ó
¥™xTc           @   s•   d  d l  m Z d  d l Z d  d l m Z d  d l m Z m Z d  d l Z	 d  d l
 m Z d „  Z e d d „ Z d „  Z d	 „  Z d
 „  Z d S(   iÿÿÿÿ(   t   divisionN(   t
   restraints(   t   servert   pdb_interpretation(   t   StringIOc           C   s   t  j j d d d t ƒ S(   Nt   input_strings  
  mp_geo {
    pdb = None
      .type = path
    out_file = None
      .type = path
    bonds_and_angles = False
      .type = bool
    kinemage = False
      .type = bool
    rna_backbone = False
      .type = bool
    outliers_only = False
      .type = bool
  }
  t   process_includes(   t   iotbxt   philt   parset   True(    (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/molprobity/mp_geo.pyt   get_master_phil	   s    c         C   s4   t  j d |  d | d | d t d | d | ƒ } | S(   Nt   pdb_hierarchyt   xray_structuret   geometry_restraints_managert	   ignore_hdt   outliers_onlyt   use_segids_in_place_of_chainids(   R   t   combinedR
   (   R   R   R   t
   use_segidsR   t   typet   rc(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/molprobity/mp_geo.pyt   get_bond_and_angle_outliers   s    		c         C   sw   d } d } t  |  ƒ d k r' d } n t  |  ƒ d k rB d } n  x% |  D] } | | j j ƒ  | } qI W| j d ƒ S(   Nt    i   s   --i   t   -(   t   lent   namet   strip(   t
   atoms_infot
   return_strt	   connectort	   atom_info(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/molprobity/mp_geo.pyt   get_atoms_str,   s    		c         C   sE   d } x8 |  D]0 } | d k r | j  d k r= | j  } q= q q W| S(   Nt    R   (   t   altloc(   R   R"   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/molprobity/mp_geo.pyt
   get_altloc9   s    c   !      C   s#  t  ƒ  } d d  l } | j j d |  d | d d) ƒ } | j d | d ƒ } | j ƒ  } | j j } d  } | j j	 d  k r‹ | j j	 } n  | j j
 } | j j }	 | j j }
 | j j } t ƒ  } t j j | ƒ } | rî t | d ƒ } nT |	 rt | d	 ƒ } n< |
 rB| d  k r0d d  l } | j } qBt | d ƒ } n  i  } t | d
 <d d l m } t j d t j ƒ  d t j ƒ  d | d t d | d t d t d | ƒ } | j ƒ  } | j d | j j ƒ } | sÚ|	 rÔt  d | j j d | j! ƒ  d | d | d | ƒ } i  } x¬ | j j j" ƒ  d j# ƒ  D]Ž } | rQ| j$ d | ƒ } n	 | j% } | j& ƒ  d } | j' | ƒ d* k r0| j( ƒ  r˜d | | <q¾| j) ƒ  r±d | | <q¾d | | <q0q0Wg  } xŒ | j* j+ D]~ } | j, d } t- d | j, ƒ } t. d | j, ƒ } | j/ } | j0 | | j1 | j2 | | j3 | | j4 | j5 | | j/ g	 ƒ qÕWxŒ | j6 j+ D]~ } | j, d } t- d | j, ƒ } t. d | j, ƒ } | j/ } | j0 | | j1 | j2 | | j3 | | j4 | j5 | | j/ g	 ƒ qdW| rPxØ | D]V } | d  | | d | d! | d" | d# | d$ | d% | d& | d' | d( f
 IJqóWnw |	 rÇ| | j* j7 IJx$ | j* j+ D] } | | j8 ƒ  IJqsW| | j6 j7 IJx' | j6 j+ D] } | | j8 ƒ  IJqªWn  | j9 ƒ  nK |
 rd d l m } | j: | ƒ }  | |  IJ| d  k	 r| j9 ƒ  qn  d  S(+   Niÿÿÿÿt   argst   master_philt   input_typest   pdbt   sourcesR   t   wt   at   use_neutron_distances(   t   utilst   mon_lib_srvt   ener_libt	   file_namet   strict_conflict_handlingt   restraints_loading_flagst   force_symmetryt6   substitute_non_crystallographic_unit_cell_if_necessaryt   logt	   hierarchyR   R   R   R   R   i    t   chaint   NAt   PROTEINt   UNKR   s"   %s:%2s:%s:%s:%s:%s:%s:%.3f:%.3f:%si   i   i   i   i   i   i   i   (   s   pdb(   R7   R8   (;   R   t   iotbx.utilsR,   t   process_command_line_inputst   fetcht   extractt   mp_geoR'   t   Nonet   out_filet   bonds_and_anglest   kinemaget   rna_backboneR   R   t   ost   patht   basenamet   filet   syst   stdoutt   Falset   mmtbx.validationR   t   processR   R.   R
   R   R   t   all_chain_proxiesR   R   R   t   modelst   chainst   get_segid_as_chainidt   idt
   conformerst   gett   is_nat
   is_proteint   bondst   resultsR   R    R#   t   chain_idt   appendt   resseqt   icodet   resnamet   modelt   scoret   anglest   kinemage_headert   as_kinemaget   closet   get_rna_backbone_dihedrals(!   R$   R%   R   t   input_objectst	   work_philt   work_paramsR/   R@   t   do_bonds_and_anglest   do_kinemaget   do_rna_backboneR   R4   RF   t   outRH   R1   R,   t   processed_pdb_filet   grmR   R   t   chain_typesR6   RX   t	   main_conft   outlierst   resultR   t	   atoms_strR"   t   outliert   rna_bb(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/molprobity/mp_geo.pyt   runA   sÜ    			
									1
(   t
   __future__R    RD   RK   R   t   mmtbx.monomer_libraryR   R   t
   iotbx.philR   t	   cStringIOR   R   RJ   R?   R   R    R#   Rt   (    (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/molprobity/mp_geo.pyt   <module>   s   	
		