ó
Î™xTc           @   sž   d  d l  m Z d  d l Z d  d l m Z d  d l Z d Z d Z	 d Z
 d Z d Z d	 „  Z d
 „  Z d „  Z e d k rš e ƒ  e ƒ  e ƒ  d GHn  d S(   iÿÿÿÿ(   t   divisionN(   t   approx_equalsŸ  CRYST1   72.240   72.010   86.990  90.00  90.00  90.00 P 21 21 21    4
ATOM      1  N   ASP L  -1      49.347 -62.804  60.380  1.00 34.60           N
ATOM      2  CA  ASP L  -1      47.975 -63.194  59.946  1.00 33.86           C
ATOM      3  C   ASP L  -1      47.122 -63.665  61.114  1.00 34.02           C
ATOM      4  O   ASP L  -1      47.573 -64.451  61.947  1.00 32.23           O
ATOM      9  N   VAL L  -2      45.889 -63.176  61.175  1.00 31.94           N
ATOM     10  CA  VAL L  -2      44.978 -63.576  62.233  1.00 29.81           C
ATOM     20  CB  GLN L   0      45.127 -68.170  63.455  1.00 29.74           C
ATOM     21  CG  GLN L   0      44.676 -69.611  63.591  1.00 39.72           C
ATOM     22  CD  GLN L   0      45.288 -70.292  64.807  1.00 51.31           C

ATOM     25  N   MET L   4      41.894 -68.026  62.256  1.00 24.27           N
ATOM     26  CA CMET L   4      40.497 -68.318  62.576  0.30 22.89           C
ATOM     27  C  CMET L   4      40.326 -69.824  62.795  0.30 21.48           C
ATOM     28  O  CMET L   4      40.633 -70.625  61.911  0.30 23.73           O

ATOM     25  N   TYR L   4      41.894 -68.026  62.256  1.00 24.27           N
ATOM     26  CA DTYR L   4      40.497 -68.318  62.576  0.70 22.89           C
ATOM     27  C  DTYR L   4      40.326 -69.824  62.795  0.70 21.48           C
ATOM     28  O  DTYR L   4      40.633 -70.625  61.911  0.70 23.73           O

ATOM    186  N   GLN L  27      43.266 -62.813  67.460  1.00 23.64           N
ATOM    187  CA  GLN L  27      43.289 -61.405  67.832  1.00 24.84           C
ATOM    197  C   SER L  27A     39.920 -58.676  67.377  1.00 22.05           C
ATOM    198  O   SER L  27A     40.712 -58.050  66.678  1.00 19.83           O

ATOM    202  CA  LEU L  27B     38.173 -58.446  65.720  1.00 20.41           C
ATOM    203  C   LEU L  27B     37.484 -57.089  65.854  1.00 21.13           C

ATOM    235  N   ASN L  28      36.659 -48.175  64.751  1.00 23.50           N
ATOM    236  CA  ASN L  28      35.418 -47.408  64.733  1.00 19.92           C
TER
ATOM   1702  N   GLY H   1      19.054 -57.059  39.111  1.00 41.20           N
ATOM   1703  CA  GLY H   1      20.002 -57.281  40.238  1.00 41.19           C
ATOM   1704  C   GLY H   1      21.452 -57.171  39.802  1.00 40.03           C

