ó
Ð™xTc           @   sÚ   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 d	 d
 „ Z e d k rÖ e d e ƒ \ Z Z e Ge GHe d k  sÖ t ‚ n  d S(   iÿÿÿÿ(   t   divisionN(   t   flex(   t   monomer_library(   t   RotamerEvals«  CRYST1   14.230   10.991   17.547  90.00  90.00  90.00 P 1
ATOM     43  N   GLY A   8       3.000   7.369   9.591  1.00  6.97           N
ATOM     44  CA  GLY A   8       4.304   7.980   9.410  1.00  7.38           C
ATOM     45  C   GLY A   8       5.375   6.966   9.058  1.00  6.50           C
ATOM     46  O   GLY A   8       5.074   5.814   8.745  1.00  6.23           O
ATOM     47  N   TYR A   9       6.631   7.398   9.110  1.00  6.94           N
ATOM     48  CA  TYR A   9       7.755   6.524   8.796  1.00  7.32           C
ATOM     49  C   TYR A   9       8.787   6.527   9.918  1.00  8.00           C
ATOM     50  O   TYR A   9       9.205   7.585  10.387  1.00  9.95           O
ATOM     51  CB  TYR A   9       8.410   6.945   7.478  1.00  8.02           C
ATOM     52  CG  TYR A   9       7.484   6.880   6.284  1.00  8.02           C
ATOM     53  CD1 TYR A   9       7.345   5.709   5.552  1.00  8.16           C
ATOM     54  CD2 TYR A   9       6.750   7.991   5.889  1.00  8.88           C
ATOM     55  CE1 TYR A   9       6.500   5.645   4.459  1.00  8.74           C
ATOM     56  CE2 TYR A   9       5.903   7.937   4.798  1.00  9.46           C
ATOM     57  CZ  TYR A   9       5.782   6.761   4.087  1.00  9.31           C
ATOM     58  OH  TYR A   9       4.940   6.702   3.000  1.00 11.26           O
ATOM     59  N   ASN A  10       9.193   5.336  10.345  1.00  7.07           N
ATOM     60  CA  ASN A  10      10.177   5.199  11.413  1.00  6.83           C
ATOM     61  C   ASN A  10      11.230   4.143  11.093  1.00  6.42           C
ATOM     62  O   ASN A  10      10.900   3.000  10.778  1.00  6.41           O
ATOM     63  CB  ASN A  10       9.486   4.870  12.738  1.00  7.59           C
ATOM     64  CG  ASN A  10      10.465   4.730  13.887  1.00  8.66           C
ATOM     65  OD1 ASN A  10      10.947   3.635  14.178  1.00  8.74           O
ATOM     66  ND2 ASN A  10      10.766   5.843  14.547  1.00 11.51           N
TER
END
sÂ  CRYST1   14.230   10.991   17.547  90.00  90.00  90.00 P 1
ATOM     43  N   GLY A   8       3.000   7.369   9.591  1.00  6.97           N
ATOM     44  CA  GLY A   8       4.304   7.980   9.410  1.00  7.38           C
ATOM     45  C   GLY A   8       5.375   6.966   9.058  1.00  6.50           C
ATOM     46  O   GLY A   8       5.074   5.814   8.745  1.00  6.23           O
ATOM     47  N   TYR A   9      10.261   7.310   2.887  1.00  6.94           N
ATOM     48  CA  TYR A   9      10.362   7.269   4.341  1.00  7.32           C
ATOM     49  C   TYR A   9      11.382   6.231   4.795  1.00  8.00           C
ATOM     50  O   TYR A   9      11.354   5.084   4.350  1.00  9.95           O
ATOM     51  CB  TYR A   9       8.996   6.971   4.965  1.00  8.02           C
ATOM     52  CG  TYR A   9       9.029   6.816   6.469  1.00  8.02           C
ATOM     53  CD1 TYR A   9       9.116   7.925   7.299  1.00  8.16           C
ATOM     54  CD2 TYR A   9       8.973   5.559   7.058  1.00  8.88           C
ATOM     55  CE1 TYR A   9       9.148   7.788   8.675  1.00  8.74           C
ATOM     56  CE2 TYR A   9       9.004   5.412   8.432  1.00  9.46           C
