ó
Š™xTc           @   sU  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 m Z m Z m Z d  d l m Z m Z m Z d  d l Z d  d	 l m Z d  d l Z d  d l Z d  d l Z d  d l Z d
 „  Z d „  Z d „  Z d „  Z d Z d „  Z  d „  Z! d „  Z" d „  Z# d „  Z$ e% d k rQe$ e j& d ƒ n  d S(   iÿÿÿÿ(   t   division(   t   pdb(   t	   hybrid_36(   t   crystal(   t   flex(   t   Sorryt   hashlib_md5t   user_plus_sys_timet   format_cpu_times(   t   Exception_expectedt   approx_equalt	   show_diffN(   t   StringIOc          C   s  t  j d t j d t j ƒ x¶ d d g D]¨ \ }  } y t j d |  d d	 ƒ Wn+ t k
 r| } t | ƒ d
 k sƒ t ‚ n Xt ‚ y t j d |  d | ƒ Wn+ t k
 rÊ } t | ƒ d
 k sÑ t ‚ q) Xt ‚ q) Wt	 ƒ  } t j
 ƒ  } | j ƒ  } d | d | t d | ƒ f GH| d d d  k s0t ‚ t j d d ƒ d k sNt ‚ t j d d ƒ d k slt ‚ t j d d ƒ d k sŠt ‚ t j d d ƒ d k t j d d ƒ d k t j d d ƒ d k y t j d d ƒ Wn+ t k
 r} t | ƒ d k st ‚ n Xt ‚ d  S(!   Nt   hy36enct   hy36deci   t   AAAi   t   zzzzzzt   widtht   valuei    s   unsupported width.t   ssJ   time hy36recode_width_4_all: %.2f s (%.3f micro s per encode-decode cycle)g    €„.Ai   iç  i'  i   i   i$   iÒ  t   A123ik,  t   1s      1t   1234t   18As'   invalid residue sequence number: " 18A"(   i   R   (   i   R   i÷*  i4   i@¶  (   R   t   exerciseR   t
   hy36encodet
   hy36decodet   RuntimeErrort   strt   AssertionErrorR	   R   t   hy36recode_width_4_allt   elapsedt   maxt   resseq_decodet   resseq_encodet
   ValueError(   R   R   t   et   upst   n_ok(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt   exercise_hybrid_36   s:      
	 c             s  t  j ‰  ˆ  d  ƒ d k s! t ‚ ˆ  d ƒ d k s9 t ‚ ˆ  d ƒ d k sQ t ‚ ˆ  d ƒ d k si t ‚ ˆ  d ƒ d k s� t ‚ ˆ  d ƒ d k s™ t ‚ ˆ  d ƒ d	 k s± t ‚ ˆ  d
 ƒ d" k sÉ t ‚ ˆ  d ƒ ˆ  d
 ƒ k sè t ‚ d „  }  x[ d d d d g D]G } ˆ  | ƒ |  | ƒ k s(t ‚ ˆ  d | ƒ ˆ  | ƒ k st ‚ qW‡  f d †  } g  t d d# ƒ D] } d | ^ qn} t | | ƒ | k sŸt ‚ t  j d d d d ƒ } t  j } g  t d | d d ƒ D] } | d d d | ƒ ^ q×} t | | ƒ | k st ‚ d  S($   Ni0   t    t   0s    0s     0R   i1   s   -1iÏÿÿÿt   123i   i2   i3   s   -123c         S   s˜   d } |  j  ƒ  }  t } t |  ƒ d k r3 d }  n# |  d d k rV t } |  d }  n  x( |  D]  } | d 9} | t | ƒ 7} q] W| r” | d 9} n  | S(   Ni    R)   t   -i   i   iÿÿÿÿ(   t   lstript   Falset   lent   Truet   ord(   R   t   resultt   negt   c(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt   po9   s    	
s   780 s   999 s   1223 t   zzzzzR+   c            s   t  ˆ  |  ƒ ˆ  | ƒ ƒ S(   N(   t   cmp(   t   at   b(   t   o(    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt   o_cmpL   s    iüÿÿi'  i   s   %4sR   i   R   t   zzzzR   i 1  i21  i 21 i321 i'  (   R   t   utils_base_256_ordinalt   NoneR   t   xranget   sortedR   R   (   R4   R   R:   t   it   char4st   mR$   (    (   R9   s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt   exercise_base_256_ordinal-   s*    		'&	8c         C   s…  |  d  k r d GHd  Sd j ƒ  } d j ƒ  } d d g } xÔ |  D]Ì } t j t | ƒ j ƒ  ƒ } t j d | ƒ } t j	 j
 | ƒ } | | k rÉ | j d k s¦ t ‚ | j s¶ t ‚ | d c d 7<q@ | | k r@ | j d k sê t ‚ | j sù t ‚ | d c d 7<q@ q@ W| d d	 k s&t ‚ | d d	 k s<t ‚ t j d
 ƒ } t j d | ƒ } | j d k srt ‚ | j s�t ‚ d  S(   NsF   Skipping exercise_columns_73_76_evaluator(): input files not availablesb   occ_3_bad2.pdb
enk_gm.pdb
t.pdb
phe_a.pdb
f_obs_complex.pdb
phe_h_bad.pdb
one_conf_but_altloc.pdb
sT   pdb103l.ent
pdb1etn.ent
pdb118d.ent
pdb161d.ent
pdb139l.ent
pdb1anp.ent
pdb1gky.ent
i    t   liness/   Blank columns 73-76 on ATOM and HETATM records.i   s*   Exactly one common label in columns 73-76.i   s:  HEADER    HYDROLASE(METALLOPROTEINASE)            17-NOV-93   1THL
ATOM      1  N   ILE     1       9.581  51.813  -0.720  1.00 31.90      1THL 158
ATOM      2  CA  ILE     1       8.335  52.235  -0.041  1.00 52.95      1THL 159
ATOM      3  C   ILE     1       7.959  53.741   0.036  1.00 26.88      1THL 160
END
(   R=   t