ATOM   1959  N   ASN H  35A     36.815 -57.860  44.928  1.00 15.79           N
ATOM   1960  CA  ASN H  35A     37.803 -58.882  45.265  1.00 16.70           C
ATOM   1967  N   TRP H  36      39.095 -60.772  44.593  1.00 17.23           N
ATOM   1968  CA  TRP H  36      39.440 -62.016  43.926  1.00 19.02           C
TER
ATOM   3383  O   HOH S 215      45.158 -61.466  59.209  1.00 21.71           O
ATOM   3384  O   HOH S 216      26.065 -71.512  48.872  1.00 18.56           O
ATOM   3385  O   HOH S 217      26.885 -90.624  56.632  0.92 16.47           O
ATOM   3386  O   HOH S 218      22.026 -89.723  46.422  1.04 19.34           O
TER
HETATM 3387  O   WAT L 219      33.576 -94.407  39.044  1.08 30.66
HETATM 3388  O   WAT L 220      39.377 -73.892  61.395  1.40 42.96
HETATM 3389  O  AWAT L 221      21.907 -98.365  40.731  0.40 16.45
HETATM 3390  O  BWAT L 221      28.591 -95.257  59.711  0.60 20.75
TER
ATOM   1001 AU   AU    500      14.333   3.856  26.301  1.00  7.97          Au
TER
ATOM   3342  N   VAL   226      20.817 -97.348  23.861  1.00 34.12           N
ATOM   3349  N   PRO   227      19.065-100.553  23.842  1.00 41.92           N
ATOM   3350  CA  PRO   227      19.109-101.900  24.416  1.00 46.30           C
ATOM   3351  C   PRO   227      20.202-102.722  23.753  1.00 50.65           C
ATOM   3356  N   ARG   228      20.811-103.620  24.514  1.00 56.77           N
TER
ATOM     25  N   MET X   4      41.894 -68.026  62.256  1.00 24.27           N
TER
ATOM   1001 AU   AU  K 502      11.333   3.856  26.301  1.00  7.97
ATOM   1001 AU   AU  K 100      14.333   0.856  26.301  1.00  7.97          Au
ATOM   1001 AU   AU  K 900      14.333   3.856  21.301  1.00  7.97          Au
END
sÈ  CRYST1   72.240   72.010   86.990  90.00  90.00  90.00 P 21 21 21    4
ATOM      1  N   ASP L  -1      49.347 -62.804  60.380  1.00 34.60           N
ATOM      2  CA  ASP L  -1      47.975 -63.194  59.946  1.00 33.86           C
ATOM      3  C   ASP L  -1      47.122 -63.665  61.114  1.00 34.02           C
ATOM      4  O   ASP L  -1      47.573 -64.451  61.947  1.00 32.23           O
ATOM      9  N   VAL L  -2      45.889 -63.176  61.175  1.00 31.94           N
ATOM     10  CA  VAL L  -2      44.978 -63.576  62.233  1.00 29.81           C
ATOM     20  CB  GLN L   0      45.127 -68.170  63.455  1.00 29.74           C
ATOM     21  CG  GLN L   0      44.676 -69.611  63.591  1.00 39.72           C
ATOM     22  CD  GLN L   0      45.288 -70.292  64.807  1.00 51.31           C

ATOM     25  N   MET L   4      41.894 -68.026  62.256  1.00 24.27           N
ATOM     26  CA CMET L   4      40.497 -68.318  62.576  0.30 22.89           C
ATOM     27  C  CMET L   4      40.326 -69.824  62.795  0.30 21.48           C
ATOM     28  O  CMET L   4      40.633 -70.625  61.911  0.30 23.73           O

ATOM     25  N   TYR L   4      41.894 -68.026  62.256  1.00 24.27           N
ATOM     26  CA DTYR L   4      40.497 -68.318  62.576  0.70 22.89           C
ATOM     27  C  DTYR L   4      40.326 -69.824  62.795  0.70 21.48           C
ATOM     28  O  DTYR L   4      40.633 -70.625  61.911  0.70 23.73           O

ATOM    186  N   GLN L  27      43.266 -62.813  67.460  1.00 23.64           N
ATOM    187  CA  GLN L  27      43.289 -61.405  67.832  1.00 24.84           C
ATOM    197  C   SER L  27A     39.920 -58.676  67.377  1.00 22.05           C
ATOM    198  O   SER L  27A     40.712 -58.050  66.678  1.00 19.83           O

ATOM    202  CA  LEU L  27B     38.173 -58.446  65.720  1.00 20.41           C
ATOM    203  C   LEU L  27B     37.484 -57.089  65.854  1.00 21.13           C

ATOM    235  N   ASN L  28      36.659 -48.175  64.751  1.00 23.50           N
ATOM    236  CA  ASN L  28      35.418 -47.408  64.733  1.00 19.92           C
TER
ATOM   1702  N   GLY H   1      19.054 -57.059  39.111  1.00 41.20           N
ATOM   1703  CA  GLY H   1      20.002 -57.281  40.238  1.00 41.19           C
ATOM   1704  C   GLY H   1      21.452 -57.171  39.802  1.00 40.03           C

