ó
¥™xTc           @   s‡   d  d l  m Z d  d l m Z m Z d  d l Z d  d l m Z m	 Z	 d  d l
 m Z d  d l Z d „  Z e d k rƒ e ƒ  n  d S(   iÿÿÿÿ(   t   division(   t   approx_equalt	   show_diffN(   t   loadst   dumps(   t   StringIOc       	   C   s£  t  j j d d d t j j ƒ }  |  d  k r6 d GHd  Sd d l m } d d l	 m
 } | j d |  ƒ } | j j } | j d	 | d
 t ƒ } xt t g D]
} | rº t t | ƒ ƒ } n  | j t | j ƒ k oÝ d k n sè t ‚ g  | j D] } | j ƒ  ^ qò d d d d d d g k s(t ‚ t g  | j D] } | j ^ q5d d d d d d g ƒ sht ‚ t ƒ  } | j d | d t ƒ t | j ƒ  d ƒ s™ t ‚ q™ W| j d	 | d
 t ƒ } xÉ t t g D]» } | rít t | ƒ ƒ } n  x, | j D]! }	 t |	 j ƒ d k s÷t ‚ q÷W| j d k s1t ‚ t | j ƒ d k sLt ‚ t ƒ  } | j d | d t ƒ t | j ƒ  d ƒ sÌt ‚ qÌWd d l m }
 d d l	 m  } | j! d  d  d! d" ƒ j" ƒ  } | j! d  d  d! d# ƒ j" ƒ  } | j! d  d  d! d$ ƒ j" ƒ  } | j# ƒ  j$ ƒ  j% ƒ  } | j# ƒ  j$ ƒ  j% ƒ  } | j# ƒ  j$ ƒ  j% ƒ  } |
 | ƒ } |
 | ƒ } |
 | ƒ } g  | D]+ } t& g  | j' ƒ  D] } | ^ qŽƒ ^ qx} g  | D]+ } t& g  | j' ƒ  D] } | ^ qÆƒ ^ q°} g  | D]+ } t& g  | j' ƒ  D] } | ^ qþƒ ^ qè} | d% d& d' d( g d% d& d' d( g g k sIt ‚ | d% d& d' d( g d% d& d' d( g g k syt ‚ | d% d& d' d( g g k sšt ‚ d) GHd  S(*   Nt   relative_paths!   phenix_regression/pdb/pdb1jxt.entt   testsC   Skipping exercise_cbetadev(): input pdb (pdb1jxt.ent) not availableiÿÿÿÿ(   t   cbetadev(   t   file_readert	   file_namet   pdb_hierarchyt   outliers_onlyi   s    A   7 AILEs    A   8 BVALs    A   8 CVALs    A  30 BTHRs    A  39 BTHRs    A  43 BASPgÞsGh Ð?g¥ˆBíƒ~Ð?g¨¤-sä?g�Wu·ÿé?gùšbp‘í?gtðZêŒà?t   outt   verboses‡  pdb:alt:res:chainID:resnum:dev:dihedralNABB:Occ:ALT:
pdb :A:ile: A:   7 :  0.260: -46.47:   0.45:A:
pdb :B:val: A:   8 :  0.258:  80.92:   0.30:B:
pdb :C:val: A:   8 :  0.641: -53.98:   0.20:C:
pdb :B:thr: A:  30 :  0.812: -76.98:   0.30:B:
pdb :B:thr: A:  39 :  0.924:  56.41:   0.30:B:
pdb :B:asp: A:  43 :  0.500:   7.56:   0.25:B:
SUMMARY: 6 C-beta deviations >= 0.25 Angstrom (Goal: 0)
i   i3   sÊ	  pdb:alt:res:chainID:resnum:dev:dihedralNABB:Occ:ALT:
pdb : :thr: A:   1 :  0.102:  11.27:   1.00: :
pdb :A:thr: A:   2 :  0.022: -49.31:   0.67:A:
pdb : :cys: A:   3 :  0.038: 103.68:   1.00: :
pdb : :cys: A:   4 :  0.047:-120.73:   1.00: :
pdb : :pro: A:   5 :  0.069:-121.41:   1.00: :
pdb : :ser: A:   6 :  0.052: 112.87:   1.00: :
pdb :A:ile: A:   7 :  0.260: -46.47:   0.45:A:
pdb :B:ile: A:   7 :  0.153: 122.97:   0.55:B:
pdb :A:val: A:   8 :  0.184:-155.36:   0.50:A:
pdb :B:val: A:   8 :  0.258:  80.92:   0.30:B:
pdb :C:val: A:   8 :  0.641: -53.98:   0.20:C:
pdb : :ala: A:   9 :  0.061: -82.84:   1.00: :
pdb :A:arg: A:  10 :  0.023: 172.25:   1.00:A:
