ó
£™xTc           @   s½  d  Z  d d l m Z d d l m Z m Z m Z d d l m Z d d l	 m
 Z
 d d l m Z d d l Z d d	 d
 d d g Z d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d  „  ƒ  YZ d! e f d" „  ƒ  YZ d# e f d$ „  ƒ  YZ d% „  Z d e d& „ Z d' e
 f d( „  ƒ  YZ d S()   s³   
Validation of models of any type against basic covalent geometry restraints.
By default this will flag all restrained atoms deviating by more than 4 sigma
from the target value.
iÿÿÿÿ(   t   division(   t   atomst
   validationt   get_atoms_info(   t   make_sub_header(   t   slots_getstate_setstate(   t   sqrtNt   sigmat   targett   modelt   deltat   residualt	   restraintc           B   so   e  Z d	 Z e j e Z d  „  Z e d „  ƒ Z	 d „  Z
 d	 d „ Z d d „ Z d „  Z d „  Z d „  Z RS(
   c         K   so   t  j |  | � |  j d  k	 r@ t |  j ƒ |  j k s@ t ‚ n  |  j d  k rk t |  j	 |  j
 ƒ |  _ n  d  S(   N(   R   t   __init__t   n_atomst   Nonet   lent
   atoms_infot   AssertionErrort   scoret   absR
   R   (   t   selft   kwds(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR   !   s
    !c           C   s   d d	 S(
   Ns$   %-20s  %7s  %7s  %7s  %6s  %6s  %10sR   t   idealR	   R
   R   R   t	   deviation(   s   atomss   ideals   models   deltas   sigmas   residuals	   deviation(    (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   header(   s    c         C   sD   d j  g  |  j D] } | j ƒ  ^ q ƒ } | |  j |  j |  j g S(   s7   
    Values for populating ListCtrl in Phenix GUI.
    s   , (   t   joinR   t   id_strR   R	   R   (   R   t   at	   atoms_str(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   as_table_row_phenix-   s    +c         C   s)   d j  g  |  j D] } | j ƒ  ^ q ƒ S(   Nt   ,(   R   R   R   (   R   t   ignore_altlocR   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR   4   s    t    c         C   sœ   g  |  j  D] } | j ƒ  ^ q
 } t g  | D] } t | ƒ ^ q, ƒ } g  } x% | D] } | j d | | f ƒ qT W| d c d |  j ƒ  7<d j | ƒ S(   Ns   %s%-20siÿÿÿÿs     s   
(   R   R   t   maxR   t   appendt   format_valuesR   (   R   t   prefixR   t   id_strst   st   id_lent   linest   atom_str(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt	   as_string7   s    "%c         C   s,   d |  j  |  j |  j |  j |  j |  j f S(   Ns.   %7.2f  %7.2f  %7.2f  %6.2e  %6.2e  %4.1f*sigma(   R   R	   R
   R   R   R   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR$   @   s    	c         C   s   t  | j |  j ƒ S(   N(   t   cmpR   (   R   t   other(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   __cmp__D   s    c         C   sy   |  j  d } g  |  j  D] } | j j ƒ  j ƒ  ^ q } d |  j ƒ  | j j ƒ  | j | j | j d j	 | ƒ f } | S(   Ni    s   %1s%3s%2s%4s%1s %st   -(
   R   t   namet   stript   lowert
   get_altloct   resnamet   chain_idt   resseqt   icodeR   (   R   t   atom0R   t
   atom_namest   kin_key(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   kinemage_keyG   s    +N(   t   __name__t
   __module__R   R   R   t	   __slots__t   __restraint_attr__R   t   staticmethodR   R   R   R+   R$   R.   R;   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR      s   					t   bondc           B   sQ   e  Z d  Z d d g Z e j e Z d „  Z e d „  ƒ Z d „  Z	 d „  Z
 RS(   i   t   slackt   symopc         C   s6   |  j  d j ƒ  |  j  d j ƒ  |  j |  j |  j g S(   Ni    i   (   R   R   R   R	   R   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR   V   s     c        	   C   s   d d
 S(   Ns)   %-20s  %5s  %6s  %6s  %6s  %6s  %8s  %10sR   R   R	   R
