ó
Å™xTc           @   s¹  d  d l  m Z d  d l m Z d  d l Z d  d l m Z d  d l m	 Z	 d  d l
 m Z m Z d  d l m Z d  d l m Z d  d	 l m Z d  d
 l m Z d  d l Z d  d l m Z d  d l m Z d  d l Z d Z d Z d Z d Z i e d 6e d 6e d 6Z  d „  Z! e" d „ Z# d „  Z$ d „  Z% d d d d „ Z' d d d „ Z( d „  Z) d d d d d d d d d d e ƒ  d e" d „ Z* d „  Z+ d  „  Z, d! „  Z- d" „  Z. d S(#   iÿÿÿÿ(   t   division(   t	   superposeN(   t   flex(   t   idealized_aa(   t   Sorryt   null_out(   t   one_letter_given_three_letter(   t   three_letter_given_one_letter(   t   run2(   t   RotamerEval(   t   secondary_structure(   t   grand_master_phil_strs  
ATOM      1  N   ALA A   1      -5.606  -2.251 -12.878  1.00  0.00           N
ATOM      2  CA  ALA A   1      -5.850  -1.194 -13.852  1.00  0.00           C
ATOM      3  C   ALA A   1      -5.186  -1.524 -15.184  1.00  0.00           C
ATOM      4  O   ALA A   1      -5.744  -1.260 -16.249  1.00  0.00           O
ATOM      5  CB  ALA A   1      -5.350   0.142 -13.324  1.00  0.00           C
ATOM      6  N   ALA A   2      -3.991  -2.102 -15.115  1.00  0.00           N
ATOM      7  CA  ALA A   2      -3.262  -2.499 -16.313  1.00  0.00           C
ATOM      8  C   ALA A   2      -3.961  -3.660 -17.011  1.00  0.00           C
ATOM      9  O   ALA A   2      -4.016  -3.716 -18.240  1.00  0.00           O
ATOM     10  CB  ALA A   2      -1.829  -2.872 -15.965  1.00  0.00           C
s  ATOM      1  N   ALA A   1       8.836  -4.233 -14.408  1.00  0.00           N
ATOM      2  CA  ALA A   1      10.232  -4.071 -14.799  1.00  0.00           C
ATOM      3  C   ALA A   1      10.764  -5.331 -15.476  1.00  0.00           C
ATOM      4  O   ALA A   1      11.679  -5.262 -16.297  1.00  0.00           O
ATOM      5  CB  ALA A   1      11.088  -3.716 -13.593  1.00  0.00           C
ATOM      6  N   ALA A   2      10.176  -6.478 -15.143  1.00  0.00           N
ATOM      7  CA  ALA A   2      10.582  -7.741 -15.750  1.00  0.00           C
ATOM      8  C   ALA A   2      10.381  -7.714 -17.262  1.00  0.00           C
ATOM      9  O   ALA A   2      11.080  -8.410 -17.999  1.00  0.00           O
ATOM     10  CB  ALA A   2       9.815  -8.901 -15.134  1.00  0.00           C
s  ATOM      1  N   ALA A   1      -3.365  -3.446  -8.396  1.00  0.00           N
ATOM      2  CA  ALA A   1      -4.568  -4.249  -8.592  1.00  0.00           C
ATOM      3  C   ALA A   1      -5.809  -3.386  -8.805  1.00  0.00           C
ATOM      4  O   ALA A   1      -6.559  -3.591  -9.759  1.00  0.00           O
ATOM      5  CB  ALA A   1      -4.775  -5.185  -7.411  1.00  0.00           C
ATOM      6  N   ALA A   2      -6.025  -2.424  -7.914  1.00  0.00           N
ATOM      7  CA  ALA A   2      -7.221  -1.588  -7.976  1.00  0.00           C