   splitlinesR   t   split_linest   opent   readR   t   columns_73_76_evaluatort   ost   patht   basenamet   findingR   t   is_old_style(   t   pdb_file_namest   known_blankt   known_exactly_onet   n_knownt	   file_nameRD   R$   t   bn(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt    exercise_columns_73_76_evaluatorT   s2    			c          C   sò  t  j d d  d t j d g ƒ ƒ y# t  j d d d t j d ƒ ƒ Wn/ t k
 rv }  t t |  ƒ d ƒ s} t	 ‚ n Xt
 ‚ y) t  j d d d t j d ƒ d t ƒ Wn t k
 r¹ n Xt
 ‚ y# t  j d d  d t j d ƒ ƒ Wn/ t k
 r}  t t |  ƒ d	 ƒ st	 ‚ n Xt
 ‚ y# t  j d d  d t j d
 ƒ ƒ Wn/ t k
 ro}  t t |  ƒ d ƒ svt	 ‚ n Xt
 ‚ y& t  j d d d t j d g ƒ ƒ Wn/ t k
 rÍ}  t t |  ƒ d ƒ sÔt	 ‚ n Xt
 ‚ y& t  j d d d t j d g ƒ ƒ Wn/ t k
 r+}  t t |  ƒ d ƒ s2t	 ‚ n Xt
 ‚ y& t  j d d d t j d g ƒ ƒ Wn/ t k
 r‰}  t t |  ƒ d ƒ s�t	 ‚ n Xt
 ‚ y& t  j d d d t j d g ƒ ƒ Wn/ t k
 rç}  t t |  ƒ d ƒ sît	 ‚ n Xt
 ‚ d  S(   Nt   source_infoRD   t   ATOMs   some.pdbsŠ   HETATM    9 2H3  MPR B   5      16.388   0.289   6.613  1.00  0.08
ANISOU    9 2H3  MPR B   5      8+8    848    848      0      0      0
s—   some.pdb, line 2:
  ANISOU    9 2H3  MPR B   5      8+8    848    848      0      0      0
  ---------------------------------^
  unexpected plus sign.t   raise_sorry_if_format_errorsÍ   HETATM    9 2H3  MPR B   5      16.388   0.289   6.613  1.00  0.08
HETATM    9 2H3  MPR B   5      16.388   0.289   6.613  1.00  0.08
ANISOU    9 2H3  MPR B   5      84-    848    848      0      0      0
s•   input line 3:
  ANISOU    9 2H3  MPR B   5      84-    848    848      0      0      0
  ----------------------------------^
  unexpected minus sign.sŠ   HETATM    9 2H3  MPR B   5      16.388   0.289   6.613  1.00  0.08
ANISOU    9 2H3  MPR B   5    c        848    848      0      0      0
s�   input line 2:
  ANISOU    9 2H3  MPR B   5    c        848    848      0      0      0
  ------------------------------^
  unexpected character.sB   ATOM   1045  O   HOH    30    x  0.530  42.610  45.267  1.00 33.84s—   some.pdb, line 1:
  ATOM   1045  O   HOH    30    x  0.530  42.610  45.267  1.00 33.84
  ------------------------------^
  not a floating-point number.sB   ATOM   1045  O   HOH    30     x 0.530  42.610  45.267  1.00 33.84s˜   some.pdb, line 1:
  ATOM   1045  O   HOH    30     x 0.530  42.610  45.267  1.00 33.84
  -------------------------------^
  not a floating-point number.sB   HETATM 4160  O   HOH S 272         nan   0.000   0.000  1.00 54.72sœ   some.pdb, line 1:
  HETATM 4160  O   HOH S 272         nan   0.000   0.000  1.00 54.72
  -----------------------------------^
  not a floating-point number.sB   ATOM   1045  O   HOH    30       0x530  42.610  45.267  1.00 33.84s”   some.pdb, line 1:
  ATOM   1045  O   HOH    30       0x530  42.610  45.267  1.00 33.84
  ----------------------------------^
  unexpected character.(   R   t	   pdb_inputR=   R   t
   std_stringRF   R#   R   R   R   R	   R/   R   (   R$   (    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt   exercise_line_info_exceptions†   s’    "									sÏ  HEADER    ISOMERASE                               02-JUL-92   1FKB
ONHOLD    26-JUN-99
OBSLTE     07-DEC-04 1A0Y      1Y4P
TITLE     ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-
SPLIT      2QNH 1VSP
COMPND    FK506 BINDING PROTEIN (FKBP) COMPLEX WITH IMMUNOSUPPRESSANT
SOURCE    HUMAN (HOMO SAPIENS) RECOMBINANT FORM EXPRESSED IN
KEYWDS    ISOMERASE
EXPDTA    X-RAY DIFFRACTION
NUMMDL    8
MDLTYP    CA ATOMS ONLY, CHAIN B, C, D, E, F, G, H, I, J, K, L, M, N,
MDLTYP   2 O, P, Q, R, S, T, U
AUTHOR    G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.C.CLARDY
REVDAT   1   31-OCT-93 1FKB    0
JRNL        AUTH   G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.CLARDY
SPRSDE     02-SEP-03 1O58      1J6N
CAVEAT     1B7F    INCORRECT CHIRALITY AT C1* OF U2, CHAIN Q

REMARK   2 RESOLUTION. 1.7  ANGSTROMS.
