ó
Â™xTc           @   sz   d  d l  m Z d  d l m Z d  d l m Z d  d l m Z m Z d  d l Z d „  Z	 e
 d k rv e	 ƒ  d GHn  d S(	   iÿÿÿÿ(   t   division(   t   easy_mp(   t   easy_pickle(   t   Sorryt   null_outNc          C   s,  d d  l  }  |  j j ƒ  d  k	 r* d GHd  St j d k rB d GHd  Sd d l m } m } m	 } d d  l
 } d d  l } d d l m } d d  l }  d d l m } m } m } d d l m }	 | j j d	 d  d
 d ƒ }
 | j j d j ƒ  ƒ } | d |
 j ƒ  d | g d t ƒ  d d ƒ } |	 ƒ  } | j d | ƒ | | j ƒ  d ƒ sRt ‚ | j ƒ  } t  | d ƒ d g k s}t ‚ | | d d d d d d g ƒ s¥t ‚ | | d d d d d d g ƒ sÍt ‚ | | d  d d d d d! g ƒ sõt ‚ | | d" d d d d d# g ƒ st ‚ | d$ d% d& k s7t ‚ | j j d' ƒ } | d |
 j ƒ  d | g d t ƒ  d d ƒ } |	 ƒ  } | j d | ƒ | | j ƒ  d( ƒ sªt ‚ y. | d |
 j ƒ  d g  d t ƒ  d d ƒ } Wn t k
 rën X| ‚ | j ƒ  } t  | d ƒ d) g k st ‚ | | d d d d d d* g ƒ sEt ‚ | | d" d d d d d g ƒ smt ‚ | j j d	 d  d
 d+ ƒ } | j j d, ƒ } | d | j ƒ  d | | g d t ƒ  d d d- t! ƒ } |	 ƒ  } | j d | ƒ | j ƒ  } | | d d' d, g ƒ st ‚ | | d d d d d. d/ d0 g ƒ s?t ‚ | | d d d d d1 d/ d g ƒ sjt ‚ t" | j# d2 j$ ƒ  ƒ d3 k s�t ‚ t" | j% ƒ  ƒ d% k s­t ‚ | | j# d2 j& d4 d4 ƒ du ƒ sÕt ‚ | | j# d2 j& d4 d8 ƒ dv ƒ sýt ‚ | j# d2 j' ƒ  d4 d< d8 g k s%t ‚ | | j ƒ  d= ƒ s@t ‚ | | j ƒ  d> ƒ s[t ‚ t( j) | ƒ } | j j d? ƒ } y7 | d | j ƒ  d | g d t ƒ  d d d- t! ƒ } Wn t k
 rÆn X| ‚ | j j d	 d  d
 d@ ƒ }
 | j j* j+ dA ƒ \ } } | d |
 j ƒ  d | d t ƒ  d d ƒ } |	 ƒ  } | j d | ƒ | j# d2 j, d2 k sbt ‚ | j# d2 j- d2 k s~t ‚ | j# d2 j. d2 k sšt ‚ t" | j# d2 j/ j0 ƒ  ƒ d4 k sÂt ‚ | j j d	 d  d
 dB ƒ }
 | j j dC ƒ } | d |
 j ƒ  d | g d t ƒ  d d ƒ } |	 ƒ  } | j d | ƒ | j# d2 j, d2 k sQt ‚ | j# d2 j- d2 k smt ‚ | j# d2 j. d2 k s‰t ‚ t" | j# d2 j/ j0 ƒ  ƒ dD k s±t ‚ | j j d	 d  d
 dE ƒ }
 | j j* j+ dF ƒ \ } } | d |
 j ƒ  d | d t ƒ  d d ƒ } |	 ƒ  } | j d | ƒ | j# d2 j. d3 k sFt ‚ | j# d2 j- d3 k sbt ‚ | j# d2 j1 dG k s~t ‚ | j# d2 j/ j2 dH k s�t ‚ | j j d	 d  d
 dI ƒ }
 | j j dJ ƒ } | d |
 j ƒ  d | g d t ƒ  d d ƒ } |	 ƒ  } | j d | ƒ | j# d2 j. d k s,	t ‚ | j# d2 j- d2 k sH	t ‚ | j# d2 j1 dG k sd	t ‚ | j# d2 j/ j2 dK k sƒ	t ‚ | j j d	 d  d
 dL ƒ }
 | j j dM ƒ } | d |
 j ƒ  d | g d t ƒ  d d ƒ } |	 ƒ  } | j d | ƒ | j# d2 j. dN k s
t ‚ | j# d2 j- d k s.