   R   RB   R   R   (   s   atomss   ideals   models   deltas   sigmas   slacks   residuals	   deviation(    (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR   Z   s    c      	   C   s8   d |  j  |  j |  j |  j |  j |  j t |  j ƒ f S(   Ns5   %5.3f  %6.2f  %6.3f  %6.3f  %6.2e  %8.2e  %4.1f*sigma(   R   R	   R
   R   RB   R   R   R   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   formate_values_   s    c         C   s   d d l  m } | |  ƒ S(   Niÿÿÿÿ(   t   bond_outlier_as_kinemage(   t   mmtbx.kinemage.validationRE   (   R   RE   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   as_kinemaged   s    (   R<   R=   R   t   __bond_attr__R   R>   R   R@   R   RD   RG   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRA   O   s   			t   anglec           B   s   e  Z d  Z d „  Z RS(   i   c         C   s   d d l  m } | |  ƒ S(   Niÿÿÿÿ(   t   angle_outlier_as_kinemage(   RF   RJ   (   R   RJ   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRG   j   s    (   R<   R=   R   RG   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRI   h   s   t   dihedralc           B   s   e  Z d  Z d „  Z RS(   i   c         C   s   d  S(   N(   R   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRG   p   s    (   R<   R=   R   RG   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRK   n   s   t	   chiralityc           B   s   e  Z d  „  Z RS(   c         C   s   d  S(   N(   R   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRG   t   s    (   R<   R=   RG   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRL   s   s   t	   planarityc           B   sH   e  Z e j d  d d g Z d „  Z e d „  ƒ Z d „  Z d „  Z RS(   t
   rms_deltast	   delta_maxR   c         C   sD   d j  g  |  j D] } | j ƒ  ^ q ƒ } | |  j |  j |  j g S(   Ns   , (   R   R   R   RO   RN   R   (   R   R   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR   }   s    +c           C   s   d d S(   Ns   %-20s  %10s  %10s  %10s  %10sR   RN   RO   R   R   (   s   atomss
   rms_deltass	   delta_maxs   residuals	   deviation(    (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR   �   s    c         C   s    d |  j  |  j |  j |  j f S(   Ns#   %10.3f  %10.3f  %10.2f  %4.1f*sigma(   RN   RO   R   R   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR$   †   s    	c         C   s   d  S(   N(   R   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRG   Š   s    (	   R<   R=   R   R>   R   R@   R   R$   RG   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRM   w   s   
		t   restraint_validationc           B   sÒ   e  Z d  Z d Z d Z d d d d g Z d d d d g Z d d	 d	 d
 g Z d d d d d d d g Z	 e
 j e	 Z e d e e d „ Z d „  Z d „  Z e j d e d „ Z e j d d „ Z d d „ Z RS(   s‹   
  Base class for collecting information about all restraints of a certain
  type, including overall statistics and individual outliers.
  t   Atomss   Ideal values   Model values   Deviation (sigmas)s   %ss   %.3fs   %.1fiô  id   i´   t   minR"   t   meant   z_mint   z_maxt   z_meanR   g      @c
         C   sP  t  j |  ƒ d  |  _ |  _ |  _ t | d |  j ƒ }
 |
 ƒ  \ |  _ |  _	 |  _
 t | d |  j ƒ } t | d |  j ƒ |  _ |  j d k r¦ | |  j |  _ n	 d |  _ t | d |  j d  ƒ } | d  k	 rû | ƒ  } | ƒ  \ |  _ |  _ |  _ n  t |  j d | d | d | d	 | d
 | d | d |	 ƒ ƒ |  _ t |  j ƒ |  _ d  S(   Ns   %s_deviationss   %s_residual_sums   n_%s_proxiesi    s   %s_deviations_zt   proxiest	   unit_cellt