FTNOTE   1 CIS PEPTIDE: GLY     190  - PHE     191

DBREF  1HTQ A  601   468  SWS    Q10377   GLN1_MYCTU       2    478
DBREF1 1JZX A    1  2880  GB                   15805042
DBREF2 1JZX A     NC_001263                     2587937     2590817
SEQRES   1 A  477  THR GLU LYS THR PRO ASP ASP VAL PHE LYS LEU ALA LYS
SEQADV 1KEH ALA A  170  SWS  Q9L5D6    SER   199 ENGINEERED
MODRES 6NSE CYS A  384  CYS  MODIFIED BY CAD

HET    GLC  A 810      12
HETNAM     G6D 6-DEOXY-ALPHA-D-GLUCOSE
HETSYN     G6D QUINOVOSE
FORMUL   2   CA    4(CA1 2+)

HELIX    1   1 GLN A   18  GLY A   34  1                                  17
SHEET    1   A 7 PHE A 257  ALA A 260  0
TURN     1  T1 GLY E   2  THR E   5     BETA, TYPE II

SSBOND  12 CYS B  191    CYS B  220
LINK         N   PRO C  61                 C   GLY A   9            1556
HYDBND       N   GLY A  148                 O   PHE B   41
SLTBRG       N   ILE A  16                 OD2 ASP A 194
CISPEP   1 ALA A  183    PRO A  184          1         0.96

SITE     1 CAB  3 HIS B  57  ASP B 102  SER B 195

CRYST1   45.920   49.790   89.880  90.00  97.34  90.00 P 1 21 1      4
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.021777  0.000000  0.002805        0.00000
SCALE2      0.000000  0.020084  0.000000        0.00000
SCALE3      0.000000  0.000000  0.011218        0.00000
MTRIX1   1  0.739109  0.012922 -0.673462       17.07460    1
MTRIX2   1  0.015672 -0.999875 -0.001986       21.64730    1
MTRIX3   1 -0.673404 -0.009087 -0.739219       44.75290    1
TVECT    1   0.00000   0.00000  20.42000

FOOBAR BAR FOO

MODEL        1
ATOM      1  N   MET A   1       6.215  22.789  24.067  1.00  0.00           N
ATOM      2  CA  MET A   1       6.963  22.789  22.822  1.00  0.00           C
BREAK
HETATM    3  C   MET A   2       7.478  21.387  22.491  1.00  0.00           C
ATOM      4  O   MET A   2       8.406  20.895  23.132  1.00  0.00           O
ENDMDL
MODEL 3
HETATM    9 2H3  MPR B   5      16.388   0.289   6.613  1.00  0.08
SIGATM    9 2H3  MPR B   5       0.155   0.175   0.155  0.00  0.05
ANISOU    9 2H3  MPR B   5      848    848    848      0      0      0
SIGUIJ    9 2H3  MPR B   5      510    510    510      0      0      0
TER
ATOM     10  N   CYSCH   6      14.270   2.464   3.364  1.00  0.07
SIGATM   10  N   CYSCH   6       0.012   0.012   0.011  0.00  0.00
ANISOU   10  N   CYSCH   6      788    626    677   -344    621   -232
SIGUIJ   10  N   CYSCH   6        3     13      4     11      6     13
TER
ENDMDL

CONECT 5332 5333 5334 5335 5336

MASTER       81    0    0    7    3    0    0    645800   20    0   12
END
c          C   sî  xÙt  d ƒ D]Ë}  t j d d  d t j d ƒ ƒ } | j ƒ  d k sL t ‚ | j ƒ  d k sd t ‚ t	 | j