ATOM     57  CZ  TYR A   9       9.091   6.530   9.235  1.00  9.31           C
ATOM     58  OH  TYR A   9       9.122   6.388  10.604  1.00 11.26           O
ATOM     59  N   ASN A  10       9.193   5.336  10.345  1.00  7.07           N
ATOM     60  CA  ASN A  10      10.177   5.199  11.413  1.00  6.83           C
ATOM     61  C   ASN A  10      11.230   4.143  11.093  1.00  6.42           C
ATOM     62  O   ASN A  10      10.900   3.000  10.778  1.00  6.41           O
ATOM     63  CB  ASN A  10       9.486   4.870  12.738  1.00  7.59           C
ATOM     64  CG  ASN A  10      10.465   4.730  13.887  1.00  8.66           C
ATOM     65  OD1 ASN A  10      10.947   3.635  14.178  1.00  8.74           O
ATOM     66  ND2 ASN A  10      10.766   5.843  14.547  1.00 11.51           N
TER      25      ASN A  10
END
g      ð?g      Ð?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 ƒ  j ƒ  ƒ d
 j ƒ  j ƒ  }
 t j j ƒ  } t  j j d t j j j d t ƒ j ƒ  } d | _ t j j d | 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 j' j( d | j) d t* ƒ d t ƒ } t+ ƒ  } t  j j, } xæ | j- ƒ  D]Ø } xÏ | j. ƒ  D]Á } x¸ | j/ ƒ  j0 ƒ  D]¤ } | | j1 ƒ d k r	t2 | j3 ƒ d k r	t4 j4 ƒ  } t j5 j6 j7 j8 d | d | d | d | d | d | d  d! | ƒ } | j ƒ  j ƒ  } t4 j4 ƒ  | } q	q	WqðWqÝW| j9 | j% ƒ | j d d" ƒ t  j: t  j; |
 | j< ƒ  ƒ ƒ } | | f S(#   Nt   source_infot   linest	   file_names
   answer.pdbt   d_mint   resolution_factort   column_root_labelt   FCmaps
   answer.mtzi   t   input_stringt   process_includesiç  t   mon_lib_srvt   paramst   ener_libt   raw_recordst   strict_conflict_handlingt   force_symmetryt   logs   poor.pdbt   geometryt   show_energiest   normalizationt   common_amino_acidi	   t
   target_mapt   residuet   xray_structuret   rotamer_managert   real_space_gradients_deltai   t   geometry_restraints_managers   refined.pdb(=   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   writet   listt   construct_hierarchyt   residue_groupst   atomst   extract_xyzR   t   servert   philt   parset   mmtbxt   pdb_interpretationt   master_params_strt   Truet   extractt   link_distance_cutofft   processR   R   t
   std_stringt
   splitlinest   all_chain_proxiest   pdb_hierarchyR   t
   sites_cartt
   restraintst   managerR   t   FalseR   t   common_residue_names_get_classt   modelst   chainst   only_conformert   residuest   resnamet   intt   resseqt   timet
   refinementt
   real_spacet   fit_residuet   runt   adopt_xray_structuret   meant   sqrtt   dot(   t   pdb_poor_strR   R   t   pdb_inpt
   xrs_answerR&   R'   R   t   mtz_datasetR+   t   sites_answerR   t   master_paramst   processed_pdb_filet   pdb_hierarchy_poort   xrs_poort   sites_cart_poort   grmR   t	   get_classt   modelt   chainR   t   t0t   rot   sites_finalt   t1t   dist(    (    s[   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/real_space/tst_fit_residue_5.pyt   exerciseG   sl    
%				
	"t   __main__RU   g      À?(   t
   __future__R    t(   mmtbx.monomer_library.pdb_interpretationR5   t	   iotbx.mtzR   t   cctbx.array_familyR   RL   R   t'   mmtbx.refinement.real_space.fit_residuet	   iotbx.pdbt   mmtbx.rotamer.rotamer_evalR   R"   t   pdb_poorRh   t   __name__Rg   t   tt   AssertionError(    (    (    s[   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/real_space/tst_fit_residue_5.pyt   <module>   s   >	