   sites_cartt	   pdb_atomst   sigma_cutofft   outliers_onlyt   use_segids_in_place_of_chainids(   R   R   R   RT   RU   RV   t   getattrt   restraint_typeRR   R"   RS   t   n_totalR   t   sortedt   get_outlierst   resultsR   t
   n_outliers(   R   RZ   RY   t   energies_sitest   restraint_proxiesRX   t	   ignore_hdR[   R\   R]   t   deviations_methodR   t   deviations_z_methodt   deviations_z(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR   ¡   s4    
						c         C   s   t  ƒ  ‚ d  S(   N(   t   NotImplementedError(   R   RW   RX   RY   RZ   R[   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRb   Ç   s    c         O   s   t  ƒ  ‚ d  S(   N(   Rk   (   R   t   argsR   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   show_old_outputË   s    s     c         C   sv   t  |  j ƒ d k r\ | | |  j ƒ  j ƒ  IJx* |  j D] } | | j d | ƒ IJq9 Wn  |  j d | d | ƒ d  S(   Ni    R%   t   out(   R   Rc   t   get_result_classR   R+   t   show_summary(   R   Rn   R%   t   verboset   result(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   showÎ   s
    R!   c         C   sú   |  j  d k r! | | d IJd  S|  j d k rA | | d IJn  | d IJ|  j d  k	 r· | | d |  j |  j f IJ| | d |  j |  j f IJ| | d |  j |  j f IJn? | | d |  j IJ| | d	 |  j IJ| | d
 |  j IJd  S(   Ni    s   No restraints of this type.s6   All restrained atoms within 4.0 sigma of ideal values.R!   s   Min. delta:  %7.3f (Z=%7.3f)s   Max. delta:  %7.3f (Z=%7.3f)s   Mean delta:  %7.3f (Z=%7.3f)s   Min. delta:  %7.3fs   Max. delta:  %7.3fs   Mean delta:  %7.3f(	   R`   Rd   RV   R   RR   RT   R"   RU   RS   (   R   Rn   R%   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRp   Õ   s"    

c         C   sŠ   |  j  } | d  k	 r† g  } xW |  j D]L } | j ƒ  r% | j | ƒ r% | j ƒ  } | d  k	 rq | j | ƒ qq q% q% W| d j | ƒ Sd  S(   Ns   
(   t   kinemage_headerR   Rc   t
   is_outliert   is_in_chainRG   R#   R   (   R   R5   R   t
   kin_blocksRr   t   outlier_kin_txt(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRG   é   s    	N(   R<   R=   t   __doc__R   R_   Rt   t   gui_list_headerst   gui_formatst   wx_column_widthst   __restraints_attr__R   R>   t   Truet   FalseR   Rb   Rm   t   syst   stdoutRs   Rp   RG   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRP   �   s.   			t   bondsc           B   sq   e  Z d  Z d Z d Z d d d d d g Z d d d	 d	 d
 g Z d d d d d g Z d „  Z e	 e
 d „ Z RS(   RA   s   Bond lengths!   @subgroup {length devs} dominant
s   Atom 1s   Atom 2s   Ideal values   Model values   Deviation (sigmas)s   %ss   %.3fs   %.1fi–   id   iP   c         C   s   t  S(   N(   RA   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRo   þ   s    c         C   sB  d d l  m } | j | j ƒ  t ƒ j ƒ  }	 | j d d d | d |	 ƒ \ }
 } |
 d  k rb g  Sg  } xÓ |
 D]Ë } | \
 } } } } } } } } } } t | d | d | ƒ} t	 d	 | d
 | d | d | d | d | d | d | d t d t
 | ƒ ƒ 
} | j | k r| j | ƒ qo | so t | _ | j | ƒ qo qo W| S(   Niÿÿÿÿ(   t   flext   by_valueR   RY   t   site_labelst
   iselectionR]   R   R   R	   R   RB   R
   RC   t   outliert   xyz(   t   scitbx.array_familyRƒ   t   boolt   sizeR~   R†   t
   get_sortedR   R   RA   t   get_mean_xyzR   R#   R   R‡   (   R   RW   RX   RY   RZ   R[   R\   R]   Rƒ   R…   t   sorted_tablet	   not_shownt   outlierst   restraint_infot   i_seqsR   R	   RB   R
   R   t   weightR   t   sym_op_jt   rt_mxt
   bond_atomsR‡   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRb      s<    	$		(   R<   R=   R_   t   restraint_labelRt   Rz   R{   R|   Ro   R~   R   Rb   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR‚   õ   s   		t   anglesc           B   s2   e  Z d  Z d Z d Z d „  Z e e d „ Z RS(   RI   s
