ó
D™xTc           @   s  d  d l  m Z d  d l m Z d  d l m Z d  d l Z d  d l m Z d  d l m	 Z	 d  d l
 m Z d  d l Z d  d l m Z m Z m Z d  d l Z d  d l Z d  d l Z d	 „  Z d
 Z d „  Z d „  Z d „  Z e d k re e j d ƒ n  d S(   iÿÿÿÿ(   t   division(   t   geometry_restraints(   t$   distance_and_repulsion_least_squaresN(   t   crystal(   t   flex(   t   StringIO(   t   approx_equalt	   show_difft   blocks_show_diffc         C   s‹	  t  j j d ƒ s d GHd  Sd d l m } t  j j d d d t j j ƒ } | d  k ra d GHd  S| j
 t | ƒ ƒ } | j d	 ƒ } | j ƒ  } |  r£ t j } n	 t ƒ  } t d
 | d d d d d d d | ƒ } t ƒ  } | j j d | ƒ |  rt j j | j ƒ  ƒ n  t | j ƒ  d d t d ƒ t d d ƒ g ƒsEt ‚ | j j ƒ  j } | j ƒ  d k sot ‚ | j j ƒ  j ƒ  }	 t ƒ  } | j j d |	 d | ƒ |  rÅt j j | j ƒ  ƒ n  t | j ƒ  d d t d ƒ t d d ƒ g ƒsüt ‚ t ƒ  } d  | j _ | j j d | ƒ |  rCt j j | j ƒ  ƒ n  t | j ƒ  d d t d ƒ t d  d! ƒ g ƒszt ‚ | j j ƒ  j ƒ  }	 t ƒ  } | j j d |	 d | ƒ |  rÐt j j | j ƒ  ƒ n  t | j ƒ  d" d t d# ƒ t d$ d ƒ g ƒst ‚ | j  j! ƒ  }
 | j j ƒ  } t ƒ  } | j" j# d% d& d' |
 d |	 d | ƒ |  rrt j j | j ƒ  ƒ n  t$ | j ƒ  j% ƒ  ƒ dQ k s–t ‚ | j ƒ  j% ƒ  d j& d) ƒ d* k  sÁt ‚ t ƒ  } | j" j# d% d& d' |
 d |	 d | d+ d, d- d. ƒ |  rt j j | j ƒ  ƒ n  t | j ƒ  j' d/ d0 ƒ d1 d t d ƒ t d2 d* ƒ g ƒs]t ‚ t ƒ  } | j" j# d% d3 d' |
 d |	 d | d+ d, d- d. ƒ |  r¶t j j | j ƒ  ƒ n  t | j ƒ  j' d/ d0 ƒ d4 d t d ƒ d g g ƒsót ‚ g  |	 D] } d5 | d6 ^ qú} t ƒ  } | j" j# d% d& d' |
 d | d | d+ d7 d- d. ƒ |  rmt j j | j ƒ  ƒ n  t | j ƒ  j' d/ d0 ƒ d8 d t d ƒ t d2 d* ƒ g ƒs°t ‚ t ƒ  } | j" j# d% d& d' |
 d | d+ d9 d- d. ƒ |  rt j j | j ƒ  ƒ n  t | j ƒ  j' d/ d0 ƒ d: d t d ƒ t d2 d* ƒ g ƒsFt ‚ t ƒ  } | j" j# d% d& d' |
 d | d+ d; d- d< ƒ |  r™t j j | j ƒ  ƒ n  t | j ƒ  j' d/ d0 ƒ d= ƒ sÁt ‚ t ƒ  } | j" j# d% d& d' |
 d | d+ d> d- d* ƒ |  rt j j | j ƒ  ƒ n  t | j ƒ  d? ƒ s0t ‚ | j! ƒ  }
 g  | j ƒ  D] } | j( ^ qI}	 | j) d@ d ƒ } xd* d# g D]} t* j+ dA | d | j, ƒ  dB t- dC | ƒ } t. j/ dA | ƒ } x; | j0 ƒ  süt. j1 dD | j2 ƒ  dE d ƒ } | j3 | ƒ qÂWt ƒ  } | j# d% d3 d' |
 d |	 d | d+ dF ƒ |  rMt j j | j ƒ  ƒ n  t | j ƒ  dG d t d ƒ t dH dI ƒ t dJ d ƒ g ƒs�t ‚ t ƒ  } | j# d% d3 d' |
 d | d+ dK d- d# ƒ |  ràt j j | j ƒ  ƒ n  t | j ƒ  dL d t d ƒ t dM d* ƒ g ƒs	t ‚ t ƒ  } | j# d% d3 d' |
 d | d+ dN d- d* ƒ |  rg	t j j | j ƒ  ƒ n  t | j ƒ  dO ƒ s}t ‚ q}Wd  S(R   Nt   iotbxs5   Skipping exercise_with_zeolite(): iotbx not availableiÿÿÿÿ(   t   strudatt   relative_paths,   phenix_regression/misc/strudat_zeolite_atlast   tests:   Skipping exercise_with_zeolite(): input file not availablet   YUGt   si_structuret   distance_cutoffg      @t!   nonbonded_repulsion_function_typet   prolsqt   n_macro_cyclesi   t   outt   fs¾   bond simple: (0, 1)
  distance_model: 3.22437
  distance_ideal: 3.07097
  weight: 0.2308
...
