ó
Ù™xTc           @   s…   d  d l  m Z d  d l Z d  d l m Z m Z d e f d „  ƒ  YZ d „  Z d d d d d „ Z
 d d	 d
 d g d d „ Z d S(   iÿÿÿÿ(   t   divisionN(   t   veclent	   vectorizet   linked_residuec           B   s˜   e  Z e j d  „ Z e e j d „ Z d d „ Z d „  Z d „  Z	 d „  Z
 d „  Z d „  Z d	 „  Z d
 „  Z d d d d d d d d g d „ Z RS(   c         C   s„   d |  j  d |  j ƒ  d g } xA | D]9 } y | j t |  j | ƒ ƒ Wq) t k
 ra d  SXq) W| j d j | ƒ d ƒ d  S(   Nt   {t    t   }s   
(   t   pdbidt   id_with_resnamet   appendt   strt   measurest   KeyErrort   writet   join(   t   selft   kinordert   writetot   outlinet   order(    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt
   printtokin3   s    "	c         C   sä   |  j  ƒ  g } xM | D]E } y | j t |  j | ƒ ƒ Wq t k
 rZ | j d ƒ q Xq W| rÆ |  j r‡ | j |  j j  ƒ  ƒ n | j d ƒ |  j r¶ | j |  j j  ƒ  ƒ qÆ | j d ƒ n  | j d j | ƒ d ƒ d  S(   Nt   NULLt   ,s   
(	   R   R	   R
   R   R   t   prevrest   nextresR   R   (   R   R   t   doconnectionsR   R   R   (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt
   printtocsv=   s    	 	 R   c         C   s7   | j  |  j |  j |  j t |  j ƒ |  j g ƒ } | S(   N(   R   R   t   modelt   chainR
   t   resnumt   icode(   R   t   sept   resid_string(    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt	   id_to_strM   s    -c         C   s!   |  j  j ƒ  d j ƒ  d } | S(   Ni    i   (   t   rgt   atomst   pdb_label_columns(   R   R    (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyR   R   s    c         C   sŠ   |  j  ƒ  } | d d !} | d d !} | d d !} | d d !} |  j d ƒ } | d  k sg | d k rp d } n  | | | | | } | S(	   Ni    i   i   i	   i
   t   CAt    R   (   R   t   firstaltt   None(   R   R    t   resnameR   R   t   inst   altt   mpid_string(    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt   mp_idW   s    
	c         C   s4   |  j  r d  |  j  _ n  |  j r0 d  |  j _  n  d  S(   N(   R   R(   R   (   R   (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt   removelinksp   s    		c         C   sO   xH |  j  D]9 } y |  j | | r( | Sw
 Wq
 t k
 rB q
 q
 Xq
 Wd  Sd  S(   N(   t   altst   atomxyzR   R(   (   R   t   atomnameR+   (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyR'   y   s    c         C   s;   |  j  | ƒ } y |  j | | SWn t k
 r6 d  SXd  S(   N(   R'   R0   R   R(   (   R   R1   R'   (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt
   getatomxyz†   s
    c         C   s�   | r… | r… y8 | j  | j d ƒ d } | j  | j d ƒ d } Wn t k
 rX t SXt t | | ƒ ƒ } | d k r~ t St Sn t Sd  S(   Nt   Ct   Ng       @(   R0   R'   R   t   FalseR   R   t   True(   R   t   res1t   res2R3   R4   t   bondlen(    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt   consecutiveŽ   s    c         C   sÞ   |  | k r d S|  j  | j  k r& d  S|  j | j k r€ d } |  } x9 | d  k r| | d 7} | j | k rp | S| j } qG Wn  |  j | j k rÚ d } |  } x9 | d  k rÖ | d 8} | j | k rÊ | S| j } q¡ Wn  d  S(   Ni    i   (   R   R(   R   R   R   (   R   t   otherrest   deltat   cur(    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt   seq_dist¥   s*    
 
 R   R&   R%   t   OR3   R4   c   
      C   s
  | |  _  | |  _ | |  _ | |  _ t | j j ƒ  ƒ |  _ | j |  _ t	 |  j |  j |  j |  j ƒ |  _
 t |  _ i  |  _ i  |  _ i  |  _ xð | j ƒ  D]â } i | j d 6| j d 6|  j | j <i  |  j | j <i  |  j | j <x• | j ƒ  D]‡ } | j r$| j j ƒ  d k r$t |  _ n  xT | D]L }	 | j j ƒ  |	 k r+| j |  j | j |	 <| j |  j | j |	 <q+q+Wqô Wq� W| r°|  j | |  ƒ r°| |  _ |  | _ n	 d  |  _ d  |  _ i i  d 6i  d 6|  _ g  |  _ g  |  _ i  |  _  i  |  _! i  |  _" d  S(   NR+   R)   t   MSER?   t   H(#   R"   R   R   R   t   intt   resseqt   stripR   R   t
   cablam_keyt   residR5   t   heteroR/   R0   t   atombt   atom_groupst   altlocR)   R#   t   upperR6   t   namet   xyzt   bR:   R   R   R(   t   probet   probeHt   probeOR   t   motifst   results(
   R   R"   R   R   t   modelidt   chainidt   targetatomst   agt   atomt
   targetatom(    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt   __init__Ã   sB    				$				$&							N(   t   __name__t
   __module__t   syst   stdoutR   R5   R   R!   R   R-   R.   R'   R2   R:   R>   R(   RZ   (    (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyR   0   s   
								c         C   s{   |  j  ƒ  } xh | D]` } xW |  | j D]H } |  | j | d j ƒ  | k r' |  | j ƒ  |  j | ƒ } Pq' q' Wq Wd  S(   NR)   (   t   keysR/   RD   R.   t   pop(   t   resdatat   restypet   reslistt   residueR+   t   trash(    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt   prunerestype  s    !c         C   sY   d  |  | | | g k r; d j |  | d | | g ƒ } | St j j d ƒ t j ƒ  d  S(   NR   s   %04isx   
Missing value for cablam_res.cablam_key(pdbid, modelid, chainid, resnum, icode)
Please pass complete information
      (   R(   R   R]   t   stderrR   t   exit(   RT   RU   R   R   R    (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyRE     s    	R%   R?   R3   R4   R   c   
      C   sÂ   i  } xµ |  j  ƒ  D]§ } xž | j ƒ  D]� } d  } x� | j ƒ  D]s } t | d | d | d | j d | j d | ƒ} t | j | j | j | j ƒ }	 | j	 s? | | |	 <| } q? q? Wq& Wq W| S(   NR   R   RT   RU   RV   (
   t   modelst   chainsR(   t   residue_groupsR   t   idRE   R   R   RG   (
   t	   hierarchyRV   R   t   proteinR   R   R   R"   Rd   R    (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt   construct_linked_residues4  s    $	!	
(   t
   __future__R    R]   t   mmtbx.cablam.cablam_mathR   R   t   objectR   Rf   R(   RE   Ro   (    (    (    sE   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/cablam/cablam_res.pyt   <module>   s   Ø	