ó
ħxTc           @   s   d  d l  m Z d  d l Z d  d l Z d  d l m Z d  d l Z d   Z	 d Z
 e j d d  Z e d k r e e j d  n  d S(	   i˙˙˙˙(   t   divisionN(   t   Usagec           C   s   t  j j d  S(   Ns  
model = None
  .type = path

verbose = True
  .type = bool

keep_hydrogens = True
  .type = bool
  .help = '''Keep hydrogens in input file'''

nuclear = False
  .type = bool
  .help = '''Use nuclear hydrogen positions'''

time_limit = 120
  .type = int
  .help = '''Time limit (sec) for Reduce optimization'''

b_factor_cutoff = None
  .type = int
  .help = '''B factor cutoff for use with MolProbity'''
(   t   iotbxt   philt   parse(    (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/clashscore.pyt   get_master_phil	   s    	s  phenix.clashscore file.pdb [params.eff] [options ...]

Options:

  model=input_file      input PDB file
  keep_hydrogens=True   keep input hydrogen files (otherwise regenerate)
  nuclear=False         use nuclear x-H distances and vdW radii
  verbose=True          verbose text output
  b_factor_cutoff=40    B factor cutoff for clash analysis

Example:

  phenix.clashscore model=1ubq.pdb keep_hydrogens=True

c         C   sä   t  j j d |  d t   d d d t  } | j j   } | j d  k rW t	 t   n  | j
 | j d d } | j j } t j j j d | d	 | j d
 | j d | d | j oµ | d | j  } | j rà | j d |  n  d  S(   Nt   argst   master_philt   pdb_file_deft   modelt   usage_stringt
   force_typet   pdbt   pdb_hierarchyt   keep_hydrogenst   nucleart   outt   verboset   b_factor_cutoff(   R   R   t   process_command_line_with_filesR   R
   t   workt   extractR	   t   NoneR   t   get_filet   file_objectt	   hierarchyt   mmtbxt
   validationt
   clashscoreR   R   R   R   t   show_old_output(   R   R   t   quiett   cmdlinet   paramst   pdb_inR   t   result(    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/clashscore.pyt   run3   s&    					t   __main__i   (   t
   __future__R    t   mmtbx.validation.clashscoreR   t
   iotbx.philR   t   libtbx.utilsR   t   sysR   R
   t   stdoutR   R#   t   __name__t   argv(    (    (    sK   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/clashscore.pyt   <module>   s   	(