ATOM      8  C   ALA A   2      -7.101  -0.486  -9.025  1.00  0.00           C
ATOM      9  O   ALA A   2      -8.089  -0.114  -9.659  1.00  0.00           O
ATOM     10  CB  ALA A   2      -7.511  -0.985  -6.610  1.00  0.00           C
s  
ATOM      1  N   ALA A   1      27.961   0.504   1.988  1.00  0.00           N
ATOM      2  CA  ALA A   1      29.153   0.205   2.773  1.00  0.00           C
ATOM      3  C   ALA A   1      30.420   0.562   2.003  1.00  0.00           C
ATOM      4  O   ALA A   1      30.753  -0.077   1.005  1.00  0.00           O
ATOM      5  CB  ALA A   1      29.170  -1.262   3.172  1.00  0.00           C
ATOM      6  N   ALA A   2      31.123   1.587   2.474  1.00  0.00           N
ATOM      7  CA  ALA A   2      32.355   2.031   1.832  1.00  0.00           C
ATOM      8  C   ALA A   2      33.552   1.851   2.758  1.00  0.00           C
ATOM      9  O   ALA A   2      33.675   2.539   3.772  1.00  0.00           O
ATOM     10  CB  ALA A   2      32.232   3.483   1.399  1.00  0.00           C
i   i   i   c         C   s^   |  j  d k r |  j d S|  j  d k r4 |  j d S|  j  d k rN |  j d St d ƒ ‚ d  S(   Ni   i   i   i   s   Unsupported helix type.(   t   helix_classt   lengthR   (   t   helix(    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt    get_expected_n_hbonds_from_helixJ   s    c   
   
   C   s~  | j  ƒ  } | r$ t d d ƒ } n  t j ƒ  } x|  j j ƒ  D]} | j | | d j | | d ƒ ƒ | | d j ƒ  d | | d j ƒ  | | d j | | d ƒ | d | d f GH| r@ | | d j ƒ  } | | d j ƒ  } d | d d !| d	 d
 !| d d !| d d !| d	 d
 !| d d !f }	 | j	 |	 ƒ q@ q@ Wd G| j
 ƒ  j ƒ  G| j ƒ  GH| rz| j ƒ  n  d S(   sM    Print hydrogen bonds in geometry restraints manager for debugging
  purposess
   dashes.pmlt   wi    i   s   <====>sL   dist chain "%s" and resi %s and name %s, chain "%s" and resi %s and name %s
i   i   i   i   i   i   s    min, max, mean, sd hbond lenghtsN(   t   atomst   openR   t   doublet   generic_restraints_managert   hbonds_as_simple_bondst   appendt   distancet   id_strt   writet   min_max_meant   as_tuplet    standard_deviation_of_the_samplet   close(
   t   geometryt	   hierarchyt   pymolR   t   dashest   hbondlent   hbt   s1t   s2t   ps(    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt   print_hbond_proxiesU   s$    &%/9c         C   s4  t  j j d d d |  ƒ j ƒ  } | j ƒ  d j ƒ  d j ƒ  d } | j ƒ  } t	 j
 ƒ  } t	 j
 ƒ  } d d d d g } t | ƒ d k r x| | d | f | d	 | f g D]K \ } } x< | j ƒ  D]. }	 |	 j j ƒ  | k rÇ | j |	 j ƒ qÇ qÇ Wq® Wn t d
 ƒ ‚ t j d | d | ƒ }
 |
 j |
 j f S(   s¾    Return rotation and translation matrices for the ideal structure.

  The function determines r and t matrices from alingment of 1st and 2nd
  residues of the structure passed in pdb_str.