 ƒ  ƒ d k s‚ t ‚ | j ƒ  j ƒ  d k s  t ‚ | j ƒ  j ƒ  d k s¾ t ‚ | j ƒ  j ƒ  d k sÜ t ‚ | j ƒ  j ƒ  d k sú t ‚ | j ƒ  j ƒ  d k st ‚ | j ƒ  j ƒ  d k s6t ‚ | j ƒ  j ƒ  d k sTt ‚ | j ƒ  j ƒ  d k srt ‚ | j ƒ  j ƒ  d k s�t ‚ t	 | j ƒ  ƒ d k s®t ‚ | j ƒ  j ƒ  d k sÌt ‚ | j ƒ  j ƒ  d k sêt ‚ | j ƒ  j ƒ  d k st ‚ | j ƒ  j ƒ  d k s&t ‚ | j ƒ  j ƒ  d k sDt ‚ | j ƒ  j ƒ  d k sbt ‚ | j ƒ  j ƒ  d k s€t ‚ | j ƒ  j ƒ  d k sžt ‚ | j ƒ  j ƒ  d k s¼t ‚ t j d d d t ƒ } | j ƒ  d k sìt ‚ | j
 ƒ  i> d d	 6d d
 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d 6d d  6d d! 6d" d# 6d d$ 6d d% 6d d& 6d d' 6d d( 6d d) 6d d* 6d d+ 6d d, 6d d- 6d d. 6d d/ 6d d0 6d d1 6d d2 6d d3 6d4 d5 6d d6 6d d7 6d d8 6d d9 6d d: 6d d; 6d d< 6d d= 6d d> 6d d? 6d d@ 6d dA 6d dB 6d dC 6d dD 6d dE 6d dF 6d dG 6d dH 6d dI 6k s¶t ‚ t  | j ƒ  ƒ dJ g k s×t ‚ t! dK j" | j ƒ  ƒ dL ƒ süt ‚ t! dK j" | j ƒ  ƒ dM ƒ s!t ‚ t! dK j" | j ƒ  ƒ dN ƒ sFt ‚ t! dK j" | j ƒ  ƒ dO ƒ skt ‚ t! dK j" | j ƒ  ƒ dP ƒ s�t ‚ t! dK j" | j ƒ  ƒ dQ ƒ sµt ‚ t! dK j" | j ƒ  ƒ dR ƒ sÚt ‚ t! dK j" | j ƒ  ƒ dS ƒ sÿt ‚ t	 | j ƒ  ƒ dT k st ‚ g  | j ƒ  D] } | j# ^ q*dU dV dW dX dY dZ g k s]t ‚ g  | j ƒ  D] } | j$ ^ qjd[ d\ d\ d] d^ d^ g k s�t ‚ t  | j ƒ  ƒ d_ d` g k sÁt ‚ t  | j ƒ  ƒ d" dT g k såt ‚ t  | j ƒ  ƒ da dT g k s	t ‚ g  | j ƒ  D] } t  | ƒ ^ qd" g da dT g g k sIt ‚ t  | j ƒ  ƒ d g k sjt ‚ t! dK j" | j ƒ  ƒ db ƒ s�t ‚ t! dK j" | j ƒ  ƒ dc ƒ s´t ‚ t  | j ƒ  ƒ d" d g k s t ‚ q Wt j d d  d t j dd ƒ ƒ } de j% ƒ  } x? t& | j ƒ  | ƒ D]( \ } } t! | j' ƒ  | ƒ st ‚ qWt j d d  d t j df ƒ ƒ } x¿ | j ƒ  D]± } | j( dg k s”t ‚ | j) dh k s©t ‚ | j* di k s¾t ‚ | j+ dj k sÓt ‚ | j, dk k sèt ‚ | j- dl k sýt ‚ | j. dm k s	t ‚ | j' ƒ  dn k syt ‚ qyWt j d d  d t j do ƒ ƒ } x¿ | j ƒ  D]± } | j( dg k sw	t ‚ | j) dh k sŒ	t ‚ | j* di k s¡	t ‚ | j+ dj k s¶	t ‚ | j, dk k sË	t ‚ | j- dl k sà	t ‚ | j. dp k sõ	t ‚ | j' ƒ  dq k s\	t ‚ q\	Wt j d d  d t j dr ƒ ƒ } x¿ | j ƒ  D]± } | j( dp k sZ
t ‚ | j) ds k so
t ‚ | j* dt k s„
t ‚ | j+ ds k s™
t ‚ | j, dp k s®
t ‚ | j- ds k sÃ
t ‚ | j. dp k sØ
t ‚ | j' ƒ  du k s?
t ‚ q?
Wt j d d  d t j d ƒ ƒ } t  | j ƒ  ƒ g  k s3t ‚ t  | j ƒ  ƒ g  k sQt ‚ t j d d  d t j dv ƒ ƒ } t  | j ƒ  ƒ d g k s“t ‚ g  | j ƒ  D] } t  | ƒ ^ q d g g k sÊt ‚ t j d d  d t j dw ƒ ƒ } t  | j ƒ  ƒ d g k st ‚ g  | j ƒ  D] } t  | ƒ ^ qg  g k s@t ‚ t j d d  d t j dx ƒ ƒ } t  | j ƒ  ƒ d g k s‚t ‚ g  | j ƒ  D] } t  | ƒ ^ q�d g g k s¹t ‚ t j d d  d t j dy ƒ ƒ } t  | j ƒ  ƒ d d g k sþt ‚ g  | j ƒ  D] } t  | ƒ ^ qg  g  g k s5t ‚ t j d d  d t j dz ƒ ƒ } t  | j ƒ  ƒ d d g k szt ‚ g  | j ƒ  D] } t  | ƒ ^ q‡g  d g g k s´t ‚ y# t j d d  d t j d{ ƒ ƒ Wn/ t/ k
 r} t! t0 | ƒ d| ƒ st ‚ n Xt1 ‚ y# t j d d  d t j d} ƒ ƒ Wn/ t/ k
 rc} t! t0 | ƒ d~ ƒ sjt ‚ n Xt1 ‚ y# t j d d  d t j d ƒ ƒ Wn/ t/ k
 r¾} t! t0 | ƒ d€ ƒ sÅt ‚ n Xt1 ‚ y# t j d d  d t j d� ƒ ƒ Wn/ t/ k
 r} t! t0 | ƒ d‚ ƒ s t ‚ n Xt1 ‚ xy d d d  g D]h } y& t j d d  d t j2 | g ƒ ƒ Wn3 t/ k