bond asu: (0, 0) -x+1,y,-z+1
  distance_model: 3.4233
  distance_ideal: 3.07097
  weight: 0.2308
t
   selectionsi   i   i   i2   t   site_labelssÖ   bond simple: (0, 1)
  SI1
  SI2
  distance_model: 3.22437
  distance_ideal: 3.07097
  weight: 0.2308
...
bond asu: (0, 0)
  SI1
  SI1 -x+1,y,-z+1
  distance_model: 3.4233
  distance_ideal: 3.07097
  weight: 0.2308
i   i   i$   s‹   bond simple: (0, 1)
  distance_ideal: 3.07097
  weight: 0.2308
...
bond asu: (0, 0) -x+1,y,-z+1
  distance_ideal: 3.07097
  weight: 0.2308
i   i   i   s£   bond simple: (0, 1)
  SI1
  SI2
  distance_ideal: 3.07097
  weight: 0.2308
...
bond asu: (0, 0)
  SI1
  SI1 -x+1,y,-z+1
  distance_ideal: 3.07097
  weight: 0.2308
i   i   t   by_valuet   residualt
   sites_carti0   t	   remainingi    t   prefixs   0^t	   max_itemsi   s   e-00s   e-0s`  0^Bond restraints: 48
0^Sorted by residual:
0^bond O3
0^     O4
0^  ideal  model  delta    sigma   weight residual
0^  2.629  2.120  0.509 1.56e+00 4.10e-01 1.06e-01
...
0^bond SI1
0^     SI1
0^  ideal  model  delta    sigma   weight residual sym.op.
0^  3.071  3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
0^... (remaining 20 not shown)
iûÿÿÿt   deltasÆ   0^Bond restraints: 48
0^Sorted by delta:
0^bond O3
0^     O4
0^  ideal  model  delta    sigma   weight residual
0^  2.629  2.120  0.509 1.56e+00 4.10e-01 1.06e-01
...
0^... (remaining 20 not shown)
t   abct   defs   ^0sx  ^0Bond restraints: 48
^0Sorted by residual:
^0bond abcO3def
^0     abcO4def
^0  ideal  model  delta    sigma   weight residual
^0  2.629  2.120  0.509 1.56e+00 4.10e-01 1.06e-01
...
^0bond abcSI1def
^0     abcSI1def
^0  ideal  model  delta    sigma   weight residual sym.op.
^0  3.071  3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
^0... (remaining 20 not shown)
s   .=sZ  .=Bond restraints: 48
.=Sorted by residual:
.=bond 4
.=     5
.=  ideal  model  delta    sigma   weight residual
.=  2.629  2.120  0.509 1.56e+00 4.10e-01 1.06e-01
...
.=bond 0
.=     0
.=  ideal  model  delta    sigma   weight residual sym.op.
