ó
­xTc           @   s`   d  d l  m Z d  d l m Z d  d l m Z m Z d  d l m Z d e	 f d     YZ
 d S(   i˙˙˙˙(   t   division(   t   adopt_init_args(   t   hbondt   ramachandran(   t   flext   managerc        
   B   s  e  Z d d d d d d d d d d  	 Z d   Z d   Z d   Z d   Z d   Z d   Z	 d   Z
 d d  Z d	   Z d
   Z d d d  Z d   Z d d d  Z d   Z d   Z d d  Z d d d d d  Z d d  Z d d d d d  Z d d  Z RS(   c
         C   sÖ   t  |  t    |  j d  k rI d d  l }
 |
 j j j d t  |  _ n  | d  k sg | d  k	 sg t  |  j d  k rĄ d d l	 m
 } | j j   j   |  _ n  |  j d  k rŇ d d l	 m } | j   |  _ n  d  S(   Ni˙˙˙˙t   default(   R   (   t	   reference(   R   t   localst   flagst   Nonet   mmtbx.geometry_restraints.flagst   geometry_restraintst   Truet   AssertionErrort   hydrogen_bond_paramst   mmtbx.geometry_restraintsR   t   master_philt   fetcht   extractt   reference_managerR   R   (   t   selft   ramachandran_proxiest   ramachandran_lookupt   hydrogen_bond_proxiesR   R   t   den_managert   ncs_managert   c_beta_dihedral_proxiesR	   t   mmtbxR   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   __init__   s    
c         C   s<   |  j    |  j   |  j   |  j   |  j   |  j   S(   N(   t   get_n_ramachandran_proxiest   get_n_hbondst"   get_n_reference_coordinate_proxiest   get_n_reference_torsion_proxiest   get_n_den_proxiest   get_n_c_beta_dihedral_proxies(   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   get_n_proxies"   s    1c         C   s    |  j  d  k	 r t |  j   Sd S(   Ni    (   R   R
   t   len(   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR   *   s    c         C   sB   |  j  d  k	 r> t |  j  t  r. t |  j   S|  j  j   Sn  d S(   Ni    (   R   R
   t
   isinstancet   listR%   t   size(   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR   /   s
    c         C   s8   |  j  d  k	 r4 |  j  j d  k	 r4 t |  j  j  Sn  d S(   Ni    (   R   R
   t   reference_coordinate_proxiesR%   (   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR    7   s    c         C   s8   |  j  d  k	 r4 |  j  j d  k	 r4 t |  j  j  Sn  d S(   Ni    (   R   R
   t   reference_torsion_proxiesR%   (   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR!   =   s    c         C   s#   |  j  d  k	 r t |  j  j  Sd S(   Ni    (   R   R
   R%   t   den_proxies(   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR"   C   s    c         C   s    |  j  d  k	 r t |  j   Sd S(   Ni    (   R   R
   R%   (   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR#   H   s    c   
      C   sű  | d  k r7 d d l m } | j | j   d  } n  d } |  j d  k	 r |  j j r | |  j j	 d | d |  j d |  7} n  |  j
 d  k	 r÷ |  j j r÷ d d l m } |  j j j } | | j d |  j
 d | d | d	 |  j j d
 |  7} n  |  j d  k	 r[|  j j r[|  j j d  k	 s6|  j j d  k	 r[| |  j j d | d |  7} q[n  |  j d  k	 r|  j j r|  j j d | d |  } | | 7} n  |  j d  k	 r÷|  j j r÷d d l m } | j d | d |  j d |  }	 | |	 7} n  | S(   Ni˙˙˙˙(   R   g        i    t
   sites_cartt   proxiest   gradient_array(   R   t   falloff_distancet   lennard_jones_potential(   t   c_betaR   (   g        g        g        (   R
   t   scitbx.array_familyR   t   vec3_doubleR(   R   R	   R   R   t   restraints_residual_sumR   t   hydrogen_bondR   R   R   t   lennard_jonest	   potentialt   target_and_gradientsR/   R   R   R)   R*   R   t   denR   R1   (
   R   R,   R.   R   t   targetR   t   lj_potentialt
   den_targetR1   t   c_beta_target(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR4   N   sT    						c         C   s3   |  j  d  k	 r/ d d l m } | j |  j   Sg  S(   Ni˙˙˙˙(   R   (   R   R
   R   R   t   get_simple_bonds(   R   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   hbonds_as_simple_bonds~   s    c         C   s   d  S(   N(   R
   (   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   rotamers   s    c      	   C   sY   d d l  m } | d  k r( |  j } n  | j d | d | d |  j d |  j |  _ d  S(   Ni˙˙˙˙(   R   t   pdb_hierarchyt   xray_structuret   paramst   log(   R   R   R
   R   t   find_implicit_hydrogen_bondsR-   R   (   R   RA   RB   RC   RD   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   update_hydrogen_bonds   s    		c         C   s  d  } } } d  } } |  j d  k	 r? |  j j | |  } n  |  j d  k	 rf |  j j | |  } n  |  j d  k	 r |  j j | |  } n  |  j d  k	 r´ |  j j | |  } n  |  j d  k	 rŰ |  j j | |  } n  t d | d |  j	 d | d |  j
 d | d | d | d |  j  S(	   NR   R   R   R   R   R   R   R	   (   R
   R   t   proxy_selectR   R   t   selectR   R   R   R   R   R	   (   R   t   n_seqt
   iselectionR   R   R   R   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyRH      s0    
					g      @c         C   s5   d d l  m } | j d | d | d d  |  _ d  S(   Ni˙˙˙˙(   R1   RA   t	   selectiont   sigmag      @(   R   R1   t   get_c_beta_torsion_proxiesR   (   R   RA   RK   RL   R1   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   add_c_beta_torsion_restraintsą   s