 r‘} t! t0 | ƒ dƒ | ƒ s˜t ‚ q0Xt1 ‚ q0Wt j d d  d t j d„ ƒ ƒ } t  | j ƒ  ƒ da d… d† d‡ g k sçt ‚ g  | j ƒ  D] } t  | ƒ ^ qôd d da g dˆ d‰ d… g d4 dŠ d† g d‹ d‡ g g k sEt ‚ t3 dŒ d� ƒ t j dŽ dŒ ƒ } | j ƒ  d� k s|t ‚ t3 dŒ d� ƒ j4 d� ƒ t j dŽ dŒ ƒ } y t j dŽ d ƒ Wn. t5 k
 rè} t0 | ƒ j6 d‘ ƒ sït ‚ n Xt1 ‚ d’ t j7 k st ‚ d“ t j8 k st ‚ d” t j9 k s.t ‚ d• t j: k sCt ‚ d– t j; k sXt ‚ d— t j< k smt ‚ t j= }	 |	 d˜ d™ ƒ dš k s‘t ‚ |	 d˜ d› ƒ dœ k s¬t ‚ |	 d˜ d• ƒ d� k sÇt ‚ |	 d˜ d– ƒ dž k sât ‚ |	 d˜ dŸ ƒ d  k sýt ‚ |	 d˜ d¡ ƒ d¢ k st ‚ |	 d˜ d” ƒ d  k s3t ‚ |	 d˜ d” d£ t> ƒ d¤ k sTt ‚ t j? d¥ d™ ƒ d  k srt ‚ x{ t j8 t j9 g D]g }
 x^ |
 D]V } t j? d¥ | ƒ } | d  k	 s¼t ‚ t j? d¥ ds | j@ ƒ  ds ƒ | k s’t ‚ q’Wq…Wx®d¦ j% ƒ  D] } t j d d  d t j2 | g ƒ ƒ } | jA ƒ  } t0 | jB ƒ  ƒ d§ k sQt ‚ t0 | jC ƒ  ƒ d¨ k sot ‚ | jD ƒ  } | jE | ƒ s�t ‚ tF | jG ƒ  d© ƒ s«t ‚ xï tH t> g D]á } | jA dª tI jJ d« d¶ ƒ d­ | ƒ } | r	t0 | jB ƒ  ƒ d§ k s't ‚ n t0 | jB ƒ  ƒ d® k s't ‚ t0 | jC ƒ  ƒ d¨ k sEt ‚ | jD d¯ | jD d° d ƒ d­ | ƒ } | jE | ƒ s~t ‚ tF | jG ƒ  d ƒ s¸t ‚ q¸WqýW| jK ƒ  d  k s¹t ‚ | jL d± d ƒ g  k s×t ‚ t j d d  d t j d² ƒ ƒ } | jK ƒ  d³ k st ‚ | jL d± d ƒ d´ g k s1t ‚ t j d d  d t j dµ ƒ ƒ } | jM ƒ  } t	 | ƒ d" k svt ‚ t  | d ƒ d d d g k r®t  | d ƒ d g k s´t ‚ t  | d ƒ t  | d ƒ k oßg  k n sêt ‚ d  S(·   Ni   RV   RD   R(   R   i    s	   file/namei   t   KEYWDSt   SEQRESs   LINK  t   ORIGX1s   SITE  t   FTNOTEt   HETSYNi   t   SIGATMt   MTRIX2t   MTRIX3s   HELIX t   MTRIX1s   END   t   ANISOUs   TITLE t   SLTBRGt   REMARKs   TURN  t   SCALE1t   SCALE2t   AUTHORt   CRYST1t   SIGUIJt   CISPEPi   s   ATOM  t   ENDMDLt   ORIGX2t   MODRESt   SOURCEt   FORMULt   MASTERt   CAVEATs   HET   t   COMPNDs   MODEL t   REVDATt   SSBONDt   OBSLTEt   CONECTs   JRNL  t   SPRSDEi   s         t   FOOBARt   HETNAMt   HEADERt   ORIGX3s   BREAK t   ONHOLDs   SHEET s   TVECT t   HYDBNDs   TER   s   DBREF t   EXPDTAt   SCALE3t   HETATMt   SEQADVs   SPLIT t   NUMMDLt   MDLTYPt   DBREF1t   DBREF2s   FOOBAR BAR FOOs   
sÿ  HEADER    ISOMERASE                               02-JUL-92   1FKB
ONHOLD    26-JUN-99
OBSLTE     07-DEC-04 1A0Y      1Y4P
TITLE     ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-
SPLIT      2QNH 1VSP
COMPND    FK506 BINDING PROTEIN (FKBP) COMPLEX WITH IMMUNOSUPPRESSANT
SOURCE    HUMAN (HOMO SAPIENS) RECOMBINANT FORM EXPRESSED IN
KEYWDS    ISOMERASE
EXPDTA    X-RAY DIFFRACTION
NUMMDL    8
MDLTYP    CA ATOMS ONLY, CHAIN B, C, D, E, F, G, H, I, J, K, L, M, N,
MDLTYP   2 O, P, Q, R, S, T, U
AUTHOR    G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.C.CLARDY
REVDAT   1   31-OCT-93 1FKB    0
JRNL        AUTH   G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.CLARDY
SPRSDE     02-SEP-03 1O58      1J6N
CAVEAT     1B7F    INCORRECT CHIRALITY AT C1* OF U2, CHAIN QsY   REMARK   2 RESOLUTION. 1.7  ANGSTROMS.
