ó
Á™xTc           @   sÉ   d  d l  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	 m
 Z
 d  d l Z d Z d	 d
 „ Z d „  Z d „  Z e d k rÅ e j j d ƒ s¶ d GHqÅ e ƒ  d GHn  d S(   iÿÿÿÿ(   t   division(   t   build_alt_confs(   t   fmodel(   t   rotalyze(   t   file_reader(   t   null_outNs“7  CRYST1   21.937    6.000   23.477  90.00 107.08  90.00 P 1 21 1
SCALE1      0.045585  0.000000  0.014006        0.00000
SCALE2      0.000000  0.166667  0.000000        0.00000
SCALE3      0.000000  0.000000  0.044560        0.00000
ATOM      1  N   GLY A   1      -9.047   4.634   6.066  1.00 16.37           N
ATOM      2  CA  GLY A   1      -9.040   4.191   4.677  1.00 16.17           C
ATOM      3  C   GLY A   1      -7.991   3.118   4.432  1.00 15.46           C
ATOM      4  O   GLY A   1      -7.507   2.493   5.371  1.00 16.71           O
ATOM      5  H1  GLY A   1      -9.744   5.171   6.203  1.00 16.37           H
ATOM      6  H2  GLY A   1      -9.108   3.927   6.603  1.00 16.37           H
ATOM      7  H3  GLY A   1      -8.294   5.075   6.240  1.00 16.37           H
ATOM      8  HA2 GLY A   1      -9.911   3.831   4.446  1.00 16.17           H
ATOM      9  HA3 GLY A   1      -8.853   4.945   4.096  1.00 16.17           H
ATOM     10  N  AASN A   2      -7.663   2.878   3.168  0.60 14.94           N
ATOM     11  CA AASN A   2      -6.533   2.012   2.845  0.60 14.28           C
ATOM     12  C  AASN A   2      -5.242   2.518   3.452  0.60 12.87           C
ATOM     13  O  AASN A   2      -5.000   3.723   3.505  0.60 12.55           O
ATOM     14  CB AASN A   2      -6.356   1.880   1.341  0.60 15.48           C
ATOM     15  CG AASN A   2      -7.500   1.158   0.693  0.60 13.90           C
ATOM     16  OD1AASN A   2      -8.052   1.622  -0.304  0.60 17.99           O
ATOM     17  ND2AASN A   2      -7.867   0.008   1.252  0.60 11.61           N
ATOM     18  H  AASN A   2      -8.073   3.200   2.484  0.60 15.11           H
ATOM     19  HA AASN A   2      -6.701   1.129   3.209  0.60 13.97           H
ATOM     20  HB2AASN A   2      -6.298   2.766   0.949  0.60 15.07           H
ATOM     21  HB3AASN A   2      -5.544   1.382   1.160  0.60 15.07           H
ATOM     22 HD21AASN A   2      -8.569  -0.402   0.970  0.60 11.52           H
ATOM     23 HD22AASN A   2      -7.404  -0.326   1.894  0.60 11.52           H
ATOM     24  N  BASN A   2      -7.626   2.899   3.175  0.40 15.11           N
ATOM     25  CA BASN A   2      -6.447   2.085   2.893  0.40 13.97           C
ATOM     26  C  BASN A   2      -5.209   2.731   3.488  0.40 13.04           C
ATOM     27  O  BASN A   2      -5.077   3.953   3.479  0.40 11.55           O
ATOM     28  CB BASN A   2      -6.250   1.906   1.394  0.40 15.07           C
ATOM     29  CG BASN A   2      -7.412   1.207   0.741  0.40 13.81           C
ATOM     30  OD1BASN A   2      -7.953   1.683  -0.257  0.40 17.17           O
ATOM     31  ND2BASN A   2      -7.805   0.067   1.298  0.40 11.52           N
ATOM     32  H  BASN A   2      -8.032   3.202   2.480  0.40 15.11           H
ATOM     33  HA BASN A   2      -6.556   1.209   3.295  0.40 13.97           H
ATOM     34  HB2BASN A   2      -6.153   2.778   0.981  0.40 15.07           H
ATOM     35  HB3BASN A   2      -5.454   1.374   1.240  0.40 15.07           H
ATOM     36 HD21BASN A   2      -8.484  -0.355   0.980  0.40 11.52           H
