e GHn  d S(   iÿÿÿÿ(   t   divisionN(   t   flex(   t   monomer_library(   t   RotamerEvalsû  CRYST1   14.074   16.834   17.360  90.00  90.00  90.00 P 1
ATOM      1  N   ARG A  21       8.318  11.834   9.960  1.00 10.00           N
ATOM      2  CA  ARG A  21       7.146  11.154   9.422  1.00 10.00           C
ATOM      3  C   ARG A  21       6.012  11.120  10.440  1.00 10.00           C
ATOM      4  O   ARG A  21       5.000  10.449  10.235  1.00 10.00           O
ATOM      5  CB  ARG A  21       7.505   9.732   8.987  1.00 10.00           C
ATOM      6  CG  ARG A  21       7.923   8.820  10.129  0.70 20.00           C
ATOM      7  CD  ARG A  21       8.312   7.441   9.621  0.70 20.00           C
ATOM      8  NE  ARG A  21       8.694   6.545  10.708  0.70 20.00           N
ATOM      9  CZ  ARG A  21       7.839   5.785  11.385  0.70 20.00           C
ATOM     10  NH1 ARG A  21       6.546   5.811  11.088  0.70 20.00           N
ATOM     11  NH2 ARG A  21       8.275   5.000  12.360  0.70 20.00           N
TER
HETATM    1  U   ION B   1       9.074   7.848   5.000  1.00 10.00           U
TER
END
sû  CRYST1   14.074   16.834   17.360  90.00  90.00  90.00 P 1
ATOM      1  N   ARG A  21       8.318  11.834   9.960  1.00 10.00           N
ATOM      2  CA  ARG A  21       7.248  10.924   9.570  1.00 10.00           C
ATOM      3  C   ARG A  21       6.012  11.120  10.440  1.00 10.00           C
ATOM      4  O   ARG A  21       5.064  10.337  10.375  1.00 10.00           O
ATOM      5  CB  ARG A  21       7.724   9.472   9.652  1.00 10.00           C
ATOM      6  CG  ARG A  21       8.797   9.112   8.637  1.00 10.00           C
ATOM      7  CD  ARG A  21       9.187   7.647   8.741  1.00 10.00           C
ATOM      8  NE  ARG A  21      10.266   7.301   7.820  1.00 10.00           N
ATOM      9  CZ  ARG A  21      10.871   6.118   7.790  1.00 10.00           C
ATOM     10  NH1 ARG A  21      10.505   5.162   8.634  1.00 10.00           N
ATOM     11  NH2 ARG A  21      11.844   5.891   6.920  1.00 10.00           N
TER
HETATM   12  U   ION B   1       9.074   7.848   5.000  1.00 10.00           U
TER
END
s)  CRYST1   14.074   16.834   17.360  90.00  90.00  90.00 P 1
ATOM      1  N   ARG A  21       8.318  11.834   9.960  1.00 10.00           N
ATOM      2  CA  ARG A  21       7.146  11.154   9.422  1.00 10.00           C
ATOM      3  C   ARG A  21       6.012  11.120  10.440  1.00 10.00           C
ATOM      4  O   ARG A  21       5.000  10.449  10.235  1.00 10.00           O
ATOM      5  CB  ARG A  21       7.505   9.732   8.987  1.00 10.00           C
ATOM      6  CG  ARG A  21       8.469   9.666   7.814  0.70 20.00           C
ATOM      7  CD  ARG A  21       8.724   8.229   7.388  0.70 20.00           C
ATOM      8  NE  ARG A  21       9.667   8.147   6.277  0.70 20.00           N
ATOM      9  CZ  ARG A  21       9.331   8.301   5.000  0.70 20.00           C
ATOM     10  NH1 ARG A  21       8.070   8.545   4.668  0.70 20.00           N
ATOM     11  NH2 ARG A  21      10.255   8.208   4.054  0.70 20.00           N