ATOM   1959  N   ASN H  35A     36.815 -57.860  44.928  1.00 15.79           N
ATOM   1960  CA  ASN H  35A     37.803 -58.882  45.265  1.00 16.70           C
ATOM   1967  N   TRP H  36      39.095 -60.772  44.593  1.00 17.23           N
ATOM   1968  CA  TRP H  36      39.440 -62.016  43.926  1.00 19.02           C
TER
ATOM   3342  N   VAL   226      20.817 -97.348  23.861  1.00 34.12           N
ATOM   3349  N   PRO   227      19.065-100.553  23.842  1.00 41.92           N
ATOM   3350  CA  PRO   227      19.109-101.900  24.416  1.00 46.30           C
ATOM   3351  C   PRO   227      20.202-102.722  23.753  1.00 50.65           C
ATOM   3356  N   ARG   228      20.811-103.620  24.514  1.00 56.77           N
TER
END
sÎ  CRYST1   72.240   72.010   86.990  90.00  90.00  90.00 P 21 21 21    4
ATOM      1  O5'  DC A   1      29.670  19.013  -2.305  1.00 11.26           O
ATOM      2  C5'  DC A   1      30.109  19.727  -1.144  1.00  2.03           C
ATOM      3  C4'  DC A   1      30.024  19.014   0.202  1.00  4.76           C
ATOM      4  O4'  DC A   1      28.912  18.160   0.419  1.00  7.08           O
ATOM      5  C3'  DC A   1      31.204  18.275   0.705  1.00  9.25           C
ATOM      6  O3'  DC A   1      31.448  18.682   2.066  1.00 11.24           O
ATOM     20  P    DG A   2      32.339  20.004   2.406  1.00 11.95           P
ATOM     45  P    DC A   3      28.538  23.069   6.214  1.00 19.73           P
ATOM     46  OP1  DC A   3      29.232  24.056   7.091  1.00 19.15           O
ATOM     47  OP2  DC A   3      29.008  21.652   6.240  1.00 19.23           O
ATOM     48  O5'  DC A   3      26.905  23.120   6.436  1.00 16.82           O
TER
ATOM    139  O5'  DC B   7      13.405  26.346   3.336  1.00 15.19           O
ATOM    140  C5'  DC B   7      13.472  24.969   2.944  1.00  4.19           C
ATOM    158  P    DG B   8      11.130  21.728   3.702  1.00 12.13           P
ATOM    159  OP1  DG B   8      10.341  22.682   2.901  1.00 14.52           O
ATOM    186  O5'  DC B   9      16.676  16.828   1.638  1.00 13.48           O
ATOM    187  C5'  DC B   9      17.151  15.620   2.196  1.00  3.67           C
ATOM    188  C4'  DC B   9      17.855  15.745   3.510  1.00  2.48           C
TER
HETATM  277  O   HOH A  13      32.050  21.145   7.029  1.00 28.46           O
HETATM  278  O   HOH A  14      29.068  18.914   5.393  1.00 44.50           O
HETATM  279  O   HOH A  15      29.984  22.375  10.338  1.00 42.18           O
END
sá  CRYST1   72.240   72.010   86.990  90.00  90.00  90.00 P 21 21 21    4
ATOM      1  O5'  DC A   1      29.670  19.013  -2.305  1.00 11.26           O
ATOM      2  C5'  DC A   1      30.109  19.727  -1.144  1.00  2.03           C
ATOM      3  C4'  DC A   1      30.024  19.014   0.202  1.00  4.76           C
ATOM      4  O4'  DC A   1      28.912  18.160   0.419  1.00  7.08           O
ATOM      5  C3'  DC A   1      31.204  18.275   0.705  1.00  9.25           C
ATOM      6  O3'  DC A   1      31.448  18.682   2.066  1.00 11.24           O
ATOM     20  P    DG A   2      32.339  20.004   2.406  1.00 11.95           P
ATOM     45  P    DC A   3      28.538  23.069   6.214  1.00 19.73           P
ATOM     46  OP1  DC A   3      29.232  24.056   7.091  1.00 19.15           O
ATOM     47  OP2  DC A   3      29.008  21.652   6.240  1.00 19.23           O
ATOM     48  O5'  DC A   3      26.905  23.120   6.436  1.00 16.82           O
TER
ATOM    139  O5'  DC B   7      13.405  26.346   3.336  1.00 15.19           O
ATOM    140  C5'  DC B   7      13.472  24.969   2.944  1.00  4.19           C
ATOM    158  P    DG B   8      11.130  21.728   3.702  1.00 12.13           P
ATOM    159  OP1  DG B   8      10.341  22.682   2.901  1.00 14.52           O
ATOM    186  O5'  DC B   9      16.676  16.828   1.638  1.00 13.48           O
ATOM    187  C5'  DC B   9      17.151  15.620   2.196  1.00  3.67           C