.=  3.071  3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
.=... (remaining 20 not shown)
s   -+i   sÃ   -+Bond restraints: 48
-+Sorted by residual:
-+bond 4
-+     5
-+  ideal  model  delta    sigma   weight residual
-+  2.629  2.120  0.509 1.56e+00 4.10e-01 1.06e-01
-+... (remaining 47 not shown)
s   =+s   =+Bond restraints: 48
t   buffer_thicknesst   asu_mappingst   minimalt   min_cubicle_edget   pairt   vdw_distances   d%sñ   d%Nonbonded interactions: 7
d%Sorted by model distance:
...
d%nonbonded SI2
d%          SI2
d%   model   vdw sym.op.
d%   3.092 3.000 -x+1,y,-z
...
d%nonbonded SI1
d%          SI1
d%   model   vdw sym.op.
d%   3.216 3.000 -x+1/2,-y+1/2,-z+1
i
   i   i   s   *jsê   *jNonbonded interactions: 7
*jSorted by model distance:
...
*jnonbonded 0
*j          1
*j   model   vdw
*j   3.107 3.000
*jnonbonded 0
*j          0
*j   model   vdw sym.op.
*j   3.130 3.000 -x+1,y,-z+1
*j... (remaining 2 not shown)
i÷ÿÿÿs   @rs   @rNonbonded interactions: 7
iÀ   iÂ   (4   t   libtbxt   envt
   has_modulet   iotbx.kriberR
   t   find_in_repositoriest   ost   patht   isfilet   Nonet   read_all_entriest   opent   gett   as_xray_structuret   syst   stdoutR   R   t   geometry_restraints_managert   show_interactionst   writet   getvalueR   t   ranget   AssertionErrort   pair_proxiest   nonbonded_proxiest   n_totalt   minimized_structuret
   scattererst   extract_labelst!   _sites_cart_used_for_pair_proxiest   start_structureR   t   bond_proxiest   show_sortedt   lent
   splitlinest   findt   replacet   labelR!   R   t   neighbors_fast_pair_generatorR    t   FalseR   t   nonbonded_sorted_asu_proxiest   at_endt   nonbonded_asu_proxyt   nextt   process(   t   verboseR
   t
   atlas_filet   strudat_contentst   strudat_entryR   R   t   drlst   nbpR   R   R;   RI   t   site_labels_longt   scR!   R#   t   pair_generatort   sorted_asu_proxiest   p(    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/regression/tst_geometry_restraints_2.pyt   exercise_with_zeolite   s„   			
%	%	%	%	$+	%		!	%	%		"								1		%		s  CRYST1   10.851   13.095   21.192  90.00  90.00  90.00 P 21 21 21
ATOM      1  CA  TYR A   1       8.787   2.175   5.487  1.00  0.91           C
ATOM      2  CB  TYR A   1       8.968   2.012   6.998  1.00  1.05           C
ATOM      3  CG  TYR A   1       9.527   0.669   7.410  1.00  1.04           C
ATOM      4  CD2 TYR A   1       8.768  -0.222   8.157  1.00  1.37           C
ATOM      5  CE2 TYR A   1       9.275  -1.449   8.537  1.00  1.50           C
ATOM      6  CZ  TYR A   1      10.559  -1.798   8.175  1.00  1.15           C
ATOM      7  CE1 TYR A   1      11.334  -0.929   7.437  1.00  1.37           C
ATOM      8  CD1 TYR A   1      10.818   0.296   7.062  1.00  1.34           C
ATOM      9  C   TYR A   1       7.767   1.172   4.959  1.00  0.85           C
ATOM     10  OH  TYR A   1      11.069  -3.019   8.553  1.00  1.40           O
ATOM     11  O   TYR A   1       6.576   1.472   4.870  1.00  1.01           O
ATOM     12  N   TYR A   1       8.388   3.541   5.166  1.00  1.11           N
ATOM     13  CA  GLY A   2       7.387  -1.050   4.044  1.00  1.14           C
ATOM     14  C   GLY A   2       6.345  -1.569   5.016  1.00  0.97           C
ATOM     15  O   GLY A   2       5.234  -1.918   4.619  1.00  1.15           O
ATOM     16  N   GLY A   2       8.241  -0.020   4.608  1.00  0.93           N
ATOM     17  CA  GLY A   3       5.804  -2.100   7.324  1.00  1.36           C
ATOM     18  C   GLY A   3       4.651  -1.149   7.578  1.00  1.01           C