   Bond angles   @subgroup {geom devs} dominant
c         C   s   t  S(   N(   RI   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRo   (  s    c         C   s  d d  l  } t | d | d | d | d | ƒ}	 g  }
 xÑ |	 D]É \ } } | j j d | d | d | ƒ } t d | d | j d	 | j d
 | j d | j j | j ƒ d | j	 ƒ  d t
 d | d j ƒ } | j | k rç |
 j | ƒ q= | s= t | _ |
 j | ƒ q= q= W|
 S(   NiÿÿÿÿRX   RY   RZ   R]   t   proxyR   R   R
   R	   R   R   R‡   Rˆ   i   (   t   cctbx.geometry_restraintst   _get_sortedt   geometry_restraintsRI   t   angle_idealR
   t   angle_modelt   weight_as_sigmaR“   R   R~   Rˆ   R   R#   R   R‡   (   R   RW   RX   RY   RZ   R[   R\   R]   t   cctbxRa   R�   R™   t   proxy_atomsR   R‡   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRb   *  s6    							(	   R<   R=   R_   R—   Rt   Ro   R~   R   Rb   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR˜   $  s   	t	   dihedralsc           B   s,   e  Z d  Z d Z d „  Z e e d „ Z RS(   RK   s   Dihedral anglec         C   s   t  S(   N(   RK   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRo   L  s    c         C   s  d d  l  } t | d | d | d | ƒ}	 g  }
 xÞ |	 D]Ö \ } } | j j d | d | d | ƒ } t d | d | j d | j d	 | j d
 | j j | j ƒ d | j	 ƒ  d t
 | d | d g ƒ d t ƒ } | j | k rî |
 j | ƒ q7 | s7 t | _ |
 j | ƒ q7 q7 W|
 S(   NiÿÿÿÿRX   RY   RZ   R™   R   R   R
   R	   R   R   Rˆ   i   i   R‡   (   Rš   R›   Rœ   RK   R�   R
   Rž   RŸ   R“   R   R�   R~   R   R#   R   R‡   (   R   RW   RX   RY   RZ   R[   R\   R]   R    Ra   R�   R™   R¡   R   R‡   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRb   N  s4    								(   R<   R=   R_   R—   Ro   R~   R   Rb   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR¢   I  s
   	t   chiralitiesc           B   s,   e  Z d  Z d Z d „  Z e e d „ Z RS(   RL   s   Chiral volumec         C   s   t  S(   N(   RL   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRo   o  s    c         C   s  d d  l  } t | d d  d | d | ƒ}	 g  }
 xÊ |	 D]Â \ } } | j j d | d | ƒ } t d | d | j d | j d	 | j d
 | j j | j	 ƒ d | j
 ƒ  d t d t | ƒ ƒ } | j | k rÚ |
 j | ƒ q7 | s7 t | _ |
 j | ƒ q7 q7 W|
 S(   NiÿÿÿÿRX   RY   RZ   R™   R   R   R
   R	   R   R   R‡   Rˆ   (   Rš   R›   R   Rœ   RL   t   volume_idealR
   t   volume_modelRŸ   R“   R   R~   R�   R   R#   R   R‡   (   R   RW   RX   RY   RZ   R[   R\   R]   R    Ra   R�   R™   R¡   R   R‡   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRb   q  s2    							(   R<   R=   R_   R—   Ro   R~   R   Rb   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR£   l  s
   	t   planaritiesc           B   sb   e  Z d  Z d Z d d d d g Z d d d d g Z d	 d
 d
 d g Z d „  Z e e	 d „ Z
 RS(   RM   s   Planar groupRQ   s
   Max. deltas
   RMS(delta)s   Deviation (sigmas)s   %ss   %.3fs   %.1fiú   id   i‚   c         C   s   t  S(   N(   RM   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRo   •  s    c         C   sŒ  d d  l  } d d l m }	 |	 j | j ƒ  t ƒ j ƒ  }
 | j d d d | d |
 d | ƒ \ } } | d  k rt g  Sg  } x| D]} | \ } } } g  | D] } | d ^ q� } t	 g  | D] } | d	 | d
 ^ q½ ƒ } t