t ‚ | j# d2 j1 dG k sJ
t ‚ | j j d	 d  d
 dO ƒ }
 | j j dP ƒ } | d |
 j ƒ  d | g d t ƒ  d d ƒ } |	 ƒ  } | j d | ƒ | j# d2 j/ j3 dQ k sÜ
t ‚ | j# d2 j/ j4 dP k sû
t ‚ | j j d	 d  d
 dR ƒ }
 | j j dS ƒ } | d |
 j ƒ  d | g d t ƒ  d d ƒ } |	 ƒ  } | j d | ƒ |  j5 j6 dT ƒ s‰dU GHd  S|  j5 j7 dV dW dX t j8 j9 ƒ } | d  k	 r(| j j dY ƒ } | j: | dZ d[ ƒ}
 |
 j; j< } | d | d | g d t ƒ  d d d\ t! d- t! ƒ } |	 ƒ  } | j d | ƒ | j# d2 j= d] t! ƒ \ } } } d^ | k r{d_ | k r{d` | k s�t ‚ | j ƒ  } | d | j k s¦t ‚ t  | d ƒ d1 da g k sÈt ‚ t  | d ƒ db dc g k sêt ‚ t  | dd ƒ de df g k st ‚ t  | dg ƒ dh di g k s.t ‚ | d | d | g d% dj d% d t ƒ  ƒ } | d k skt ‚ | j> ƒ  } | j? ƒ  j# ƒ  d2 j@ ƒ  } | j? ƒ  jA | ƒ | d | d | g d% dj dN d t ƒ  ƒ } | d k sãt ‚ | d | d | g dj dN d t ƒ  ƒ } | d% k st ‚ y/ | d | d | g d3 dj dN d t ƒ  ƒ } Wn+ tB k
 rx} dk tC | ƒ k st ‚ n X| ‚ | d | d | g d3 dj dN dl t! d t ƒ  ƒ } | d k sÂt ‚ y/ | d | d | g d% dj d d t ƒ  ƒ } Wn+ tB k
 r} dm tC | ƒ k s%t ‚ n X| ‚ | d | d | g d% dj d dn t! d t ƒ  ƒ } | do k sht ‚ | j> ƒ  } | j? ƒ  j# ƒ  d2 j@ ƒ  } | j? ƒ  jA | ƒ y/ | d | d | g dN dj dN d t ƒ  ƒ } Wn+ tB k
 rÿ} dk tC | ƒ k st ‚ n X| ‚ | d | d | g dj d d t ƒ  ƒ } | d3 k s?t ‚ | j> ƒ  } | j? ƒ  j# ƒ  d2 j@ ƒ  } | j? ƒ  jA | ƒ | d | d | g dN dj dN d t ƒ  ƒ } | d% k s·t ‚ dp } tD | dq ƒ jE dr | j ƒ | ds | dt | dj d% d t ƒ  ƒ } z | d% k st ‚ Wd  t jF | ƒ Xn  d  S(w   Niÿÿÿÿs1   multiprocessing not available, skipping this testt   ntsB   easy_mp fixed_func not supported under Windows, skipping this test(   t
   validationt   get_sequence_n_copiest    get_sequence_n_copies_from_files(   t   file_reader(   t   Exception_expectedt   contains_linest   approx_equal(   t   StringIOt   source_infot   liness‘  ATOM      2  CA  ARG A  10      -6.299  36.344   7.806  1.00 55.20           C
ATOM     25  CA  TYR A  11      -3.391  33.962   7.211  1.00 40.56           C
ATOM     46  CA  ALA A  12      -0.693  34.802   4.693  1.00 67.95           C
ATOM     56  CA  ALA A  13       0.811  31.422   3.858  1.00 57.97           C
ATOM     66  CA  GLY A  14       4.466  31.094   2.905  1.00 49.24           C
ATOM     73  CA  ALA A  15       7.163  28.421   2.671  1.00 54.70           C
ATOM     83  CA  ILE A  16       6.554  24.685   2.957  1.00 51.79           C
ATOM    102  CA  LEU A  17       7.691  23.612   6.406  1.00 42.30           C
ATOM    121  CA  PTY A  18       7.292  19.882   5.861  1.00 36.68           C
ATOM    128  CA  PHE A  19       5.417  16.968   4.327  1.00 44.99           C
ATOM    148  CA  GLY A  20       3.466  14.289   6.150  1.00 41.99           C
ATOM    155  CA  GLY A  21       1.756  11.130   4.965  1.00 35.77           C
ATOM    190  CA  ALA A  24       1.294  19.658   3.683  1.00 47.02           C