ATOM     19  O   GLY A   3       3.598  -1.553   8.071  1.00  1.38           O
ATOM     20  N   GLY A   3       6.706  -1.622   6.294  1.00  1.11           N
ATOM     21  CA  PHE A   4       3.819   1.134   7.419  1.00  0.89           C
ATOM     22  CB  PHE A   4       4.397   2.380   8.094  1.00  1.13           C
ATOM     23  CG  PHE A   4       4.930   2.130   9.475  1.00  1.00           C
ATOM     24  CD1 PHE A   4       6.267   1.825   9.673  1.00  1.51           C
ATOM     25  CE1 PHE A   4       6.760   1.595  10.943  1.00  1.80           C
ATOM     26  CZ  PHE A   4       5.916   1.667  12.033  1.00  1.59           C
ATOM     27  CE2 PHE A   4       4.582   1.970  11.850  1.00  1.49           C
ATOM     28  CD2 PHE A   4       4.095   2.199  10.577  1.00  1.24           C
ATOM     29  C   PHE A   4       3.185   1.509   6.084  1.00  0.94           C
ATOM     30  N   PHE A   4       4.852   0.121   7.242  1.00  0.88           N
ATOM     31  O   PHE A   4       2.361   2.421   6.010  1.00  1.47           O
ATOM     32  CA  LEU A   5       3.055   1.059   3.693  1.00  0.87           C
ATOM     33  CB  LEU A   5       3.965   0.435   2.634  1.00  1.13           C
ATOM     34  CG  LEU A   5       3.531   0.603   1.177  1.00  1.16           C
ATOM     35  CD1 LEU A   5       3.411   2.076   0.818  1.00  1.88           C
ATOM     36  CD2 LEU A   5       4.502  -0.103   0.245  1.00  1.67           C
ATOM     37  C   LEU A   5       1.634   0.527   3.541  1.00  0.87           C
ATOM     38  N   LEU A   5       3.576   0.800   5.030  1.00  0.92           N
ATOM     39  OXT LEU A   5       1.246  -0.440   4.196  1.00  1.23           O
ATOM     41  O   HOH B   1      14.655  -4.248   8.995  1.00  1.51           O
ATOM     81  H1  HOH B   1      14.954  -3.400   8.664  1.00  1.13           H
ATOM     82  H2  HOH B   1      13.712  -4.246   8.805  1.00  0.76           H
ATOM     42  O   HOH B   2      12.055  -3.540   8.243  1.00  1.81           O
ATOM     83  H1  HOH B   2      11.456  -4.167   7.841  1.00  0.96           H
ATOM     84  H2  HOH B   2      11.476  -3.010   8.803  1.00  1.17           H
ATOM     43  O   HOH B   3       9.622  -2.103   5.551  1.00  2.24           O
ATOM     85  H1  HOH B   3      10.394  -1.650   5.193  1.00  1.02           H
ATOM     86  H2  HOH B   3       9.588  -2.843   4.937  1.00  1.29           H
END
c         C   sý  t  j j d d ƒ s" d Gd GHd  St  j j d d ƒ d  k rF d GHd  Sd d	 l m } |  rh t j } n	 t	 ƒ  } t
 d
 d ƒ j t ƒ | j d d
 g d t d | ƒ } | j ƒ  } | j ƒ  j ƒ  j ƒ  } t	 ƒ  } | j d | ƒ |  rt j j | j ƒ  ƒ n  t | j ƒ  d ƒ s t ‚ t	 ƒ  } | j d | d | ƒ |  r^t j j | j ƒ  ƒ n  t | j ƒ  d ƒ szt ‚ t t j | j ƒ  ƒ d ƒ sžt ‚ d  | _ t	 ƒ  } | j d | ƒ |  rßt j j | j ƒ  ƒ n  t | j ƒ  d ƒ sût ‚ t	 ƒ  } | j d | d | ƒ |  r9t j j | j ƒ  ƒ n  t | j ƒ  d ƒ sUt ‚ | j ƒ  } t | ƒ d k syt ‚ | d  dE dF dG dH g k s›t ‚ | d dI dJ dK dL g k s½t ‚ d# | j d$ d% _ d& | j d' d( _ | j ƒ  } t  t! | ƒ t! | ƒ ƒ dM dN g k st ‚ | j d) d* ƒ } t  t! | ƒ t! | ƒ ƒ dO g k s\t ‚ | j" d+ dP ƒ } | j# j$ ƒ  j% ƒ  d k s�t ‚ | j& d. d, ƒ }	 t  g  |	 D] }
 t' t  |
 ƒ ƒ ^ q«ƒ dQ dR dS dT dU dV dW dX dY dZ d[ g k sùt ‚ d  S(\   Nt   namet   mmtbxs   Skipping exercise_with_pdb():s6   mmtbx.monomer_library.pdb_interpretation not availableR   t	   chem_datas?   Skipping exercise_with_pdb(): chem_data directory not availableiÿÿÿÿ(   t   pdb_interpretations!   tmp_cctbx_geometry_restraints.pdbt   wt   argst   strict_conflict_handlingt   logR   sÄ  bond simple: (0, 1)
  distance_model: 1.53051
  distance_ideal: 1.53
  weight: 2500
...