 | d | ƒ} t d | d | d | d t	 g  | D] } | d	 ^ qƒ d | d t d t | ƒ ƒ } | j | k re| j | ƒ q� | s� t | _ | j | ƒ q� q� W| S(   Niÿÿÿÿ(   Rƒ   R„   R   RY   R…   RX   i    i   i   R†   R   RN   RO   R   R‡   Rˆ   (   Rš   R‰   Rƒ   RŠ   R‹   R~   R†   RŒ   R   R"   R   RM   R�   R   R#   R   R‡   (   R   RW   RX   RY   RZ   R[   R\   R]   R    Rƒ   R…   RŽ   t   n_not_shownR�   R‘   t   plane_atomst	   rms_deltaR   R   R’   R   t   plane_atoms_R‡   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRb   —  s<    	 +#	(   R<   R=   R_   R—   Rz   R{   R|   Ro   R~   R   Rb   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR¦   Ž  s   	c         C   sY   d d l  m } | |  d j ƒ } x% |  d D] } | | | j ƒ 7} q. W| t |  ƒ S(   Niÿÿÿÿ(   t   coli    i   (   t   scitbx.matrixR«   Rˆ   R   (   R   R«   t   sumt   atom(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR�   ¸  s
    c         C   s/  | d k s t  ‚ |  j ƒ  d k r( g  Sd d  l } d d l m } | j |  j d | ƒ ƒ } |  j d | ƒ }	 | d k r† |	 }
 n | d k r› | }
 n  | j d |
 d t	 ƒ } g  } xo | D]g } |  | } | j
 j | j ƒ } t |	 | ƒ | } t | d	 | j d
 | ƒ} | j | | f ƒ qÀ W| S(   NR   R
   i    iÿÿÿÿ(   Rƒ   RY   t   datat   reverseR†   R]   (   s   residuals   delta(   R   R‹   Rš   R‰   Rƒ   R   t   deltast	   residualst   sort_permutationR~   Rœ   RŸ   R“   R   R   R’   R#   (   t   ORX   RY   RZ   R„   R]   R    Rƒ   R±   R²   t   data_to_sortt   i_proxies_sortedRŽ   t   i_proxyR™   R   R   R¡   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR›   ¿  s*     		
	t   combinedc           B   sr   e  Z d  Z d d d d d g Z e d g Z e d e e d d „ Z e	 j
 d	 e d
 „ Z d „  Z d d „ Z RS(   s\   
  Container for individual validations of each of the five covalent restraint
  classes.
  R‚   R˜   R¢   R£   R¦   t   _use_cdlg      @c	         C   su  | |  _  d d l m }	 |	 j d | ƒ }
 | j ƒ  } | j ƒ  } | j ƒ  } | r  | j t ƒ d k r  |
 j	 d | ƒ }
 | j	 | ƒ } | j	 | ƒ } n  |
 j
 d | d t ƒ j } x³ |  j D]¨ } t ƒ  | } | d k rÿ |
 j j d | ƒ j } n t |
 j d	 | j ƒ } | d
 | d | d | d | d | j ƒ  d | d | d | d | ƒ 	} t |  | | ƒ qÅ Wd  S(   Niÿÿÿÿ(   t
   restraintst   geometryi    t	   selectionRY   t   compute_gradientsR‚   s
   %s_proxiesRZ   Re   Rf   RX   Rg   R[   R\   R]   (   R¹   t   mmtbxRº   t   managerRY   t   hd_selectionR   t   countR~   t   selectRe   R   R»   t   __geo_types__t   globalst   pair_proxiest   bond_proxiesR^   R_   RX   t   setattr(   R   t   pdb_hierarchyt   xray_structuret   geometry_restraints_managerRg   R[   R\   R]   t   cdlRº   t   restraints_managerRY   RÀ   RZ   Re   t   geo_typet   restraint_validation_classRf   t   rv(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR   á  s@    							R!   c         C   s�   x† |  j  D]{ } t |  | ƒ } t | j d d | ƒ| d k ro t |  d t ƒ ro | d d IJ| d IJn  | j d | d | ƒ q
 Wd  S(	   NR'   Rn   R˜   R¹   s5     Using conformation-dependent library for mainchain s   bond angle targetsR!   R%   (   RÃ   R^   R   R—   R   Rs   (   R   Rn   R%   Rq   RÍ   RÏ   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRs     s    c         C   s   |  j  j |  j j f S(   N(   R‚   RS   R˜   (   R   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   get_bonds_angles_rmsds  s    c         C   s<   |  j  j d | ƒ } | d 7} | |  j j d | ƒ 7} | S(   NR5   s   
(   R˜   RG   R‚   (   R   R5   t   kin_txt(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyRG     s    
N(   R<   R=   Ry   RÃ   R>   R~   R   R   R   R€   R�   Rs   RÐ   RG   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyR¸   Ú  s   #
	(   Ry   t
   __future__R    t   mmtbx.validationR   R   R   t   libtbx.str_utilsR   t   libtbxR   t   mathR   R€   R?   R   RA   RI   RK   RL   RM   RP   R‚   R˜   R¢   R£   R¦   R�   R   R›   R¸   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/restraints.pyt   <module>   s6   	8h/%#"*	