ATOM     37 HD22BASN A   2      -7.381  -0.249   1.976  0.40 11.52           H
ATOM     38  N  AASN A   3      -4.414   1.582   3.898  0.60 12.35           N
ATOM     39  CA AASN A   3      -3.182   1.908   4.599  0.60 11.68           C
ATOM     40  C  AASN A   3      -1.933   1.346   3.923  0.60 11.09           C
ATOM     41  O  AASN A   3      -1.858   0.142   3.653  0.60 10.18           O
ATOM     42  CB AASN A   3      -3.259   1.407   6.050  0.60 11.62           C
ATOM     43  CG AASN A   3      -2.011   1.746   6.852  0.60 13.00           C
ATOM     44  OD1AASN A   3      -1.704   2.921   7.070  0.60 15.44           O
ATOM     45  ND2AASN A   3      -1.287   0.720   7.295  0.60 12.87           N
ATOM     46  H  AASN A   3      -4.547   0.737   3.805  0.60 12.00           H
ATOM     47  HA AASN A   3      -3.078   2.871   4.634  0.60 11.53           H
ATOM     48  HB2AASN A   3      -4.019   1.821   6.488  0.60 12.90           H
ATOM     49  HB3AASN A   3      -3.362   0.442   6.047  0.60 12.90           H
ATOM     50 HD21AASN A   3      -0.573   0.863   7.753  0.60 12.97           H
ATOM     51 HD22AASN A   3      -1.533  -0.086   7.123  0.60 12.97           H
ATOM     52  N  BASN A   3      -4.310   1.908   4.015  0.40 12.00           N
ATOM     53  CA BASN A   3      -3.078   2.406   4.614  0.40 11.53           C
ATOM     54  C  BASN A   3      -1.844   1.661   4.111  0.40 11.70           C
ATOM     55  O  BASN A   3      -1.810   0.428   4.100  0.40 10.95           O
ATOM     56  CB BASN A   3      -3.152   2.335   6.142  0.40 12.90           C
ATOM     57  CG BASN A   3      -4.074   3.380   6.732  0.40 13.32           C
ATOM     58  OD1BASN A   3      -4.367   4.398   6.099  0.40 15.04           O
ATOM     59  ND2BASN A   3      -4.528   3.143   7.958  0.40 12.97           N
ATOM     60  H  BASN A   3      -4.390   1.052   4.038  0.40 12.00           H
ATOM     61  HA BASN A   3      -2.956   3.336   4.370  0.40 11.53           H
ATOM     62  HB2BASN A   3      -3.483   1.461   6.402  0.40 12.90           H
ATOM     63  HB3BASN A   3      -2.265   2.476   6.508  0.40 12.90           H
ATOM     64 HD21BASN A   3      -5.055   3.706   8.338  0.40 12.97           H
ATOM     65 HD22BASN A   3      -4.295   2.426   8.372  0.40 12.97           H
ATOM     66  N  AGLN A   4      -0.970   2.230   3.649  0.60 10.54           N
ATOM     67  CA AGLN A   4       0.385   1.832   3.248  0.60 10.42           C
ATOM     68  C  AGLN A   4       1.438   2.482   4.154  0.60 11.71           C
ATOM     69  O  AGLN A   4       1.592   3.742   4.128  0.60  8.92           O
ATOM     70  CB AGLN A   4       0.671   2.161   1.771  0.60  9.88           C
ATOM     71  CG AGLN A   4       1.921   1.446   1.228  0.60 10.02           C
ATOM     72  CD AGLN A   4       2.481   2.048  -0.057  0.60 12.86           C
ATOM     73  OE1AGLN A   4       2.716   3.260  -0.143  0.60 14.16           O
ATOM     74  NE2AGLN A   4       2.719   1.195  -1.059  0.60  9.04           N
ATOM     75  H  AGLN A   4      -1.078   3.082   3.689  0.60 10.83           H
ATOM     76  HA AGLN A   4       0.472   0.872   3.352  0.60 10.25           H
ATOM     77  HB2AGLN A   4      -0.088   1.885   1.234  0.60  9.74           H
ATOM     78  HB3AGLN A   4       0.810   3.117   1.682  0.60  9.74           H
ATOM     79  HG2AGLN A   4       2.620   1.485   1.899  0.60 10.05           H