angle: (1, 0, 8)
  angle_model: 110.543
  angle_ideal: 110.1
  weight: 0.277008
...
dihedral: (2, 0, 1, 11)
  angle_model: 173.684
  angle_ideal: -180
  weight: 0.00444444
  periodicity: 3
...
chirality: (0, 1, 8, 11)
  volume_model: -2.50215
  volume_ideal: -2.50318
  both_signs: 0
  weight: 25
...
planarity: (0, 8, 10, 15)
  delta: -0.00012, weight: 2500
  delta:  0.00042, weight: 2500
  delta: -0.00016, weight: 2500
  delta: -0.00014, weight: 2500
...
nonbonded asu: (36, 46) -x+1,y+1/2,-z+1/2
  distance_model: 4.89425
  vdw_distance: 2.8
nonbonded simple: (0, 23)
  distance_model: 4.89852
  vdw_distance: 3.77
R   sÃ  bond simple: (0, 1)
  pdb=" CA  TYR A   1 "
  pdb=" CB  TYR A   1 "
  distance_model: 1.53051
  distance_ideal: 1.53
  weight: 2500
bond simple: (0, 8)
...
angle: (1, 0, 8)
  pdb=" CB  TYR A   1 "
  pdb=" CA  TYR A   1 "
  pdb=" C   TYR A   1 "
  angle_model: 110.543
  angle_ideal: 110.1
  weight: 0.277008
...
dihedral: (2, 0, 1, 11)
  pdb=" CG  TYR A   1 "
  pdb=" CA  TYR A   1 "
  pdb=" CB  TYR A   1 "
  pdb=" N   TYR A   1 "
  angle_model: 173.684
  angle_ideal: -180
  weight: 0.00444444
  periodicity: 3
...
chirality: (0, 1, 8, 11)
  pdb=" CA  TYR A   1 "
  pdb=" CB  TYR A   1 "
  pdb=" C   TYR A   1 "
  pdb=" N   TYR A   1 "
  volume_model: -2.50215
  volume_ideal: -2.50318
  both_signs: 0
  weight: 25
...
planarity: (0, 8, 10, 15)
  pdb=" CA  TYR A   1 " delta: -0.00012, weight: 2500
  pdb=" C   TYR A   1 " delta:  0.00042, weight: 2500
  pdb=" O   TYR A   1 " delta: -0.00016, weight: 2500
  pdb=" N   GLY A   2 " delta: -0.00014, weight: 2500
gø�Kw2“Þ?s¸  bond simple: (0, 1)
  distance_ideal: 1.53
  weight: 2500
...
angle: (1, 0, 8)
  angle_ideal: 110.1
  weight: 0.277008
...
dihedral: (2, 0, 1, 11)
  angle_ideal: -180
  weight: 0.00444444
  periodicity: 3
...
chirality: (0, 1, 8, 11)
  volume_ideal: -2.50318
  both_signs: 0
  weight: 25
...
planarity: (0, 8, 10, 15)
  weight: 2500
...
nonbonded simple: (5, 39)
  vdw_distance: 3.26
...
nonbonded asu: (7, 29) x+1,y,z
  vdw_distance: 3.42
sÕ  bond simple: (0, 1)
  pdb=" CA  TYR A   1 "
  pdb=" CB  TYR A   1 "
  distance_ideal: 1.53
  weight: 2500
...
angle: (1, 0, 8)
  pdb=" CB  TYR A   1 "
  pdb=" CA  TYR A   1 "
  pdb=" C   TYR A   1 "
  angle_ideal: 110.1
  weight: 0.277008
...