FTNOTE   1 CIS PEPTIDE: GLY     190  - PHE     191so  DBREF  1HTQ A  601   468  SWS    Q10377   GLN1_MYCTU       2    478
DBREF1 1JZX A    1  2880  GB                   15805042
DBREF2 1JZX A     NC_001263                     2587937     2590817
SEQRES   1 A  477  THR GLU LYS THR PRO ASP ASP VAL PHE LYS LEU ALA LYS
SEQADV 1KEH ALA A  170  SWS  Q9L5D6    SER   199 ENGINEERED
MODRES 6NSE CYS A  384  CYS  MODIFIED BY CADsv   HET    GLC  A 810      12
HETNAM     G6D 6-DEOXY-ALPHA-D-GLUCOSE
HETSYN     G6D QUINOVOSE
FORMUL   2   CA    4(CA1 2+)s«   HELIX    1   1 GLN A   18  GLY A   34  1                                  17
SHEET    1   A 7 PHE A 257  ALA A 260  0
TURN     1  T1 GLY E   2  THR E   5     BETA, TYPE IIs  SSBOND  12 CYS B  191    CYS B  220
LINK         N   PRO C  61                 C   GLY A   9            1556
HYDBND       N   GLY A  148                 O   PHE B   41
SLTBRG       N   ILE A  16                 OD2 ASP A 194
CISPEP   1 ALA A  183    PRO A  184          1         0.96s1   SITE     1 CAB  3 HIS B  57  ASP B 102  SER B 195sv  CRYST1   45.920   49.790   89.880  90.00  97.34  90.00 P 1 21 1      4
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.021777  0.000000  0.002805        0.00000
SCALE2      0.000000  0.020084  0.000000        0.00000
SCALE3      0.000000  0.000000  0.011218        0.00000
MTRIX1   1  0.739109  0.012922 -0.673462       17.07460    1
MTRIX2   1  0.015672 -0.999875 -0.001986       21.64730    1
MTRIX3   1 -0.673404 -0.009087 -0.739219       44.75290    1
TVECT    1   0.00000   0.00000  20.42000i   s       1s       2s       3s       4s       9s      10s    Ns    Cs    Os     s      1s      3i   s   CONECT 5332 5333 5334 5335 5336sJ   MASTER       81    0    0    7    3    0    0    645800   20    0   12
ENDs(  ATOM      1  CB  LYS   109      16.113   7.345  47.084  1.00 20.00      A
ATOM      2  CG  LYS   109      17.058   6.315  47.703  1.00 20.00      A
ATOM      3  CB  LYS   109      26.721   1.908  15.275  1.00 20.00      B
ATOM      4  CG  LYS   109      27.664   2.793  16.091  1.00 20.00      B
sŒ   pdb=" CB  LYS   109 " segid="A   "
pdb=" CG  LYS   109 " segid="A   "
pdb=" CB  LYS   109 " segid="B   "
pdb=" CG  LYS   109 " segid="B   "
s¢   ATOM  12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdefS123E1C1
HETATM12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdefS123E1C1
t   N123t   At   R12t   CR   t   It   S123s"   pdb="N123AR12 C1234I" segid="S123"s¢   ATOM  12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdef    E1C1
HETATM12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdef    E1C1
s       s   pdb="N123AR12 C1234I"s   ATOM
HETATM
t    s      s   pdb="               "s   ATOM
s   MODEL        1
ENDMDL
s   MODEL        1
ATOM
ENDMDL
s,   MODEL        1
ENDMDL
MODEL        2
ENDMDL
s1   MODEL        1
ENDMDL
MODEL        2
ATOM
ENDMDL
s   MODEL        1
ENDMDL
ATOM
sO   input line 3:
  ATOM
  ^
  ATOM or HETATM record is outside MODEL/ENDMDL block.s   MODEL        1
MODEL        2
sN   input line 2:
  MODEL        2
  ^
  Missing ENDMDL for previous MODEL record.s   ATOM
MODEL        1
s`   input line 2:
  MODEL        1
  ^
  MODEL record must appear before any ATOM or HETATM records.s   ATOM
ENDMDL
s6   input line 2:
  ENDMDL
  ^
  No matching MODEL record.s;   input line 1:
  %s
  ^
  no matching ATOM or HETATM record.s¼  MODEL        1
ATOM                 C
ATOM                 C
ATOM                 D
ATOM                 E
ATOM                 E
ENDMDL
MODEL        2
ATOM                 C
ATOM                 C
ATOM                 D
ATOM                 D
ATOM                 E
ENDMDL
MODEL        3
ATOM                                                                    C
ATOM                                                                    D
ATOM                                                                    D
ATOM                 E                                                  X
ATOM                 E
ENDMDL
MODEL        4
ATOM                                                                    C
ATOM                                                                    D
ATOM                                                                    C
ATOM                 E                                                  X
ATOM                 E
ENDMDL
i
   i   i   i   i	   i   i   s   tmp.pdbt   wRS   s   file tmp.pdbs†   ATOM      1  CA  SER     1       1.212 -12.134   3.757  1.00  0.00
ATOM      2  CA  LEU     2       1.118  -9.777   0.735  1.00  0.00
s    Cannot open file for reading: ""t   HISt   GUAs   CD t   HOHt   SO4s    FEt   namet   ALAt   common_amino_acids     Ut   common_rna_dnat   common_watert   common_small_molecules   CL t   common_elementt   ABCt   othert   consider_ccp4_mon_lib_rna_dnat   ccp4_mon_lib_rna_dnat   common_names›   CRYST1   61.410   54.829   43.543  90.00  90.00  90.00 P 21 21 21    8
REMARK sg= P2(1)2(1)2(1) a= 61.410 b= 54.829 c= 43.543 alpha= 90 beta= 90 gamma= 90
s#   (61.41, 54.829, 43.543, 90, 90, 90)s
   P 21 21 21g      à?t   crystal_symmetryt	   unit_celliZ   t   weak_symmetrys   (10, 10, 10, 90, 90, 90)t   special_position_settingst   min_distance_sym_equivt   iiisc   HEADER                                            02-JUL-92
REMARK   2 RESOLUTION. 1.7  ANGSTROMS.