  t   source_infot   linesi    t   Nt   CAt   Ct   Oi   i   s*   pdb_str should contain at least 2 residuest   reference_sitest   other_sitesN(   t   iotbxt   pdbt   inputt   Nonet   construct_hierarchyt   modelst   chainst
   conformerst   residuesR   t   vec3_doublet   lenR   t   namet   stripR   t   xyzR   R   t   least_squares_fitt   rt   t(   t   pdb_strt   pdb_hierarchyt	   conformerR8   t   fixed_sitest   moving_sitest   main_chain_atomsR?   t   arrt   at   lsq_fit_obj(    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt   get_r_t_matrices_from_structurem   s    !$-	c         C   sû  t  | j j ƒ  } | d k r# d  St | |  _ | d k r€ x= |  j ƒ  D]/ } | j j ƒ  d k rI |  j d | ƒ PqI qI Wd  St j	 ƒ  } t j	 ƒ  } d d d g } xe |  | f | | f g D]K \ } }	 x< | j ƒ  D]. } | j j ƒ  | k rÙ |	 j
 | j ƒ qÙ qÙ WqÀ Wt j d | d | ƒ }
 | j ƒ  } | j ƒ  j |
 j j | j ƒ  j ƒ  |
 j j ƒ | j ƒ  j | j | ƒ ƒ |  j d	 t | j ƒ  ƒ d
 ƒ xR | j ƒ  D]D } | j j ƒ  d k r¯| j ƒ  } | j ƒ  |  j d | ƒ q¯q¯Wd  S(   Nt   At   Gt   CBt   atomR+   R*   R.   R/   t   number_of_additional_atomsi   R,   R-   (   R*   s   CAR,   R-   RM   (   t	   one_threet   resnamet   uppert	   three_oneR   R;   R<   t   remove_atomR   R9   R   R=   R   R>   t   detached_copyt   set_xyzR?   t   elemst   extract_xyzR@   t   nearest_rotamer_sites_cartt   pre_allocate_atomsR:   t	   uij_eraset   append_atom(   t   ag_to_placet   current_reference_agt   rotamer_managert   cRH   RD   RE   t   reper_atomst   agRG   RI   t   ideal_correct_agt   at(    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt   side_chain_placement†   sB    		
c         C   sŒ  | d k r t ƒ  } n  | } | | g j d ƒ d k s? t ‚ | d k	 r« t | j ƒ  j ƒ  ƒ } | d k r~ t d ƒ ‚ q« t | j ƒ  j ƒ  ƒ d k s« t d ƒ ‚ n  | d k rÃ t | ƒ n- t | j ƒ  d j	 ƒ  d j
 ƒ  d j ƒ  ƒ } | d k  rt d ƒ ‚ n  t j ƒ  } d } | rI| j ƒ  d j	 ƒ  d j ƒ  } n  t j j d d d |  ƒ j ƒ  }	 |	 j ƒ  d j	 ƒ  d }
 |
 j ƒ  d j ƒ  d } t j j j d d	 ƒ } | j d
 | ƒ t |  ƒ \ } } xü t | ƒ D]î } t j j j d d ƒ } | d | _ | j d | ƒ | j ƒ  } | j d | ƒ | j ƒ  j | j  | j ƒ  j! ƒ  | j  ƒ | rƒ| | j ƒ  d n= | t" | | j# ƒ  j ƒ  d j	 ƒ  d j ƒ  d j ƒ  d } t$ | | | ƒ qåWt j j j% | ƒ } | d k rˆ| j ƒ  j! ƒ  } | j ƒ  j! ƒ  } t | ƒ t | ƒ k s:t ‚ t& j' d | d | ƒ } | j ƒ  j | j( j  | j ƒ  j! ƒ  | j) j  ƒ n  | S(   s~   Return pdb.hierarchy with secondary structure according to sequence or
  reference hierarcy. If reference hierarchy provided, the resulting hierarchy
  will be rigid body aligned to it. Residue numbers will start from 1.

  pdb_str - "ideal" structure at least 2 residues long.
  sequence - string with sequence (one-letter codes)
  pdb_hierarchy_template - reference hierarchy.