    	c         C   s.   |  j  d  k	 r* |  j  j d |  |  _  n  d  S(   NRK   (   R   R
   t   proxy_remove(   R   RK   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt    remove_c_beta_torsion_restraintsź   s    c         C   s   d  |  _ d  |  _ d  S(   N(   R
   R   R   (   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   remove_ramachandran_restraintsÁ   s    	c         C   s^  d d d     Y} | d k s% t   | d  k sO t |  | j   k sO t   d d  l } d d  l } | j j d  } | j | |  j	  } t
 j |  j	  }	 | d  k	 r˛ | n( g  t | j    D] }
 t |
  ^ qĹ } g  } x$t |	  D]\ }
 } | j | | d d | | d d d	 | | d d | | d d d	 | | d d	 | | d d	 d	  } | d
 | | d d | | d d |  j	 |
 j d | d |  j	 |
 j | d d | j |  j	 |
 j  d |  j	 |
 j d | |
  } | j |  qđ W| d k r2| j d d   d t  n( | d k rZ| j d d   d t  n  | S(   Nt   hbond_for_showc           B   s   e  Z d    Z RS(   c	   	      S   s   t  |  t    d  S(   N(   R   R   (	   R   t   ilabelt   jlabelt   idealt   modelt   deltaRL   t   weightt   residual(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR   Ę   s    	(   t   __name__t
   __module__R   (    (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyRR   É   s   RY   RW   i˙˙˙˙t   mmtbx_hbond_restraints_exti    i   i   RS   RT   RU   RV   RL   RX   t   keyc         S   s   |  j  S(   N(   RY   (   t   x(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   <lambda>í   s    t   reversec         S   s   t  |  j  S(   N(   t   absRW   (   R^   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR_   ď   s    (    (   s   residuals   delta(   R   R
   R%   R(   t   boost.pythont   matht   pythont
   import_extt   h_bond_simple_residualsR   R   R>   t   ranget   strt	   enumeratet   sqrtt   distance_idealRX   t   appendt   sortR   (   R   t   by_valueR,   t   site_labelsRR   t   boostRc   t   extt	   residualst   simple_bondst   it   labelst   resultt   prRV   t   hbond_fs(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt"   _get_sorted_hbond_proxies_for_showĹ   s<    *+G*t    c   	   
   C   sŮ   | d  k r t j } n  |  j d | d | d |  } | d t |  IJ| d | IJxp | D]h } | d I| j IJ| d I| j IJ| d IJ| d	 | j | j | j	 | j
 | j | j f IJq_ W| d
 IJd  S(   NRn   R,   Ro   s   Hydrogen bond restraints: %ds   Sorted by %s:R   s        s1     ideal  model  delta     sigma   weight residuals'     %5.3f  %5.3f %5.3f  %5.2e %5.2e %5.2eRz   (   R
   t   syst   stdoutRy   R%   RS   RT   RU   RV   RW   RL   RX   RY   (	   R   Rn   R,   Ro   t   ft   prefixt	   max_itemst   sorted_proxies_for_showt   p(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   show_sorted_hbondsň   s     		
/c      
   C   s  d d d     Y} | d k s% t   | d  k sO t |  | j   k sO t   |  j   d k sp |  j d  k rt d  St j   } |  j j | |  j	 d | g  } | d  k	 r´ | n( g  t
 | j    D] } t |  ^ qÇ } xz t |  j	  D]i \ } }	 |	 j   }
 | j | | |
 d | |
 d | |
 d | |
 d	 | |
 d
 g | |   qď W| d k r| j d d   d t  n  | S(   Nt   rama_for_showc           B   s   e  Z d    Z RS(   c         S   s   t  |  t    d  S(   N(   R   R   (   R   Ru   RY   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR     s    (   RZ   R[   R   (    (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR     s   RY   RW   i    t   residuals_arrayi   i   i   i   R]   c         S   s   |  j  S(   N(   RY   (   R^   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR_   )  s    R`   (    (   s   residuals   delta(   R   R
   R%   R(   R   R   R   t   doubleR4   R   Rg   Rh   Ri   t
   get_i_seqsRl   Rm   R   (   R   Rn   R,   Ro   R   R   Rv   Rt   Ru   Rw   t   i_seqs(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt)   _get_sorted_ramachandran_proxies_for_show	  s4    *		+	c   
      C   sů   |  j    d k r d  S| d  k r. t j } n  | d k rC d } n  |  j d | d | d |  } | d t |  IJ| d | IJxe | D]] } | d IJ| d	 | j d | j f IJx, t d
 d  D] }	 | d | j |	 IJqČ Wq W| d IJd  S(   Ni    RY   Rn   R,   Ro   s    Ramachandran plot restraints: %ds   Sorted by %s:s-   phi-psi angles formed by             residuals       %s            %5.2ei   i   s       %sRz   (	   R   R
   R{   R|   R   R%   Ru   RY   Rg   (
   R   Rn   R,   Ro   R}   R~   R   R   R   Rt   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   show_sorted_ramachandran,  s$     			
c         C   s   t  j |  j |  S(   N(   R   R8   R   (   R   R,   R.   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   get_hbonds_residual_sumE  s    N(   RZ   R[   R
   R   R$   R   R   R    R!   R"   R#   R4   R?   R@   RF   RH   RN   RP   RQ   Ry   R   R   R   R   (    (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyR      sJ   							.		
			-#N(   t
   __future__R    t   libtbxR   R   R   R   R2   R   t   objectR   (    (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry_restraints/__init__.pyt   <module>   s   