ó
¤™xTc           @   s°   d  d l  m Z d  d l m Z d  d l Z d  d l Z d  d l m	 Z	 d  d l
 m Z d  d l m Z d  d l m Z d „  Z d	 „  Z e d
 k r¬ e ƒ  e ƒ  d GHn  d S(   iÿÿÿÿ(   t   division(   t
   molprobityN(   t   flex(   t   approx_equal(   t   null_out(   t   StringIOc          C   sµ  d d l  m }  t j j j d |  j ƒ } | j j ƒ  } t | j	 d d ƒ j
 ƒ  ƒ } | j d d ƒ j ƒ  } | j d | ƒ } | j d t j | j ƒ  t ƒ ƒ } | j d | ƒ } | j d	 d
 ƒ } | j | d	 d ƒ| j ƒ  j d ƒ t d d ƒ j |  j ƒ d d d d d d g }	 t j d |	 d t d t ƒ  ƒ j }
 t ƒ  } |
 j d | ƒ | j d t j | j ƒ  t ƒ ƒ } | j d | ƒ } | j d	 d
 ƒ } | j | d	 d ƒt j d |	 d t d t ƒ  ƒ j }
 t ƒ  } |
 j d | ƒ | j } | j  ƒ  j! ƒ  } | j" | ƒ d | j# ƒ  d _$ d | j# ƒ  d _$ t d d ƒ j | j% ƒ  ƒ d d d d d g }	 t j d |	 d t d t ƒ  ƒ j }
 t ƒ  } |
 j d | ƒ t d d ƒ j |  j ƒ d d d d g }	 t j d |	 d t d t ƒ  ƒ j }
 t ƒ  } |
 j d t d | ƒ d | j& ƒ  k s8t' ‚ d d  d d g } t ƒ  } t j d | d t d t ƒ  ƒ j }
 |
 j d t d | ƒ d! | j& ƒ  k s±t' | j& ƒ  ƒ ‚ d  S("   Niÿÿÿÿ(   t   tst_build_alt_confst
   pdb_stringt   d_ming      ø?gš™™™™™ù?t   othert   datat   column_root_labelt   Ft
   FreeR_flags   tst_molprobity_1.mtzs   tst_molprobity_1.pdbt   ws
   --kinemages   --mapss   flags.clashscore=Falses   flags.xtriage=Truet   argst   ignore_missing_modulest   outt   1i    t   2i   s   tst_molprobity_multi_model.pdbs   tst_molprobity_misc1.pdbs   rotamer_library=500s   outliers_only=Falset   outliers_onlys0   A   7  TYR              m-85  91.83   299.6,92.0s   rotamer_library=8000s3      A   7  TYR              m-85  93.10   299.6,92.0((   t   mmtbx.regressionR   t   iotbxt   pdbt	   hierarchyt   inputt   pdb_rawt   xray_structure_simplet   abst   structure_factorst   f_calct   resolution_filtert   generate_r_free_flagst   lone_sett   arrayR   t   boolt   sizet   Truet   concatenatet   as_mtz_datasett   add_miller_arrayt
   mtz_objectt   writet   openR   t   runR   t
   validationR   t   showt   Falset
   only_modelt   detached_copyt   append_modelt   modelst   idt   as_pdb_stringt   getvaluet   AssertionError(   R   t   pdb_int   xrst   fct   flagst   lst   flags2t	   flags_allt   mtz_outR   t   resultR   R   t   model2t   args2(    (    sZ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/regression/tst_molprobity_1.pyt   exercise_synthetic   sŽ    $		$								c    	      C   s	  d }  d |  } t  d d ƒ j |  ƒ t  d d ƒ j | ƒ d d g } d d g } x® t | | t t g ƒ D]” \ } } } t j d | d	 g d
 t d t ƒ  ƒ j } t	 | j
 ƒ  | d d ƒsÇ t ‚ | rm t ƒ  } | j d | ƒ d | j ƒ  k st ‚ qm qm Wd  S(   NsC	  
ATOM   1270  N   LEU A 199       6.903  55.119  -0.416  1.00 25.48           N
ATOM   1271  CA  LEU A 199       7.726  56.192  -0.941  1.00 25.93           C
ATOM   1272  C   LEU A 199       6.996  56.972  -2.047  1.00 26.39           C
ATOM   1273  O   LEU A 199       7.020  58.180  -2.064  1.00 25.38           O
ATOM   1274  CB  LEU A 199       9.033  55.633  -1.490  1.00 25.66           C