ATOM     80  HG3AGLN A   4       1.694   0.521   1.045  0.60 10.05           H
ATOM     81 HE21AGLN A   4       2.557   0.357  -0.958  0.60  8.91           H
ATOM     82 HE22AGLN A   4       3.034   1.485  -1.805  0.60  8.91           H
ATOM     83  N  BGLN A   4      -0.835   2.425   3.699  0.40 10.83           N
ATOM     84  CA BGLN A   4       0.428   1.863   3.233  0.40 10.25           C
ATOM     85  C  BGLN A   4       1.600   2.421   4.037  0.40 10.29           C
ATOM     86  O  BGLN A   4       2.033   3.551   3.826  0.40 10.50           O
ATOM     87  CB BGLN A   4       0.633   2.137   1.738  0.40  9.74           C
ATOM     88  CG BGLN A   4       1.808   1.376   1.129  0.40 10.05           C
ATOM     89  CD BGLN A   4       2.359   2.037  -0.120  0.40 12.79           C
ATOM     90  OE1BGLN A   4       2.503   3.262  -0.175  0.40 15.08           O
ATOM     91  NE2BGLN A   4       2.674   1.228  -1.135  0.40  8.91           N
ATOM     92  H  BGLN A   4      -0.859   3.284   3.680  0.40 10.83           H
ATOM     93  HA BGLN A   4       0.422   0.902   3.357  0.40 10.25           H
ATOM     94  HB2BGLN A   4      -0.169   1.873   1.260  0.40  9.74           H
ATOM     95  HB3BGLN A   4       0.791   3.086   1.615  0.40  9.74           H
ATOM     96  HG2BGLN A   4       2.526   1.323   1.778  0.40 10.05           H
ATOM     97  HG3BGLN A   4       1.513   0.484   0.889  0.40 10.05           H
ATOM     98 HE21BGLN A   4       2.561   0.379  -1.059  0.40  8.91           H
ATOM     99 HE22BGLN A   4       2.990   1.556  -1.865  0.40  8.91           H
ATOM    100  N  AGLN A   5       2.125   1.651   4.991  0.60 10.59           N
ATOM    101  CA AGLN A   5       3.274   2.224   5.659  0.60 11.43           C
ATOM    102  C  AGLN A   5       4.582   1.732   5.073  0.60 11.24           C
ATOM    103  O  AGLN A   5       4.749   0.545   4.827  0.60 11.99           O
ATOM    104  CB AGLN A   5       3.229   2.076   7.170  0.60 12.07           C
ATOM    105  CG AGLN A   5       2.235   3.000   7.859  0.60 10.78           C
ATOM    106  CD AGLN A   5       1.562   2.322   9.034  0.60 12.94           C
ATOM    107  OE1AGLN A   5       1.005   1.233   8.899  0.60 10.72           O
ATOM    108  NE2AGLN A   5       1.621   2.959  10.197  0.60 12.32           N
ATOM    109  H  AGLN A   5       1.948   0.827   5.163  0.60 10.59           H
ATOM    110  HA AGLN A   5       3.279   3.179   5.509  0.60 11.43           H
ATOM    111  HB2AGLN A   5       2.987   1.162   7.384  0.60 12.07           H
ATOM    112  HB3AGLN A   5       4.109   2.273   7.527  0.60 12.07           H
ATOM    113  HG2AGLN A   5       2.702   3.784   8.188  0.60 10.78           H
ATOM    114  HG3AGLN A   5       1.548   3.260   7.225  0.60 10.78           H
ATOM    115 HE21AGLN A   5       2.025   3.716  10.253  0.60 12.32           H
ATOM    116 HE22AGLN A   5       1.255   2.615  10.895  0.60 12.32           H
ATOM    117  N  BGLN A   5       2.125   1.651   4.991  0.40 10.59           N
ATOM    118  CA BGLN A   5       3.274   2.224   5.659  0.40 11.43           C
ATOM    119  C  BGLN A   5       4.582   1.732   5.073  0.40 11.24           C
ATOM    120  O  BGLN A   5       4.749   0.545   4.827  0.40 11.99           O
ATOM    121  CB BGLN A   5       3.229   2.076   7.170  0.40 12.07           C
ATOM    122  CG BGLN A   5       2.235   3.000   7.859  0.40 10.78           C