dihedral: (2, 0, 1, 11)
  pdb=" CG  TYR A   1 "
  pdb=" CA  TYR A   1 "
  pdb=" CB  TYR A   1 "
  pdb=" N   TYR A   1 "
  angle_ideal: -180
  weight: 0.00444444
  periodicity: 3
...
chirality: (0, 1, 8, 11)
  pdb=" CA  TYR A   1 "
  pdb=" CB  TYR A   1 "
  pdb=" C   TYR A   1 "
  pdb=" N   TYR A   1 "
  volume_ideal: -2.50318
  both_signs: 0
  weight: 25
...
planarity: (0, 8, 10, 15)
  pdb=" CA  TYR A   1 " weight: 2500
  pdb=" C   TYR A   1 " weight: 2500
  pdb=" O   TYR A   1 " weight: 2500
  pdb=" N   GLY A   2 " weight: 2500
...
nonbonded simple: (5, 39)
  pdb=" CZ  TYR A   1 "
  pdb=" O   HOH B   1 "
  vdw_distance: 3.26
...
nonbonded asu: (7, 29)
  pdb=" CD1 TYR A   1 "
  pdb=" N   PHE A   4 " x+1,y,z
  vdw_distance: 3.42
i.   i   i    i   i   i   i   iüÿÿÿi*   i+   i,   i-   i/   gš™™™™™¹?i   i   g333333Ó?i   i   t   omit_slack_greater_thangš™™™™™É?t   new_unit_celli
   iZ   t(   constrain_dihedrals_with_sigma_less_thani   i   i   i   i   i   i	   i   i   i   i   i   i   i%   i   i   i   i   i   i   i   i   (   i    i   (   i    i   (   i    i   (   i   i   (   i*   i+   (   i*   i,   (   i-   i.   (   i-   i/   (   i   i   (   i   i   (   i   i   (   i
   i
   i
   iZ   iZ   iZ   (   i    i   i
   i   (   i    i   i   i   (   i   i   i   i   i   i   i   i	   (   i   i   i   i	   (   i   i   i   i   (   i   i   i   i   (   i   i   i   i   (   i   i   i   i   (   i   i   i   i%   (   i   i   i   i%   (   i   i   i   i   i   i   i   ((   R&   R'   R(   R*   R.   t   mmtbx.monomer_libraryR`   R3   R4   R   R0   R7   t   enk_pdbt   runRK   R5   t   xray_structureR?   R@   R6   R8   R   R:   R   R   t   mint   nonbonded_model_distancesRA   t   simple_edge_listRE   t   bond_params_tablet   slackt   sortedt   sett   discard_symmetryt   site_symmetry_tablet   special_position_indicest   sizet*   rigid_clusters_due_to_dihedrals_and_planest   tuple(   RQ   R`   R   t   processed_pdb_filet   geoR   t   sel0t   selt   dt   clusterst   c(    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/regression/tst_geometry_restraints_2.pyt   exercise_with_pdb„  s~    					#	*$			/"".+!		(		c       
   C   s’  t  j j d t j d2 d3 d4 d5 g ƒ d d6 d7 d8 g d d9 d: g ƒ \ }  } t |  d; d< d= d> g ƒ sl t ‚ t | j d |  ƒ j d ƒ s� t ‚ t j d? d@ dA dB g ƒ } t	 ƒ  } | j
 d | d* | ƒ d+ } t | j ƒ  | d, ƒ sð t ‚ t  j j d t j dC dD dE dF dG g ƒ d dH dI dJ g d dK dL g ƒ \ }  } | j |  d0 ƒ t	 ƒ  } | j
 d | d* | ƒ t | j ƒ  | d1 ƒ sŽt ‚ d  S(M   NR   gÙÎ÷Sãå%@gáz®G¡)@gTã¥›Ä`.@g�Âõ(\Ï$@gœÄ °rè+@g/Ý$�Õ/@g+‡ÙŽ%@g /Ý$†.@gNbX9t.@g¢E¶óýÔ#@g×£p=