  i   i    s@   Hierarchy template in secondary_structure_from_sequence is emptys+   Alternative conformations are not supporteds-   sequence should contain at least one residue.R(   R)   t   idRK   t#   number_of_additional_residue_groupst   icodet    t   residue_groupt
   atom_groupR.   R/   N(*   R3   R	   t   countt   AssertionErrorR:   t   altloc_indicest   keysR   R5   R6   R7   R8   R   t   residue_dictt   residue_groupsR0   R1   R2   R4   t   atom_groupsR   t   chaint   pre_allocate_residue_groupsRJ   t   rangeRj   t   resseqt   append_residue_groupRU   t   append_atom_groupR   RV   RW   RX   RS   t   lowerRe   t   new_hierarchy_from_chainR   R>   R?   R@   (   RA   t   sequencet   pdb_hierarchy_templateR_   t   phtt   lkt   number_of_residuest   ideal_res_dictt   real_res_listRB   Rs   t   current_ala_agt	   new_chainR?   R@   t   jt   rgR]   R^   t	   new_pdb_hRD   RE   RI   (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt!   secondary_structure_from_sequence­   s`    !!0#!	!/	*c      	   C   sD   |  t  j ƒ  k r! t d ƒ ‚ n  t d t  |  d | d | d | ƒ S(   Ns   Unsupported helix type.RA   R{   R_   R|   (   t   helix_class_to_pdb_strRo   R   R‡   (   R   R_   R{   R|   (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt	   get_helixî   s    
c          C   s.   d d  l  }  |  j j d ƒ } | j ƒ  } | S(   Niÿÿÿÿt!   mmtbx_ramachandran_restraints_ext(   t   boost.pythont   pythont
   import_extt   shared_phi_psi_proxy(   t   boostt   extt   proxies(    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt   get_empty_ramachandran_proxiesø   s    g      à?g      @i,  c   ?      C   sÀ	  | d> k r t ƒ  } n  xV |  j ƒ  D]H } x? | j ƒ  D]1 } t | j ƒ  ƒ d k r8 t d d ƒ ‚ q8 q8 Wq% Wd } | } | j ƒ  } x! | j D] } | t	 | ƒ 7} q“ Wt
 j j d d> d t j |  j ƒ  ƒ ƒ j ƒ  } |  j ƒ  j ƒ  } t j | t ƒ } |  j ƒ  } x½ | j D]² } | j ƒ  } | j | d ƒ } t j | t ƒ } | j | t ƒ | j | t ƒ |  j | d t ƒ} t d | j d	 | d
 | ƒ } | j | ƒ j ƒ  j | j ƒ  j ƒ  ƒ qWxÐ | j D]Å } x¼ | j  D]± }  |  j ƒ  } | j | ƒ } t j | t ƒ } | j | t ƒ | j | t ƒ |  j | d t ƒ} t! d t" d d> d	 | d
 | ƒ } | j | ƒ j ƒ  j | j ƒ  j ƒ  ƒ qçWq×W| }! |! j# ƒ  |  j ƒ  j ƒ  }" t j |" t ƒ }# t j |" t ƒ }$ t j |" t ƒ }% t j |" t ƒ }& t j |" t ƒ }' t j |" t ƒ }( |  j ƒ  } | j d ƒ } |& j | t ƒ |& j$ t ƒ }) | j d ƒ } |( j | t ƒ d }* | r£| j% d ƒ n  x  | j D]• } | j% d | j& ƒ  ƒ | j ƒ  d }+ |* |+ } | j | ƒ } |$ j | t ƒ |& j | t ƒ | j | ƒ } |' j | t ƒ |( j | t ƒ q­Wx§ | j D]œ }, | j% d |, j& ƒ  ƒ x| |, j ƒ  D]n }+ |* |+ } | j | ƒ } |% j | t ƒ |& j | t ƒ | j | ƒ } |' j | t ƒ |( j | t ƒ qzWqPW| j d ƒ } |& j | t ƒ |$ |% @}- |- j$ t ƒ d k r<|% |- @}% n  |$ |% B|& @j$ t ƒ d k s_t' ‚ t( }. |. d t) j* 7}. t
 j+ j, d |. d t ƒ }/ |/ j- d t