ATOM    123  CD BGLN A   5       1.562   2.322   9.034  0.40 12.94           C
ATOM    124  OE1BGLN A   5       1.005   1.233   8.899  0.40 10.72           O
ATOM    125  NE2BGLN A   5       1.621   2.959  10.197  0.40 12.32           N
ATOM    126  H  BGLN A   5       1.863   0.873   5.246  0.40 10.59           H
ATOM    127  HA BGLN A   5       3.288   3.182   5.538  0.40 11.43           H
ATOM    128  HB2BGLN A   5       2.987   1.162   7.384  0.40 12.07           H
ATOM    129  HB3BGLN A   5       4.109   2.273   7.527  0.40 12.07           H
ATOM    130  HG2BGLN A   5       2.702   3.784   8.188  0.40 10.78           H
ATOM    131  HG3BGLN A   5       1.548   3.260   7.225  0.40 10.78           H
ATOM    132 HE21BGLN A   5       2.025   3.716  10.253  0.40 12.32           H
ATOM    133 HE22BGLN A   5       1.255   2.615  10.895  0.40 12.32           H
ATOM    134  N   ASN A   6       5.508   2.663   4.851  1.00 11.72           N
ATOM    135  CA  ASN A   6       6.825   2.322   4.325  1.00 12.12           C
ATOM    136  C   ASN A   6       7.854   2.763   5.330  1.00 13.15           C
ATOM    137  O   ASN A   6       8.221   3.937   5.380  1.00 13.93           O
ATOM    138  CB  ASN A   6       7.061   3.013   2.994  1.00 11.96           C
ATOM    139  CG  ASN A   6       5.963   2.732   2.005  1.00 12.58           C
ATOM    140  OD1 ASN A   6       5.799   1.604   1.549  1.00 14.01           O
ATOM    141  ND2 ASN A   6       5.192   3.751   1.679  1.00  9.96           N
ATOM    142  HA  ASN A   6       6.919   1.367   4.193  1.00 12.12           H
ATOM    143  HB2 ASN A   6       7.099   3.972   3.133  1.00 11.96           H
ATOM    144  HB3 ASN A   6       7.896   2.697   2.615  1.00 11.96           H
ATOM    145 HD21 ASN A   6       4.551   3.642   1.116  1.00  9.96           H
ATOM    146 HD22 ASN A   6       5.330   4.524   2.029  1.00  9.96           H
ATOM    147  H  AASN A   6       5.396   3.503   4.998  0.60 11.72           H
ATOM    148  H  BASN A   6       5.396   3.503   4.998  0.40 11.72           H
ATOM    149  N   TYR A   7       8.297   1.822   6.155  1.00 14.62           N
ATOM    150  CA  TYR A   7       9.162   2.146   7.291  1.00 15.04           C
ATOM    151  C   TYR A   7      10.611   2.329   6.888  1.00 15.56           C
ATOM    152  O   TYR A   7      11.046   1.810   5.854  1.00 15.52           O
ATOM    153  CB  TYR A   7       9.056   1.072   8.370  1.00 14.86           C
ATOM    154  CG  TYR A   7       7.657   0.941   8.898  1.00 14.38           C
ATOM    155  CD1 TYR A   7       6.767   0.030   8.334  1.00 15.46           C
ATOM    156  CD2 TYR A   7       7.206   1.753   9.930  1.00 14.37           C
ATOM    157  CE1 TYR A   7       5.476  -0.089   8.802  1.00 13.24           C
ATOM    158  CE2 TYR A   7       5.905   1.644  10.409  1.00 13.84           C
ATOM    159  CZ  TYR A   7       5.049   0.722   9.836  1.00 14.98           C
ATOM    160  OH  TYR A   7       3.767   0.593  10.299  1.00 14.28           O
ATOM    161  OXT TYR A   7      11.361   3.003   7.603  1.00 17.34           O
ATOM    162  H   TYR A   7       8.113   0.985   6.081  1.00 14.62           H
ATOM    163  HA  TYR A   7       8.860   2.981   7.681  1.00 15.04           H
ATOM    164  HB2 TYR A   7       9.319   0.217   7.995  1.00 14.86           H