iÈ  s&   REMARK   2 RESOLUTION. 1.7  ANGSTROMS.s8  HETATM    1  C   ACT  1428      -0.014   0.010   0.027  1.00 20.00
HETATM    2  O   ACT  1428      -0.480  -1.088  -0.009  1.00 20.00
HETATM    3  OXT ACT  1428      -0.744   0.936  -0.009  1.00 20.00
HETATM    4  CH3 ACT  1428       1.238   0.142  -0.009  1.00 20.00
CONECT    1    2    3    4
CONECT    4    1
(   i
   i
   i
   iZ   iZ   iZ   (N   R>   R   RY   R=   R   RF   t	   file_typeR   RV   R.   t   record_type_countst   unknown_sectiont   sizet   title_sectiont   remark_sectiont   primary_structure_sectiont   heterogen_sectiont   secondary_structure_sectiont   connectivity_annotation_sectiont   miscellaneous_features_sectiont   crystallographic_sectiont   atoms_with_labelst   atomst	   model_idst   model_indicest   ter_indicest   chain_indicest   break_indicest   connectivity_sectiont   bookkeeping_sectiont   model_atom_countst   pdb_string_all_sectionst   listR   t   joint   serialt   elementRE   t   zipt   id_strR•   t   altloct   resnamet   chain_idt   resseqt   icodet   segidR#   R   R	   RZ   RG   t   writet   IOErrort
   startswitht   common_residue_names_amino_acidt   common_residue_names_rna_dnat)   common_residue_names_ccp4_mon_lib_rna_dnat   common_residue_names_watert#   common_residue_names_small_moleculet   common_residue_names_elementt   common_residue_names_get_classR/   t   rna_dna_reference_residue_namet   lowerR¡   R¢   t   space_group_infoR¤   t   is_similar_symmetryR
   R¥   R-   R   t   symmetryt   extract_header_yeart   extract_remark_iii_recordst   extract_connectivity(   t   i_trialt   pdb_inpt   atomt   vt   expected_id_strst   awlt   eidsR$   t   record_namet	   get_classt   common_namest   nt   rt   linet   cst   spsR£   t   bonds(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt   exercise_pdb_inputG  s4   			############!!!$$$@!(	" 					!7	!4	!7	$7	$:				&
	*"< 			+$				!				#>c          C   sF  t  j d d d t ƒ }  x't t g D]} | j |  d ƒ } | j | ƒ } t | j ƒ  |  j ƒ  ƒ sn t	 ‚ | j
 ƒ  d k s† t	 ‚ xQ t  j D]F } t d j t | | ƒ ƒ  ƒ d j t |  | ƒ ƒ  ƒ ƒ s� t	 ‚ q� Wd j | j ƒ  d ƒ } t | ƒ j ƒ  } t  j j j ƒ  r,| d k s>t	 ‚ q% | d k s% t	 ‚ q% Wd  S(	   NRV   s	   file/nameRD   i   t   pickles   
t    bf987c40cc8672e2f2324d91d6de3e2bt    7375e96fd52794a785284580730de20c(   R   RY   R½   Rí   t   cPicklet   dumpst   loadsR   t   as_pdb_stringR   RV   t   input_sectionsR¿   t   getattrt   __getinitargs__R   t	   hexdigestt	   hierarchyRÞ   t
   has_siguij(   RÝ   t   pR   t   lt   sectiont   d(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt   exercise_input_picklingõ  s    ")c       	   C   s´
  t  j d d  d t j d ƒ ƒ }  x� t t g D]‚ } |  j d | ƒ } t ƒ  } | j	 d | ƒ t
 | j ƒ  d ƒ s{ t ‚ t ƒ  } | j d | ƒ t
 | j ƒ  d ƒ s. t ‚ q. W|  j d t ƒ } t ƒ  } | j	 d | ƒ t
 | j ƒ  d	 ƒ sû t ‚ t ƒ  } | j d | ƒ t
 | j ƒ  d