 j+ j, d j. d | d d d g ƒ ƒ ƒ j/ ƒ  }0 t0 j1 j2 d | j3 ƒ  d |0 j4 d t5 ƒ  ƒ }1 |1 j6 d t j |  j ƒ  ƒ ƒ \ }2 }3 d> }4 | d> k	 rg| j7 ƒ  j8 ƒ  j9 ƒ  }5 d |5 k pad  |5 k }4 n  t0 j) j: d! |0 j) d" |2 d# t; j< ƒ  d t5 ƒ  d$ |4 ƒ }6 |6 j= d t5 ƒ  ƒ |6 j> d t5 ƒ  d% d> ƒ }7 |7 j? }8 |2 j@ d& t d' t d( |0 jA jB d) d* d+ |8 d$ |4 ƒ }9 t0 jC jD d, |9 d- t ƒ }: | d> k	 rH| j3 ƒ  |: _3 n  |: }; |; jE jF jG d. |  d/ d> d0 |	 ƒ |  j# ƒ  |; jE jF jH jI d1 |  j ƒ  j ƒ  j |$ ƒ d/ |$ d0 | ƒ |; jE jF jH jI d1 |  j ƒ  j ƒ  j |% ƒ d/ |% d0 | ƒ |; jE jF jH jI d1 |  j ƒ  j ƒ  j |& ƒ d/ |& d0 | ƒ |; jE jF jH jJ d. |! d1 |! j ƒ  j ƒ  j |' ƒ d/ |' d2 t d0 | ƒ |; jE jF jH jJ d. |! d1 |  j ƒ  j ƒ  j |( ƒ d/ |( d2 t d0 | ƒ |  j ƒ  j |! j ƒ  j ƒ  ƒ |; jE jF jK ƒ  }< | d> k	 r	|  jL d3 | ƒ n  |; jE jF jM ƒ  d k s"	t' ‚ |; jE jF jN ƒ  |) k s@	t' ‚ t5 ƒ  }= | re	| }= |= j% d4 ƒ n  tO d5 |; d. |  d6 | d7 |
 d8 t d9 t d: t d; t d< t d= t d |= ƒ }> |; jE jF jH jP S(?   s/  
  Substitute secondary structure elements in real_h hierarchy with ideal
  ones _in_place_.
  Returns reference torsion proxies - the only thing that cannot be restored
  with little effort outside the procedure.
  real_h - hierarcy to substitute secondary structure elements.
  xray_structure - xray_structure - needed to get crystal symmetry (to
      construct processed_pdb_file and xray_structure is needed to call
      get_geometry_restraints_manager for no obvious reason).
  helices - list with HELIX records. Types supported:
      1:alpha_pdb_str, 3:alpha_pi_pdb_str, 5: alpha310_pdb_str

  Weights (bigger number gives lighter restraints):
  sigma_on_reference_non_ss - weight on original model coordinates restraints
      where no ss present. Keeps loops close to initial model.
  sigma_on_reference_ss - weight on original model coordinates restraints
      where ss present. Bends helices a bit according to initial model.
  sigma_on_torsion_ss - weight on torsion angles restraints where ss present.
      Keeps helices torsion angles close to ideal.
  i   s2   Secondary structure substitution does not support
s*   the presence of alternative conformations.i    R(   R)   t
   copy_atomsR   R|   R_   RA   R{   s%   name ca or name n or name o or name cs*   (name ca or name n or name o or name c) %ss'   Replacing ss-elements with ideal ones:
s   %s
s8   not name ca and not name n and not name o and not name cs   secondary_structure {%s}t   input_stringt   process_includest   sources   
sB   secondary_structure {h_bond_restraints.remove_outliers = False
%s}s>   pdb_interpretation.peptide_link.ramachandran_restraints = Trues&   use_c_beta_deviation_restraints = Trues#   secondary_structure_restraints=Truet   crystal_symmetryt   pdb_interpretation_paramst   logt   raw_recordst   Ht   Dt   paramst   processed_pdb_filet   tmp_dirt   assume_hydrogens_all_missingt   hbond_paramst   show_energiest   show_nonbonded_clashscoret   params_editst   plain_pairs_radiusi   t   hydrogen_bond_proxiesR   t   normalizationRB   t	   selectiont   sigmat
   sites_cartt   chi_angles_onlyt	   file_names?   Refining geometry of substituted secondary structure elements.