ATOM    200  CA  VAL A  24A      2.361  22.009   6.464  1.00 37.13           C
ATOM    216  CA  HIS A  25       2.980  25.633   5.535  1.00 42.52           C
ATOM    234  CA  LEU A  26       4.518  28.425   7.577  1.00 47.63           C
ATOM    253  CA  ALA A  27       2.095  31.320   7.634  1.00 38.61           C
ATOM    263  CA  ARG A  28       1.589  34.719   9.165  1.00 37.04           C
ENDt   MTTPSHLSDRYELGEILGFGGMSEVHLARDt   pdb_hierarchyt	   sequencest   logt   nproci   t   outs¦     sequence identity: 76.47%
  13 residue(s) missing from PDB chain (9 at start, 1 at end)
  2 gap(s) in chain
  4 mismatches to sequence
    residue IDs:  12 13 15 24s$   _struct_ref.pdbx_seq_one_letter_codes'   _struct_ref_seq.pdbx_auth_seq_align_begt   10t   14t   16t   19t   24s'   _struct_ref_seq.pdbx_auth_seq_align_endt   11t   17t   21t   28s   _struct_ref_seq.db_align_begt   25s   _struct_ref_seq.db_align_endt   29s+   _struct_ref_seq.pdbx_seq_align_beg_ins_codei   t   At   MTTPSHLSDRYELGEILGFGGMSEVHLAs7     1 residues not found in sequence
    residue IDs:  28s   MTTPSHLSDRYELGEILGFGGMSEVHLA-t   27sø  ATOM      2  CA  ARG A  10      -6.299  36.344   7.806  1.00 55.20           C
ATOM     25  CA  TYR A  11      -3.391  33.962   7.211  1.00 40.56           C
ATOM     46  CA  ALA A  12      -0.693  34.802   4.693  1.00 67.95           C
ATOM     56  CA  ALA A  13       0.811  31.422   3.858  1.00 57.97           C
ATOM     66  CA  GLY A  14       4.466  31.094   2.905  1.00 49.24           C
ATOM     73  CA  ALA A  15       7.163  28.421   2.671  1.00 54.70           C
ATOM     83  CA  ILE A  16       6.554  24.685   2.957  1.00 51.79           C
ATOM    102  CA  LEU A  17       7.691  23.612   6.406  1.00 42.30           C
TER
ATOM   1936  P     G B   2     -22.947 -23.615  15.323  1.00123.20           P
ATOM   1959  P     C B   3     -26.398 -26.111  19.062  1.00110.06           P
ATOM   1979  P     U B   4     -29.512 -30.638  21.164  1.00101.06           P
ATOM   1999  P     C B   5     -30.524 -36.109  21.527  1.00 92.76           P
ATOM   2019  P     U B   6     -28.684 -41.458  21.223  1.00 87.42           P
ATOM   2062  P     G B   8     -18.396 -45.415  21.903  1.00 80.35           P
ATOM   2085  P     A B   9     -13.852 -43.272  24.156  1.00 77.76           P
ATOM   2107  P     G B  10      -8.285 -44.242  26.815  1.00 79.86           P
END
t
   AGCUUUGGAGt   extract_coordinatest   2t   6t   8t   4i    i   i   g“V-æ¿g-²�ï§fA@gƒÀÊ¡Å@i   gX9´Èv~@gžï§ÆKo?@g/Ý$A@i   s5     3 mismatches to sequence
    residue IDs:  12 13 15s›     sequence identity: 87.50%
  2 residue(s) missing from PDB chain (1 at start, 0 at end)
  1 gap(s) in chain
  1 mismatches to sequence
    residue IDs:  5t    se  ATOM  18932  P  B DG D   1     -12.183  60.531  25.090  0.50364.79           P