ATOM    188  C4'  DC B   9      17.855  15.745   3.510  1.00  2.48           C
TER
END
sµ  CRYST1   72.240   72.010   86.990  90.00  90.00  90.00 P 21 21 21    4
ATOM      1  N   ASP L  -1      49.347 -62.804  60.380  1.00 34.60           N
ATOM      2  CA  ASP L  -1      47.975 -63.194  59.946  1.00 33.86           C
ATOM      3  C   ASP L  -1      47.122 -63.665  61.114  1.00 34.02           C
ATOM      4  O   ASP L  -1      47.573 -64.451  61.947  1.00 32.23           O
ATOM      9  N   VAL L  -2      45.889 -63.176  61.175  1.00 31.94           N
ATOM     10  CA  VAL L  -2      44.978 -63.576  62.233  1.00 29.81           C
ATOM     20  CB  GLN L   0      45.127 -68.170  63.455  1.00 29.74           C
ATOM     21  CG  GLN L   0      44.676 -69.611  63.591  1.00 39.72           C
ATOM     22  CD  GLN L   0      45.288 -70.292  64.807  1.00 51.31           C
ATOM     25  N   MET L   4      41.894 -68.026  62.256  1.00 24.27           N
ATOM     26  CA CMET L   4      40.497 -68.318  62.576  0.30 22.89           C
ATOM     27  C  CMET L   4      40.326 -69.824  62.795  0.30 21.48           C
ATOM     28  O  CMET L   4      40.633 -70.625  61.911  0.30 23.73           O
TER
HETATM 3387  O   WAT L 219      33.576 -94.407  39.044  1.08 30.66
HETATM 3388  O   WAT L 220      39.377 -73.892  61.395  1.40 42.96
HETATM 3389  O  AWAT L 221      21.907 -98.365  40.731  0.40 16.45
HETATM 3390  O  BWAT L 221      28.591 -95.257  59.711  0.60 20.75
TER
ATOM   1001 AU   AU  L 500      14.333   3.856  26.301  1.00  7.97          Au
TER
END
c          C   s<  t  j j d d  d t ƒ }  |  j ƒ  } | j ƒ  j ƒ  t j	 j
 j d | ƒ } d d d g } x  | D] } | | k se t ‚ qe Wt | ƒ d k s™ t ‚ | j ƒ  j d d	 j | ƒ ƒ } |  j ƒ  j d
 | ƒ } t  j j d d  d t ƒ j ƒ  } t | j d d ƒ j ƒ  j ƒ  | j d d ƒ j ƒ  j ƒ  ƒ s8t ‚ d  S(   Nt   source_infot   linest   pdb_hierarchys#   (chain 'L' and resid -1 through 28)s"   (chain 'H' and resid 1 through 36)s%   (chain ' ' and resid 226 through 228)i   t   strings    or t	   selectiont   d_mini   (   t   iotbxt   pdbt   inputt   Nonet	   m1_in_strt   construct_hierarchyt   atomst   reset_i_seqt   mmtbxt
   refinementt
   rigid_bodyt   rigid_groups_from_pdb_chainst   AssertionErrort   lent   atom_selection_cacheR   t   joint   xray_structure_simplet   selectt
   m1_out_strR   t   structure_factorst   f_calct   data(   t   pdb_inpR   t   sel_stringst   answert
   sel_stringR   t   xrs_1t   xrs_2(    (    sd   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_rigid_body_groups_from_pdb_chains.pyt   exercise_00Ì   s&    		c          C   s9  t  j j d d  d t ƒ }  |  j ƒ  } | j ƒ  j ƒ  t j	 j
 j d | ƒ } d d g } x  | D] } | | k sb t ‚ qb Wt | ƒ d k s– t ‚ | j ƒ  j d d j | ƒ ƒ } |  j ƒ  j d	 | ƒ } t  j j d d  d t ƒ j ƒ  } t | j d
 d ƒ j ƒ  j ƒ  | j d
 d ƒ j ƒ  j ƒ  ƒ s5t ‚ d  S(   NR   R   R   s!   (chain 'A' and resid 1 through 3)s!   (chain 'B' and resid 7 through 9)i   R   s    or R   R   (   R   R	   R
   R   t	   m2_in_strR   R   R   R   R   R   R   R   R   R   R   R   R   R   t
   m2_out_strR   R   R   R   (   R   R   R   R    R!   R   R"   R#   (    (    sd   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_rigid_body_groups_from_pdb_chains.pyt   exercise_01â   s$    		c          C   sn   t  j j d d  d t ƒ }  |  j ƒ  } | j ƒ  j ƒ  t j	 j
 j d | d t ƒ } | d g k sj t ‚ d  S(   NR   R   R   t   group_all_by_chains0   (chain 'L' and not (resname HOH or resname WAT))(   R   R	   R
   R   t	   m3_in_strR   R   R   R   R   R   R   t   TrueR   (   R   R   R   (    (    sd   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_rigid_body_groups_from_pdb_chains.pyt   exercise_02÷   s    	t   __main__t   OK(   t
   __future__R    t	   iotbx.pdbR   t   libtbx.test_utilsR   t   mmtbx.refinement.rigid_bodyR   R   R   R%   R&   R)   R$   R'   R+   t   __name__(    (    (    sd   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/refinement/tst_rigid_body_groups_from_pdb_chains.pyt   <module>   s    D3				