t   restraints_managert   max_number_of_iterationst   number_of_macro_cyclest   bondt	   nonbondedt   anglet   dihedralt	   chiralityt	   planarityN(Q   R3   R	   R5   R6   R:   R7   R   t   as_restraint_groupst   helicesR   R0   R1   R2   R   t   split_linest   as_pdb_stringR4   R   t   sizet   boolt   Falset   atom_selection_cachet   as_atom_selectionst
   iselectiont   set_selectedt   Truet   selectR‰   R   RV   RX   t   sheetst   strandsR‡   t   beta_pdb_strt   reset_i_seq_if_necessaryRl   R   t
   as_pdb_strRm   R   R
   t   sec_str_master_phil_strt   philt   parset   fetcht   joint   extractt   mmtbxt   utilst   process_pdb_file_srvR—   t   pdb_interpretationR   t   process_pdb_filest   scattering_type_registryt   type_count_dictRo   t   process_structuret   ost   getcwdt
   initializet   create_hbond_proxiesR‘   t   geometry_restraints_managert   geometry_restraintst   editst
   restraintst   managerR   R   t   add_c_beta_torsion_restraintst   reference_managert   add_coordinate_restraintst   add_torsion_restraintst   get_n_hbondst   write_pdb_filet   get_n_den_proxiest"   get_n_reference_coordinate_proxiesR   t   reference_torsion_proxies(?   t   real_ht   xray_structuret   ss_annotationt   sigma_on_reference_non_sst   sigma_on_reference_helixt   sigma_on_reference_sheett   sigma_on_torsion_sst   sigma_on_torsion_nonsst   sigma_on_ramachandrant   sigma_on_cbetat   n_macrot   n_itert   fname_before_regularizationR™   R_   t   verboset   modelRs   t   expected_n_hbondst   annt   phil_strt   ht   edited_ht   n_atoms_in_real_ht	   cumm_bselt   selection_cachet	   selstringt   iselt   all_bselt   sel_ht   ideal_ht   sht   stt   pre_result_ht   n_atomst   bselt   helix_selectiont   sheet_selectiont   other_selectiont   ss_for_tors_selectiont   nonss_for_tors_selectiont   n_main_chain_atomst   main_chain_selection_prefixt   ss_selst   sheett   helix_sheet_intersectiont   params_lineR�   t   custom_parst   processed_pdb_files_srvRž   t   junkt   has_hdt	   sctr_keyst   sec_strt   build_proxiesR¡   R   R­   t   grmt   actual_n_hbondst   refinement_logt   obj(    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt   substitute_ssÿ   sv   $	,	0


	
#				
					
	
			
	c          C   s#   t  t d ƒ }  |  j d d ƒ d  S(   Nt   ACEDGFIHKMLNQPSRTWVYR¬   s   o_beta_seq.pdb(   R‡   RÅ   Rä   (   RB   (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt   beta÷  s    	c          C   s#   t  t d ƒ }  |  j d d ƒ d  S(   NR   R¬   s   o_helix310_seq.pdb(   R‡   t   alpha310_pdb_strRä   (   RB   (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt	   alpha_310ü  s    	c          C   s#   t  t d ƒ }  |  j d d ƒ d  S(   NR   R¬   s   o_helix_pi_seq.pdb(   R‡   t   alpha_pi_pdb_strRä   (   RB   (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt   alpha_pi  s    	c          C   s#   t  t d ƒ }  |  j d d ƒ d  S(   NR   R¬   s   o_helix_seq.pdb(   R‡   t   alpha_pdb_strRä   (   RB   (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt   alpha  s    	(/   t
   __future__R    t   scitbx.mathR   t	   iotbx.pdbR0   t   cctbx.array_familyR   t   mmtbx.monomer_libraryR   t   libtbx.utilsR   R   t   iotbx.pdb.amino_acid_codesR   RP   R   RS   t&   mmtbx.refinement.geometry_minimizationR   t   mmtbx.rotamer.rotamer_evalR	   t   mmtbx.utilsRÎ   R
   t(   mmtbx.monomer_library.pdb_interpretationR   RÖ   t   alpha_helix_strt   a310_helix_strt   pi_helix_strRÅ   Rˆ   R   R¼   R'   RJ   Re   R3   R‡   R‰   R’   R  R!  R#  R%  R'  (    (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/secondary_structure/build/__init__.pyt   <module>   sX   			(>
	
é			