ó
ąxTc           @   s_   d  d l  m Z d  d l m Z d  d l Z e j d  Z e d k r[ e e j d  n  d S(   i˙˙˙˙(   t   division(   t   SorryNc   
      C   s  d d l  m } d d  l } | j j d d d t  } d } | j j d |  d | d	 | d
 t d t d |  } | j } | j	   j
   s t d   n  | j } | j }	 | j d | d | d |	 j d |	 j d |	 j d |	 j d |	 j d |	 j d |	 j d |	 j d	 |  S(   Ni˙˙˙˙(   t   anomalous_scatterer_groupst   phil_stringsZ  
map_type = *anom_residual llg
  .type = choice
exclude_waters = False
  .type = bool
exclude_non_water_light_elements = True
  .type = bool
n_cycles_max=None
  .type = int
map_sigma_min = 3.0
  .type = float
wavelength = None
  .type = float
refine = *f_prime *f_double_prime
  .type = choice(multi=True)
reset_water_u_iso = True
  .type = bool
t   enable_automatic_twin_detections#  mmtbx.refine_anomalous_substructure model.pdb data.mtz [options]

Iterative identification of anomalously scattering atoms in the anomalous
residual map (simple or Phaser LLG), followed by refinement of the anomalous
scattering coefficients.  Intended as a diagnostic/development tool only!
t   argst   master_philt   outt   process_pdb_filet   prefer_anomaloust   usage_strings   Anomalous data required.t   fmodelt   pdb_hierarchyt
   wavelengtht   map_typet   exclude_waterst    exclude_non_water_light_elementst   n_cycles_maxt   map_sigma_mint   refinet   reset_water_u_iso(   t   mmtbx.refinementR   t   mmtbx.command_linet   command_linet    generate_master_phil_with_inputst   Truet   load_model_and_datat   FalseR   t   f_obst   anomalous_flagR   R   t   paramst   refine_anomalous_substructureR   R   R   R   R   R   R   R   (
   R   R   R   t   mmtbxR   R
   t   cmdlineR   R   R   (    (    s^   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/refine_anomalous_substructure.pyt   run   s<    														t   __main__i   (	   t
   __future__R    t   libtbx.utilsR   t   syst   stdoutR"   t   __name__t   argv(    (    (    s^   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/refine_anomalous_substructure.pyt   <module>   s
   7