ATOM  18963  P  B DG D   2      -9.738  55.258  20.689  0.50278.77           P
ATOM  18994  P  B DA D   3     -10.119  47.855  19.481  0.50355.17           P
ATOM  19025  P  B DT D   4     -13.664  42.707  21.119  0.50237.06           P
ATOM  19056  P  B DG D   5     -19.510  39.821  21.770  0.50255.45           P
ATOM  19088  P  B DA D   6     -26.096  40.001  21.038  0.50437.49           P
ATOM  19120  P  B DC D   7     -31.790  41.189  18.413  0.50210.00           P
ATOM  19149  P  B DG D   8     -34.639  41.306  12.582  0.50313.99           P
ATOM  19179  P  B DA D   9     -34.987  38.244   6.813  0.50158.92           P
ATOM  19210  P  B DT D  10     -32.560  35.160   1.082  0.50181.38           P
HETATM19241  P  BTSP D  11     -27.614  30.137   0.455  0.50508.17           P
sî  >4GFH:A|PDBID|CHAIN|SEQUENCE
MSTEPVSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNAADNKVRDPS
MKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILET
ADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYLNGK
SLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYI
TDQIVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRM
FEIADANEENALKKSDGTRKSRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLN
VREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFI
TPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDL
AFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELK
VAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADD
PLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIE
PLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGF
YERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTV
TNKPRNAIIQELENLGFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTYEYLLGMR
IWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR
>4GFH:D|PDBID|CHAIN|SEQUENCE
GGATGACGATX
s?  ATOM      2  CA  GLY A   1       1.367   0.551   0.300  1.00  7.71           C
ATOM      6  CA  CYS A   2       2.782   3.785   1.683  1.00  5.18           C
ATOM     12  CA  CYS A   3      -0.375   5.128   3.282  1.00  5.21           C
ATOM     18  CA  SER A   4      -0.870   2.048   5.492  1.00  7.19           C
ATOM     25  CA  LEU A   5       2.786   2.056   6.642  1.00  6.78           C
ATOM     33  CA  PRO A   6       3.212   4.746   9.312  1.00  7.03           C
ATOM     40  CA  PRO A   7       6.870   5.690   8.552  1.00  7.97           C
ATOM     47  CA  CYS A   8       6.021   6.070   4.855  1.00  6.48           C
ATOM     53  CA  ALA A   9       2.812   8.041   5.452  1.00  7.15           C
ATOM     58  CA  LEU A  10       4.739  10.382   7.748  1.00  8.36           C
ATOM     66  CA  SER A  11       7.292  11.200   5.016  1.00  7.00           C
ATOM     73  CA  ASN A  12       4.649  11.435   2.264  1.00  5.40           C