pdb : :ser: A:  11 :  0.028:-129.11:   1.00: :
pdb :A:asn: A:  12 :  0.021: -80.80:   0.50:A:
pdb :B:asn: A:  12 :  0.199:  50.01:   0.50:B:
pdb :A:phe: A:  13 :  0.067: -37.32:   0.65:A:
pdb :B:phe: A:  13 :  0.138:  19.24:   0.35:B:
pdb : :asn: A:  14 :  0.065: -96.35:   1.00: :
pdb : :val: A:  15 :  0.138: -96.63:   1.00: :
pdb : :cys: A:  16 :  0.102: -28.64:   1.00: :
pdb : :arg: A:  17 :  0.053:-106.79:   1.00: :
pdb : :leu: A:  18 :  0.053:-141.51:   1.00: :
pdb : :pro: A:  19 :  0.065:-146.95:   1.00: :
pdb : :thr: A:  21 :  0.086:  53.80:   1.00: :
pdb :A:pro: A:  22 :  0.092: -83.39:   0.55:A:
pdb :A:glu: A:  23 :  0.014:-179.53:   0.50:A:
pdb :B:glu: A:  23 :  0.050:-179.78:   0.50:B:
pdb : :ala: A:  24 :  0.056: -88.96:   1.00: :
pdb : :leu: A:  25 :  0.084:-106.42:   1.00: :
pdb : :cys: A:  26 :  0.074: -94.70:   1.00: :
pdb : :ala: A:  27 :  0.056: -62.15:   1.00: :
pdb : :thr: A:  28 :  0.056:-114.82:   1.00: :
pdb :A:tyr: A:  29 :  0.068:   0.22:   0.65:A:
pdb :A:thr: A:  30 :  0.180: 103.27:   0.70:A:
pdb :B:thr: A:  30 :  0.812: -76.98:   0.30:B:
pdb : :cys: A:  32 :  0.029: -84.07:   1.00: :
pdb : :ile: A:  33 :  0.048:-119.17:   1.00: :
pdb : :ile: A:  34 :  0.045:  99.02:   1.00: :
pdb : :ile: A:  35 :  0.052:-128.24:   1.00: :
pdb : :pro: A:  36 :  0.084:-142.29:   1.00: :
pdb : :ala: A:  38 :  0.039:  50.01:   1.00: :
pdb :A:thr: A:  39 :  0.093: -96.63:   0.70:A:
pdb :B:thr: A:  39 :  0.924:  56.41:   0.30:B:
pdb : :cys: A:  40 :  0.013:-144.11:   1.00: :
pdb : :pro: A:  41 :  0.039: -97.09:   1.00: :
pdb :A:asp: A:  43 :  0.130:-146.91:   0.75:A:
pdb :B:asp: A:  43 :  0.500:   7.56:   0.25:B:
pdb : :tyr: A:  44 :  0.085:-143.63:   1.00: :
pdb : :ala: A:  45 :  0.055:  33.32:   1.00: :
pdb : :asn: A:  46 :  0.066: -50.46:   1.00: :
SUMMARY: 6 C-beta deviations >= 0.25 Angstrom (Goal: 0)
(   t    extract_atoms_from_residue_group(   t   pdbt   source_infot   linessµ  ATOM   1185  N  ASER A 146      24.734  37.097  16.303  0.50 16.64           N
ATOM   1186  N  BSER A 146      24.758  37.100  16.337  0.50 16.79           N
ATOM   1187  CA ASER A 146      24.173  37.500  17.591  0.50 16.63           C
ATOM   1188  CA BSER A 146      24.237  37.427  17.662  0.50 16.87           C
ATOM   1189  C  ASER A 146      22.765  36.938  17.768  0.50 15.77           C
ATOM   1190  C  BSER A 146      22.792  36.945  17.783  0.50 15.94           C
ATOM   1191  O  ASER A 146      22.052  36.688  16.781  0.50 14.91           O
ATOM   1192  O  BSER A 146      22.091  36.741  16.779  0.50 15.17           O
ATOM   1193  CB ASER A 146      24.118  39.035  17.649  0.50 16.93           C
