ó
±™xTc           @   s³   d  d l  m Z d  d l Td  d l m Z d  d l Z d  d l Z d  d l m	 Z	 d  d l
 m Z d  d l Z d  d l Z e j e j d „ Z e d k r¯ e e j d	 ƒ n  d S(
   iÿÿÿÿ(   t   division(   t   *(   t   hbondN(   t   flex(   t   Sorryc      	   C   sU  g  } g  } t  } d t } t j j d |  d | d d ƒ } | j } | j ƒ  }	 |	 j j }
 |	 j	 rv t
 j ƒ  } n  t | ƒ d k rž |
 j j j | ƒ n  |
 j j } t | ƒ d k rË t d ƒ ‚ n  t j j d | ƒ } t j j d	 d  d
 t j | j ƒ ƒ } | j ƒ  } | j ƒ  j ƒ  t | j ƒ  ƒ d k rJt d ƒ ‚ n  t d | d | j ƒ  d |
 ƒ } | j d | ƒ d } |	 j d k r™d } n  d  } | j d t  ƒ } t  j! d | ƒ } |	 j d k rát d ƒ ‚ np|	 j d$ k rÏ| j" d | ƒ | j# d | d t$ ƒ } t | j% ƒ d k r0qQ|	 j d k rjt& j' d | j% d | d |	 j( d | ƒ qQ|	 j d k r¤t& j) d | j% d | d |	 j( d | ƒ qQt& j* d | j% d | d |	 j( d | ƒ n‚ | d IJ| d k rö| d  | IJn  |	 j+ r| j, d! d" d | ƒ n | j, d! d" d | ƒ | d k rG| d# IJn  | j- ƒ  Sd  S(%   Nsá   
show_all_params = False
  .type = bool
filter_outliers = True
  .type = bool
format = *phenix phenix_bonds pymol refmac kinemage
  .type = choice
quiet = False
  .type = bool
refinement {
  secondary_structure {
    %s
  }
}t   argst   master_phil_stringt   pdb_file_defs.   refinement.secondary_structure.input.file_namei    s   No PDB files specified.t
   file_namest   source_infot   linesi   s   Multiple models not supported.t   pdb_hierarchyt   sec_str_from_pdb_filet   paramst   logs   refinement.secondary_structuret   phenixt    t   master_philt   sourcet   phenix_bondss   Not yet implemented.t   pymolt   refmact   kinemaget   outt   as_python_objectst   proxiest   filters9   # These parameters are suitable for use in phenix.refine.s   %s {t   prefixs     t   }(   R   R   R   (.   t   Falset   sec_str_master_phil_strt   iotbxt   philt   process_command_line_with_filest   workt   extractt
   refinementt   secondary_structuret   quiett	   cStringIOt   StringIOt   lent   inputt	   file_namet   extendR   t   pdbt   combine_unique_pdb_filest   NoneR   t
   std_stringt   raw_recordst   construct_hierarchyt   atomst   reset_i_seqt   modelst   managert   extract_secondary_structuret   find_automaticallyt   formatt   as_phil_strt   sec_str_master_philt
   fetch_difft   show_summaryt   create_hbond_proxiest   TrueR   R   t   as_pymol_dashest   filter_outlierst   as_kinemaget   as_refmac_restraintst   show_all_paramst   showt   as_str(   R   R   R   t	   pdb_filest   sourcest   force_new_annotationt   master_phil_strt   pclt   working_philR   t	   ss_paramst   pdb_combinedt   pdb_structureR   t   mt   prefix_scopet   ss_philt	   phil_difft   build_proxies(    (    s_   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/secondary_structure_restraints.pyt   run   sŒ    
										
			
			

	t   __main__i   (   t
   __future__R    t   mmtbx.secondary_structuret   mmtbx.geometry_restraintsR   t	   iotbx.pdbR   t
   iotbx.philt   scitbx.array_familyR   t   libtbx.utilsR   R'   t   syst   stdoutt   stderrRU   t   __name__t   argv(    (    (    s_   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/secondary_structure_restraints.pyt   <module>   s   
Z