ATOM     81  CA  PRO A  13       1.879  13.433   3.968  1.00  5.97           C
ATOM     88  CA  ASP A  14       0.485  15.371   0.986  1.00  7.70           C
ATOM     96  CA  TYR A  15       0.565  12.245  -1.180  1.00  6.55           C
ATOM    108  CA  CYS A  16      -1.466  10.260   1.363  1.00  7.32           C
ATOM    113  N   NH2 A  17      -2.612  12.308   2.058  1.00  8.11           N
t   GCCSLPPCALSNPDYCXi   sÚ  ATOM   2518  CA  PRO C   3      23.450  -5.848  45.723  1.00 85.24           C
ATOM   2525  CA  GLY C   4      20.066  -4.416  44.815  1.00 79.25           C
ATOM   2529  CA  PHE C   5      19.408  -0.913  46.032  1.00 77.13           C
ATOM   2540  CA  GLY C   6      17.384  -1.466  49.208  1.00 83.44           C
ATOM   2544  CA  GLN C   7      17.316  -5.259  49.606  1.00 89.25           C
ATOM   2553  CA  GLY C   8      19.061  -6.829  52.657  1.00 90.67           C
sð  >1JN5:A|PDBID|CHAIN|SEQUENCE
MASVDFKTYVDQACRAAEEFVNVYYTTMDKRRRLLSRLYMGTATLVWNGNAVSGQESLSEFFEMLPSSEFQISVVDCQPV
HDEATPSQTTVLVVICGSVKFEGNKQRDFNQNFILTAQASPSNTVWKIASDCFRFQDWAS
>1JN5:B|PDBID|CHAIN|SEQUENCE
APPCKGSYFGTENLKSLVLHFLQQYYAIYDSGDRQGLLDAYHDGACCSLSIPFIPQNPARSSLAEYFKDSRNVKKLKDPT
LRFRLLKHTRLNVVAFLNELPKTQHDVNSFVVDISAQTSTLLCFSVNGVFKEVDGKSRDSLRAFTRTFIAVPASNSGLCI
VNDELFVRNASSEEIQRAFAMPAPTPSSSPVPTLSPEQQEMLQAFSTQSGMNLEWSQKCLQDNNWDYTRSAQAFTHLKAK
GEIPEVAFMK
>1JN5:C|PDBID|CHAIN|SEQUENCE
GQSPGFGQGGSV
g      ð?t   iiimmmmmmiiisÚ  ATOM      2  CA  ALA A   2      -8.453  57.214 -12.754  1.00 52.95           C
ATOM      7  CA  LEU A   3      -8.574  59.274  -9.471  1.00 24.33           C
ATOM     15  CA  ARG A   4     -12.178  60.092  -8.575  1.00 28.40           C
ATOM     26  CA  GLY A   5     -14.170  61.485  -5.667  1.00 26.54           C
ATOM     30  CA  THR A   6     -17.784  60.743  -4.783  1.00 31.78           C
ATOM     37  CA  VAL A   7     -19.080  64.405  -4.464  1.00 21.31           C
t   XALRGTVt   immmmmmsÇ  ATOM   2171  CA  ASP I 355       5.591 -11.903   1.133  1.00 41.60           C
ATOM   2175  CA  PHE I 356       7.082  -8.454   0.828  1.00 39.82           C
ATOM   2186  CA  GLU I 357       5.814  -6.112  -1.877  1.00 41.12           C
ATOM   2195  CA  GLU I 358       8.623  -5.111  -4.219  1.00 42.70           C
ATOM   2199  CA  ILE I 359      10.346  -1.867  -3.363  1.00 43.32           C
ATOM   2207  CA  PRO I 360      11.658   0.659  -5.880  1.00 44.86           C
ATOM   2214  CA  GLU I 361      14.921  -0.125  -7.592  1.00 44.32           C
ATOM   2219  CA  GLU I 362      15.848   3.489  -6.866  1.00 44.27           C
HETATM 2224  CA  TYS I 363      16.482   2.005  -3.448  1.00 44.52           C
t   NGDFEEIPEEYLi   s´  ATOM    450  CA  ASN A   1      37.242  41.665  44.160  1.00 35.89           C
ATOM    458  CA  GLY A   2      37.796  38.269  42.523  1.00 30.13           C
