ó
±xTc           @   s}   d  d l  m Z d  d l m Z d  d l Z d  d l Z d   Z d Z e j	 e
 d  Z e d k ry e e j d  n  d S(	   i’’’’(   t   division(   t   rna_validationNc           C   s   t  j j d d d t  S(   Nt   input_strings½  
  model = None
      .type = path
      .help = "Model file (PDB or mmCIF)"

  outliers_only = True
    .type = bool
    .help = "Only display outliers"

  verbose = True
    .type = bool
    .help = '''Verbose'''
  rna_sugar_pucker_analysis
    .short_caption = RNA sugar pucker analysis
    .style = box noauto auto_align menu_item parent_submenu:advanced
  {
    include scope mmtbx.monomer_library.rna_sugar_pucker_analysis.master_phil
  }
t   process_includes(   t   iotbxt   philt   parset   True(    (    (    sM   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/rna_validate.pyt   get_master_phil   s    sź   
phenix.rna_validate file.pdb [params.eff] [options ...]

Options:

  pdb=input_file        input PDB file
  outliers_only=False   print all suites, not just outliers

Example:

  phenix.rna_validate pdb=1u8d.pdb outliers_only=False

c      	   C   s0  d d l  m } d d l  m } d d  l } | j j d |  d t   d d d t  } | j j	   } | j
 d  k r t t   n  | j j d	 | j
 d
 | j
  } | j   }	 | j   }
 | j d |	 d |
 d | d t  } | j j } | j   } t d | d | d | d | j  } | j d |  | S(   Ni’’’’(   t   pdb_interpretation(   t   servert   argst   master_philt   pdb_file_deft   modelt   usage_stringt   source_infot	   file_namet   mon_lib_srvt   ener_libt   pdb_inpt6   substitute_non_crystallographic_unit_cell_if_necessaryt   pdb_hierarchyt   geometry_restraints_managert   paramst   outliers_onlyt   out(   t   mmtbx.monomer_libraryR	   R
   t	   iotbx.pdbR   t   process_command_line_with_filesR   R   t   workt   extractR   t   Nonet   Usaget   pdbt   inputR   t   processR   t   all_chain_proxiesR   R   R   R   t   show(   R   R   t   quietR	   R
   R   t   cmdlineR   t   pdb_inR   R   t   processed_pdb_fileR   t   geometryt   result(    (    sM   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/rna_validate.pyt   run+   s8    		!		t   __main__i   (   t
   __future__R    t   mmtbx.validation.rna_validateR   t
   iotbx.philR   t   sysR   R   t   stdoutt   FalseR-   t   __name__t   argv(    (    (    sM   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/rna_validate.pyt   <module>   s   	!