ATOM   1194  CB BSER A 146      24.321  38.940  17.904  0.50 17.48           C
ATOM   1195  OG ASER A 146      23.183  39.485  18.611  0.50 17.56           O
ATOM   1196  OG BSER A 146      23.468  39.645  17.028  0.50 18.32           O  sy  ATOM   1185  N   SER A 146      24.734  37.097  16.303  0.50 16.64           N
ATOM   1187  CA  SER A 146      24.173  37.500  17.591  0.50 16.63           C
ATOM   1189  C   SER A 146      22.765  36.938  17.768  0.50 15.77           C
ATOM   1191  O   SER A 146      22.052  36.688  16.781  0.50 14.91           O
ATOM   1193  CB ASER A 146      24.118  39.035  17.649  0.50 16.93           C
ATOM   1194  CB BSER A 146      24.321  38.940  17.904  0.50 17.48           C
ATOM   1195  OG ASER A 146      23.183  39.485  18.611  0.50 17.56           O
ATOM   1196  OG BSER A 146      23.468  39.645  17.028  0.50 18.32           O  s*  ATOM   1185  N   SER A 146      24.734  37.097  16.303  0.50 16.64           N
ATOM   1187  CA  SER A 146      24.173  37.500  17.591  0.50 16.63           C
ATOM   1189  C   SER A 146      22.765  36.938  17.768  0.50 15.77           C
ATOM   1191  O   SER A 146      22.052  36.688  16.781  0.50 14.91           O
ATOM   1193  CB  SER A 146      24.118  39.035  17.649  0.50 16.93           C
ATOM   1195  OG ASER A 146      23.183  39.485  18.611  0.50 17.56           O
ATOM   1196  OG BSER A 146      23.468  39.645  17.028  0.50 18.32           O  s    C  s    CA s    CB s    N  t   OK((   t   libtbxt   envt   find_in_repositoriest   ost   patht   isfilet   Nonet   mmtbx.validationR   t   iotbxR	   t   any_filet   file_objectt	   hierarchyt   Truet   FalseR   R   t
   n_outlierst   lent   resultst   AssertionErrort   id_strR   t	   deviationR   t   show_old_outputR   t   getvaluet   xyzt   mmtbx.validation.cbetadevR   R   t   inputt   construct_hierarchyt
   only_modelt
   only_chaint   only_residue_groupt   sortedt   keys(   t   regression_pdbR   R	   t   pdb_inR   t
   validationt   unpicklet   cbR   t   outlierR   R   t   pdb_1t   pdb_2t   pdb_3t   rg1t   rg2t   rg3t   all_relevant_atoms_1t   all_relevant_atoms_2t   all_relevant_atoms_3t   at   kt   keys_1t   keys_2t   keys_3(    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/regression/tst_cbetadev.pyt   exercise_cbetadev	   s|    		.		
			688800!t   __main__(   t
   __future__R    t   libtbx.test_utilsR   R   t   libtbx.load_envR   t   libtbx.easy_pickleR   R   t	   cStringIOR   t   os.pathR   RG   t   __name__(    (    (    sV   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/validation/regression/tst_cbetadev.pyt   <module>   s   	š