TER      12      ARG A  21
HETATM    1  U   ION B   1       9.074   7.848   5.000  1.00 10.00           U
TER      14      ION B   1
END
g      ð?gš™™™™™¹?c         C   s  t  j j d d  d t ƒ } | j d d ƒ | j ƒ  } | j d | ƒ j ƒ  } | j	 d | ƒ }	 |	 j
 ƒ  |	 j ƒ  }
 | j d d ƒ } | j ƒ  } | j d d	 ƒ t j j ƒ  } t j j d
 | d t j j ƒ  d t j | j ƒ  ƒ d t d t d d  ƒ } | j j } | j ƒ  } | j ƒ  } | j d d ƒ t ƒ  } t  j j } d  } x]| j ƒ  D]O} xF| j ƒ  D]8} x/| j  ƒ  j! ƒ  D]} | | j" ƒ d k r‡t# j# ƒ  } t$ j% j& j' d | d d d | j( ƒ  j) ƒ  ƒ } t$ j% j& j* d | d |
 d | d d ƒ } d t# j# ƒ  | GHt$ j% j& j+ j, d | d
 | d | j- ƒ  d | d | d |  d  | d! | ƒ | j. | j( ƒ  j) ƒ  | j( ƒ  j/ ƒ  ƒ d" t# j# ƒ  | GHq‡q‡WqnWq[W| j0 | ƒ } | j1 | ƒ | j d d# ƒ | j2 d$ | ƒ } | d% k  st3 | ƒ ‚ d  S(&   Nt   source_infot   linest	   file_names
   answer.pdbt   d_mint   resolution_factort   column_root_labelt   FCmaps
   answer.mtzt   mon_lib_srvt   ener_libt   raw_recordst   strict_conflict_handlingt   force_symmetryt   logs   poor.pdbt   common_amino_acidt   xray_structuret   selection_within_radiusi   t
   iselectiont   map_datat   negate_selectiont   atom_radiusi   s     time (negate map): %6.4ft
   target_mapt   special_position_settingst   residuet   rotamer_managert	   use_slopet   use_torsion_searcht   use_rotamer_iterators     time (refine): %6.4fs   refined.pdbt   othergyé&1¬l?(4   t   iotbxt   pdbt   inputt   Nonet
   pdb_answert   write_pdb_filet   xray_structure_simplet   structure_factorst   f_calct   fft_mapt   apply_sigma_scalingt   real_map_unpaddedt   as_mtz_datasett
   mtz_objectt   writeR   t   servert   pdb_interpretationt   processR   R   t
   std_stringt
   splitlinest   Truet   all_chain_proxiest   pdb_hierarchyR   t
   sites_cartR   t   common_residue_names_get_classt   modelst   chainst   only_conformert   residuest   resnamet   timet   mmtbxt
   refinementt
   real_spacet   selection_around_to_negatet   atomst   extract_i_seqt6   negate_map_around_selected_atoms_except_selected_atomst   fit_residuet   managerR   t   set_selectedt   extract_xyzt   replace_sites_cartt   adopt_xray_structuret   max_distancet   AssertionError(   R   R   R   t   pdb_poor_strR   R   t   pdb_inpt
   xrs_answerR(   R)   R   t   mtz_datasetR-   R   t   processed_pdb_filet   pdb_hierarchy_poort   xrs_poort   sites_cart_poorR   t	   get_classt   residue_poort   modelt   chainR   t   t0R   t   target_map_t   dist(    (    s[   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/real_space/tst_fit_residue_1.pyt   exerciseW   sr    
			"t   __main__RN   R   R   R   s   Time: %6.4f(   t
   __future__R    t(   mmtbx.monomer_library.pdb_interpretationR?   t	   iotbx.mtzR    t   cctbx.array_familyR   R>   R   t'   mmtbx.refinement.real_space.fit_residuet	   iotbx.pdbt   mmtbx.rotamer.rotamer_evalR   R$   t	   pdb_poor1t	   pdb_poor2t	   pdb_poor3R]   t   __name__RZ   t	   enumeratet   i_pdbRN   R4   t   FalseR   R   R   (    (    (    s[   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/real_space/tst_fit_residue_1.pyt   <module>   s4   D"