ATOM    165  HB3 TYR A   7       9.638   1.306   9.110  1.00 14.86           H
ATOM    166  HD1 TYR A   7       7.053  -0.517   7.638  1.00 15.46           H
ATOM    167  HD2 TYR A   7       7.785   2.372  10.313  1.00 14.37           H
ATOM    168  HE1 TYR A   7       4.895  -0.708   8.422  1.00 13.24           H
ATOM    169  HE2 TYR A   7       5.614   2.185  11.107  1.00 13.84           H
ATOM    170  HH  TYR A   7       3.563   1.261  10.764  1.00 14.28           H
TER
HETATM  171  O   HOH S   8      -6.473   5.220   7.122  1.00 22.61           O
HETATM  172  O   HOH S   9      10.427   1.864   3.212  1.00 19.32           O
HETATM  173  O   HOH S  10     -11.288   1.762  -1.464  1.00 16.97           O
HETATM  174  O   HOH S  11      11.803   4.188   9.965  1.00 23.89           O
HETATM  175  O   HOH S  12      13.608   1.315   9.196  1.00 26.08           O
HETATM  176  O   HOH S  13      -2.736   3.452  10.015  1.00 38.68           O
HETATM  177  O   HOH S  14      -1.495   0.667  10.978  1.00 44.24           O
TER
END
t   tst_build_alt_confsc   
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 ƒ  } x° | j ƒ  j ƒ  D]œ } x“ | j ƒ  D]… } | j ƒ  } t | ƒ d k r« x. t | ƒ d k rÿ | j | d ƒ | d =qÒ Wx | j ƒ  D] }	 d |	 _ qWd | d _ q« q« Wq˜ W| j ƒ  j ƒ  j d ƒ sYt ‚ t  d |  d ƒ j | j d | ƒ ƒ d  S(   Ns	   %s_in.pdbt   ws   high_resolution=1.2s	   type=reals   label=Fs   add_sigmas=Trues   r_free_flags_fraction=0.1s   random_seed=12345s   output.file_name=%s.mtzt   argst   logi   iÿÿÿÿg      ð?t    i    s   %s_start.pdbt   crystal_symmetry(   t   opent   writet   pdb_rawR   t   runR   R   t   any_filet   file_objectt	   hierarchyt   xray_structure_simplet
   only_modelt   chainst   residue_groupst   atom_groupst   lent   remove_atom_groupt   atomst   occt   altloct   extract_occt   all_eqt   AssertionErrort   as_pdb_string(
   t   prefixt   pdb_inR   t   pdb_fileR   t   xrst   chaint   residue_groupR   t   atom(    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/regression/tst_build_alt_confs.pyt   prepare_inputsÈ   s6    
!c         C   s\   t  j |  ƒ } | j j } t j d | d t ƒ } g  | j D] } | j ƒ  | j f ^ q= S(   Nt   pdb_hierarchyt   outliers_only(	   R   R   R   R   R   t   Falset   resultst   id_strt   rotamer_name(   t	   file_nameR"   R   t   validatet   r(    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/regression/tst_build_alt_confs.pyt   get_rotamersç   s
    	c       	   C   so   t  ƒ  d d d d d d d d d	 g	 }  t j d
 |  d t ƒ  ƒ t d ƒ } t d ƒ } | | k sk t ‚ d  S(   Ns   tst_build_alt_confs_start.pdbs   tst_build_alt_confs.mtzs    selection='chain A and resseq 3's,   output.file_name=tst_build_alt_confs_out.pdbs   expected_occupancy=0.4s   window_size=2s   nproc=1s   rsr_fofc_map_target=Falses	   --verboseR   t   outs   tst_build_alt_confs_in.pdbs   tst_build_alt_confs_out.pdb(   R(   R   R   R   R2   R   (   R   t   rota_int   rota_out(    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/regression/tst_build_alt_confs.pyt   exerciseî   s    	t   __main__t   probes'   probe not available, skipping this testt   OK(   t
   __future__R    t   mmtbx.command_lineR   R   t   mmtbx.validationR   t   iotbxR   t   libtbx.utilsR   t   libtbx.load_envt   libtbxR   R(   R2   R6   t   __name__t   envt
   has_module(    (    (    sR   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/regression/tst_build_alt_confs.pyt   <module>   s   ¾		