HETATM  463  CA AMSE A   3      35.878  39.005  39.326  0.54 22.83           C
HETATM  464  CA BMSE A   3      35.892  39.018  39.323  0.46 22.96           C
ATOM    478  CA  ILE A   4      37.580  38.048  36.061  1.00 22.00           C
ATOM    486  CA  SER A   5      37.593  40.843  33.476  1.00 18.73           C
ATOM    819  CA  ALA A   8      25.982  34.781  27.220  1.00 18.43           C
ATOM    824  CA  ALA A   9      23.292  32.475  28.614  1.00 19.60           C
HETATM  830  CA BMSE A  10      22.793  30.814  25.223  0.41 22.60           C
HETATM  831  CA CMSE A  10      22.801  30.850  25.208  0.59 22.54           C
ATOM    845  CA  GLU A  11      26.504  30.054  24.966  1.00 25.19           C
ATOM    854  CA  GLY A  12      25.907  28.394  28.320  1.00 38.88           C
t   NGMISAAAAMEGt   NGMISXXAAMEGsd  ATOM   4615  CA  ALA C   1       1.000   1.000   1.000  1.00 10.00
ATOM   4622  CA  ALA C   2       1.000   1.000   1.000  1.00 10.00
ATOM   4627  CA  ALA C   3       1.000   1.000   1.000  1.00 10.00
ATOM   4634  CA  ALA C   4       1.000   1.000   1.000  1.00 10.00
ATOM   4646  CA  ALA C   5       1.000   1.000   1.000  1.00 10.00
ATOM   4658  CA  ALA C   6       1.000   1.000   1.000  1.00 10.00
ATOM   4664  CA  ALA C   7       1.000   1.000   1.000  1.00 10.00
ATOM   4669  CA  ALA C   8       1.000   1.000   1.000  1.00 10.00
ATOM   4680  CA  ARG C   9       1.000   1.000   1.000  1.00 10.00
ATOM   4690  CA  GLY C  10       1.000   1.000   1.000  1.00 10.00
ATOM   4698  CA  PRO C  11       1.000   1.000   1.000  1.00 10.00
ATOM   4705  CA  LYS C  12       1.000   1.000   1.000  1.00 10.00
ATOM   4712  CA  TRP C  13       1.000   1.000   1.000  1.00 10.00
ATOM   4726  CA  GLU C  14       1.000   1.000   1.000  1.00 10.00
ATOM   4738  CA  SER C  15       1.000   1.000   1.000  1.00 10.00
ATOM   4744  CA  THR C  16       1.000   1.000   1.000  1.00 10.00
ATOM   4751  CA  GLY C  17       1.000   1.000   1.000  1.00 10.00
ATOM   4755  CA  TYR C  18       1.000   1.000   1.000  1.00 10.00
ATOM   4767  CA  PHE C  19       1.000   1.000   1.000  1.00 10.00
ATOM   4778  CA  ALA C  20       1.000   1.000   1.000  1.00 10.00
ATOM   4786  CA  ALA C  21       1.000   1.000   1.000  1.00 10.00
ATOM   4798  CA  TRP C  22       1.000   1.000   1.000  1.00 10.00
ATOM   4812  CA  GLY C  23       1.000   1.000   1.000  1.00 10.00
ATOM   4816  CA  GLN C  24       1.000   1.000   1.000  1.00 10.00
ATOM   4822  CA  GLY C  25       1.000   1.000   1.000  1.00 10.00
ATOM   4826  CA  THR C  26       1.000   1.000   1.000  1.00 10.00
ATOM   4833  CA  LEU C  27       1.000   1.000   1.000  1.00 10.00
ATOM   4841  CA  VAL C  28       1.000   1.000   1.000  1.00 10.00
ATOM   4848  CA  THR C  29       1.000   1.000   1.000  1.00 10.00