ATOM   1278  N   ARG A 200       6.361  56.258  -2.980  1.00 27.31           N
ATOM   1279  CA  ARG A 200       5.576  56.913  -3.993  1.00 28.53           C
ATOM   1280  C   ARG A 200       4.520  57.823  -3.397  1.00 27.54           C
ATOM   1281  O   ARG A 200       4.397  58.949  -3.851  1.00 27.50           O
ATOM   1282  CB  ARG A 200       4.933  55.879  -4.899  1.00 30.38           C
ATOM   1289  N   ALA A 201       3.790  57.365  -2.357  1.00 26.90           N
ATOM   1290  CA  ALA A 201       2.764  58.200  -1.713  1.00 26.49           C
ATOM   1291  C   ALA A 201       3.406  59.407  -1.045  1.00 26.59           C
ATOM   1292  O   ALA A 201       2.866  60.516  -1.082  1.00 26.58           O
ATOM   1293  CB  ALA A 201       1.959  57.412  -0.715  1.00 25.11           C
ATOM   1294  N   ARG A 202       4.566  59.205  -0.419  1.00 25.66           N
ATOM   1295  CA  ARG A 202       5.245  60.296   0.240  1.00 26.93           C
ATOM   1296  C   ARG A 202       5.676  61.346  -0.767  1.00 26.93           C
ATOM   1297  O   ARG A 202       5.555  62.541  -0.489  1.00 25.79           O
ATOM   1298  CB  ARG A 202       6.493  59.779   0.996  1.00 28.25           C
ATOM   1305  N   ILE A 203       6.154  60.912  -1.931  1.00 26.99           N
ATOM   1306  CA  ILE A 203       6.611  61.848  -2.965  1.00 27.49           C
ATOM   1307  C   ILE A 203       5.430  62.674  -3.480  1.00 28.29           C
ATOM   1308  O   ILE A 203       5.548  63.905  -3.624  1.00 27.82           O
ATOM   1309  CB  ILE A 203       7.322  61.125  -4.075  1.00 28.09           C
ATOM   1313  N   SER A 204       4.288  62.025  -3.678  1.00 27.96           N
ATOM   1314  CA  SER A 204       3.119  62.736  -4.184  1.00 28.04           C
ATOM   1315  C   SER A 204       2.683  63.793  -3.199  1.00 28.16           C
ATOM   1316  O   SER A 204       2.311  64.910  -3.605  1.00 28.25           O
ATOM   1317  CB  SER A 204       1.962  61.780  -4.504  1.00 27.64           C
s+   REMARK   3    GEOSTD + MON.LIB. + CDL v1.2
s   tst_molprobity_cdl_1.pdbR   s   tst_molprobity_cdl_2.pdbgèÙ¬ú\mð?g¡ø1æ®%ì?R   s   flags.clashscore=FalseR   R   t   epsgü©ñÒMbP?s   conformation-dependent library(   R+   R*   t   zipR/   R%   R   R,   R   R-   R   t
   rms_anglesR7   R   R.   R6   (	   R   t	   pdb_raw_2t   filest   rmsdst	   file_namet   rmsdt   cdl_expectedR@   R   (    (    sZ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/regression/tst_molprobity_1.pyt   exercise_cdlc   s     
(!	t   __main__t   OK(   t
   __future__R    t   mmtbx.command_lineR   t   mmtbx.validation.molprobityt   mmtbxt   iotbx.pdb.hierarchyR   t   scitbx.array_familyR   t   libtbx.test_utilsR   t   libtbx.utilsR   t	   cStringIOR   RC   RM   t   __name__(    (    (    sZ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/regression/tst_molprobity_1.pyt   <module>   s   	W	2