0@g¬Zd;ß-@t   edge_list_bondsi    i   i   i   t   edge_list_anglesgoƒÀÊ!@g      @gP�—n@gÛù~j¼ô@gu“VŽ@g�•C‹ì@gÁÊ¡E¶s@g}?5^ºÉ@gD‹lçû)@gÍÌÌÌÌŒ @gyé&1,@g…ëQ¸@g;ßO�—î@gÇK7‰Aà@g`åÐ"Ûy@gÝ$�•Ã@gßO�—n’@g¦›Ä °ò@g9´Èv¾@g)\�Âõ(@g33333s @g®Gáz@R   sX  Bond restraints: 5
Sorted by residual:
bond 2
     3
  ideal  model  delta    sigma   weight residual
  1.231  1.158  0.073 1.00e-01 1.00e+02 5.35e-01
bond 1
     2
  ideal  model  delta    sigma   weight residual
  1.525  1.577 -0.052 1.00e-01 1.00e+02 2.66e-01
bond 1
     3
  ideal  model  delta    sigma   weight residual
  2.401  2.338  0.063 1.41e-01 5.00e+01 1.96e-01
bond 0
     1
  ideal  model  delta    sigma   weight residual
  1.457  1.420  0.037 1.00e-01 1.00e+02 1.37e-01
bond 0
     2
  ideal  model  delta    sigma   weight residual
  2.453  2.462 -0.009 1.41e-01 5.00e+01 3.92e-03

s   Nonbonded interactions: 0

gsh‘í|%@g{®Gá:)@gºI+Ç.@iÿÿÿÿs¡   Nonbonded interactions: 2
Sorted by model distance:
nonbonded 0
          4
   model   vdw
   0.306 1.200
nonbonded 1
          4
   model   vdw
   1.274 1.200

(   gÙÎ÷Sãå%@gáz®G¡)@gTã¥›Ä`.@(   g�Âõ(\Ï$@gœÄ °rè+@g/Ý$�Õ/@(   g+‡ÙŽ%@g /Ý$†.@gNbX9t.@(   g¢E¶óýÔ#@g×£p=
0@g¬Zd;ß-@(   i    i   (   i   i   (   i   i   (   i    i   (   i   i   (   goƒÀÊ!@g      @gP�—n@(   gÛù~j¼ô@gu“VŽ@g�•C‹ì@(   gÁÊ¡E¶s@g}?5^ºÉ@gD‹lçû)@(   g      @gÍÌÌÌÌŒ @g      @(   gyé&1,@g…ëQ¸@g;ßO�—î@(   gÇK7‰Aà@g`åÐ"Ûy@gÝ$�•Ã@(   gßO�—n’@g¦›Ä °ò@g9´Èv¾@(   g)\�Âõ(@g33333s @g®Gáz@(   gÙÎ÷Sãå%@gáz®G¡)@gTã¥›Ä`.@(   g�Âõ(\Ï$@gœÄ °rè+@g/Ý$�Õ/@(   g+‡ÙŽ%@g /Ý$†.@gNbX9t.@(   g¢E¶óýÔ#@g×£p=
0@g¬Zd;ß-@(   gsh‘í|%@g{®Gá:)@gºI+Ç.@(   i    i   (   i   i   (   i   i   (   i    i   (   i   i   (   R   t   managert:   construct_non_crystallographic_conserving_bonds_and_anglesR   t   vec3_doubleR   R:   t   energies_sitest   targetR   RD   R   R8   t   append(   R   Rz   t   sites_cart_noiset   siot   expected_first_part(    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/regression/tst_geometry_restraints_2.pyt9   exercise_non_crystallographic_conserving_bonds_and_anglesb  sL    $		c         C   s?   d |  k } t  d | ƒ t d | ƒ t ƒ  t j j ƒ  GHd  S(   Ns	   --verboseRQ   (   R\   R€   RŒ   R&   t   utilst   format_cpu_times(   Rb   RQ   (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/regression/tst_geometry_restraints_2.pyt   exercise_all²  s
    t   __main__i   (   t
   __future__R    t   cctbxR   t0   cctbx.geometry_restraints.distance_least_squaresR   t!   cctbx.geometry_restraints.managerR   t   cctbx.array_familyR   t	   cStringIOR   t   libtbx.utilsR&   t   libtbx.test_utilsR   R   R   t   libtbx.load_envR3   R+   R\   Ri   R€   RŒ   R�   t   __name__t   argv(    (    (    sX   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/cctbx/regression/tst_geometry_restraints_2.pyt   <module>   s$   	ÿ u	Þ	P	