ATOM   4855  CA  VAL C  30       1.000   1.000   1.000  1.00 10.00
ATOM   4862  CA  SER C  31       1.000   1.000   1.000  1.00 10.00
ATOM   4868  CA  SER C  32       1.000   1.000   1.000  1.00 10.00
END
tA   AAAAAAAARGKWESPAALLKKAAWCSGTLVTVSSASAPKWKSTSGCYFAAPWNKRALRVTVLQSSt   ksdssps/   Skipping advanced tests (require ksdssp module)t   relative_paths   phenix_regression/pdb/1ywf.pdbt   testt(  MGSSHHHHHHSSGLVPRGSHMAVRELPGAWNFRDVADTATALRPGRLFRSSELSRLDDAGRATLRRLGITDVADLRSSREVARRGPGRVPDGIDVHLLPFPDLADDDADDSAPHETAFKRLLTNDGSNGESGESSQSINDAATRYMTDEYRQFPTRNGAQRALHRVVTLLAAGRPVLTHCFAGKDRTGFVVALVLEAVGLDRDVIVADYLRSNDSVPQLRARISEMIQQRFDTELAPEVVTFTKARLSDGVLGVRAEYLAAARQTIDETYGSLGGYLRDAGISQATVNRMRGVLLGt
   force_typet   pdbt   include_secondary_structuret   include_sec_strt   HHHt   LLLs   ---t   117t   85t   275s   _struct_ref_seq.seq_align_begt   1t   114s   _struct_ref_seq.seq_align_endt   82t   272t   copies_from_xtriages   round numbert   force_accept_compositions	   less thant(   assume_xtriage_copies_from_sequence_fileg      à?s    tmp_mmtbx_validation_sequence.fat   ws   >1ywf
%st   pdb_filet   seq_file(   g“V-æ¿g-²�ï§fA@gƒÀÊ¡Å@(   gX9´Èv~@gžï§ÆKo?@g/Ý$A@(G   t   libtbx.utilst   utilst   detect_multiprocessing_problemt   Nonet   ost   namet   mmtbx.validation.sequenceR   R   R   t   iotbx.bioinformaticst	   iotbx.pdbt   iotbxR	   t   libtbx.load_envt   libtbx.test_utilsR
   R   R   t	   cStringIOR   R8   t   inputt   bioinformaticst   sequencet   lowert   construct_hierarchyR   t   showt   getvaluet   AssertionErrort   as_cif_blockt   listt   Truet   lent   chainst   get_outliers_tablet   get_table_datat'   get_mean_coordinate_for_alignment_ranget   get_highlighted_residuesR   t   dumpst   fasta_sequence_parset   parset	   n_missingt   n_missing_endt   n_missing_startt	   alignmentt   matchest   identityt   match_codest   at   bt   envt
   has_modulet   find_in_repositoriest   patht   isfilet   any_filet   file_objectt	   hierarchyt   get_alignmentt	   deep_copyt
   only_modelt   detached_copyt   append_chainR   t   strt   opent   writet   remove(   t   libtbxR   R   R   RS   R	   R
   R   R   R   t   pdb_int   seq1t   vR   t	   cif_blockt   seq2t   pdb_in2t   seq3t   st   seq4R   t   _t   seqRH   R{   t   aln1t   aln2t   sst   n_seqt   chain2RI   (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/regression/tst_sequence_validation.pyt   exercise   s€   					

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					
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!%(						(					(									
										"											"*""		t   __main__t   OK(   t
   __future__R    R…   R   R   RJ   R   R   RN   R–   t   __name__(    (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/regression/tst_sequence_validation.pyt   <module>   s   	ÿ û