 ƒ s0t ‚ t  j d d  d t j d ƒ ƒ }  |  j d t ƒ } | j ƒ  d j d k s‚t ‚ y |  j ƒ  Wn/ t k
 rÁ} t
 t | ƒ d ƒ sÈt ‚ n Xt ‚ t  j d d  d t j d ƒ ƒ }  |  j d t ƒ } | j ƒ  d j d k st ‚ y |  j ƒ  Wn/ t k
 rY} t
 t | ƒ d ƒ s`t ‚ n Xt ‚ t  j d d  d t j d ƒ ƒ }  |  j d t ƒ } | j ƒ  d j d k s²t ‚ y |  j ƒ  Wn/ t k
 rñ} t
 t | ƒ d ƒ søt ‚ n Xt ‚ t  j d d  d t j d ƒ ƒ }  |  j ƒ  } | j ƒ  d j d k sDt ‚ |  j d t d t ƒ } | j ƒ  d j d k s{t ‚ t ƒ  } | j ƒ  j d | ƒ t
 | j ƒ  d ƒ s¶t ‚ y |  j d t ƒ Wn/ t k
 rû} t
 t | ƒ d ƒ st ‚ n Xt ‚ t  j d d  d t j d ƒ ƒ }  |  j d t ƒ } t ƒ  } | j d | ƒ t
 | j ƒ  d ƒ sjt ‚ |  j d t ƒ } t | ƒ d k s”t ‚ t ƒ  } | d j d | ƒ t
 | j ƒ  d ƒ sÍt ‚ t ƒ  } | d j d | ƒ t
 | j ƒ  d ƒ st ‚ t  j d d  d t j d  ƒ ƒ }  |  j ƒ  } | j ƒ  j ƒ  i d d! 6k sXt ‚ t | j ƒ  j ƒ d g k s|t ‚ t  j d d  d t j d" ƒ ƒ }  |  j ƒ  j ƒ  j ƒ  d k sÁt ‚ t |  j ƒ  ƒ d k sßt ‚ t  j d d  d t j d# ƒ ƒ }  |  j ƒ  j ƒ  j ƒ  d k s$t ‚ t |  j ƒ  ƒ d k sBt ‚ t  j d d  d t j d$ ƒ ƒ }  |  j ƒ  j ƒ  j ƒ  d k s‡t ‚ t |  j ƒ  ƒ d k s¥t ‚ t  j d d  d t j d% ƒ ƒ }  |  j ƒ  j ƒ  j ƒ  d k sêt ‚ |  j ƒ  } t | ƒ d k st ‚ | d j ƒ  j ƒ  d k s0t ‚ | d j ƒ  j ƒ  d k sRt ‚ | d j ƒ  d j d& k sut ‚ t  j d d  d t j d' ƒ ƒ }  |  j ƒ  j ƒ  j ƒ  d k sºt ‚ |  j ƒ  } t | ƒ d k sÞt ‚ | d j ƒ  j ƒ  d k s t ‚ | d j ƒ  j ƒ  d k s"t ‚ | d j ƒ  d j d( k sEt ‚ d) } t  j d d  d t j | ƒ ƒ }  g  |  j d t d t ƒ j ƒ  D] } | j ^ q‹d* d+ d+ d, d d d d& g k sÄt ‚ t j d- dA d2 d3 ƒ } t j d- dB d2 d: ƒ }	 d; } t  j d d  d | ƒ }  |  j ƒ  }
 |
 j | ƒ s3	t ‚ |  j d< |	 ƒ }
 |
 j |	 ƒ sZ	t ‚ d= } t  j d d  d | ƒ }  |  j ƒ  }
 |
 j | j d- |	 j ƒ  ƒ ƒ s«	t ‚ |  j d< |	 ƒ }
 |
 j |	 ƒ sÒ	t ‚ d> } t  j d d  d | ƒ }  |  j ƒ  }
 |
 j | j d? |	 j  ƒ  ƒ ƒ s#
t ‚ |  j d< |	 ƒ }
 |
 j |	 ƒ sJ
t ‚ d@ } t  j d d  d | ƒ }  |  j ƒ  }
 |
 j |	 ƒ s‰
t ‚ |  j d< | ƒ }
 |
 j | ƒ s°
t ‚ d  S(C   NRV   RD   sä  CRYST1   61.410   54.829   43.543  90.00  90.00  90.00 P 21 21 21    8
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.016284  0.000000  0.000000        0.00000
SCALE2      0.000000  0.018239  0.000000        0.00000
SCALE3      0.000000  0.000000  0.022966        0.00000
ATOM      1  N   GLN A   3      35.299  11.075  19.070  1.00 36.89           N
ATOM      2  CA  GLN A   3      34.482   9.927  18.794  0.63 37.88           C
SIGATM    2  CA  GLN A   3       1.200   2.300   3.400  0.04  0.05           C
ANISOU    2  CA  GLN A   3     7794   3221   3376  -1227   1064   2601       C
ATOM      3  Q   GLN A   3      35.130   8.880  17.864  0.84 37.52           C
ANISOU    3  Q   GLN A   3     7875   3041   3340   -981    727   2663       C
SIGUIJ    3  Q   GLN A   3       75     41     40     -1      7     63       C
ATOM      4  O   GLN A   3      34.548   7.819  17.724  1.00 38.54      STUV
ATOM      5 1CB AGLN A   3      32.979  10.223  18.469  1.00 37.80
HETATM    6 CA  AION B   1      32.360  11.092  17.308  0.92 35.96          CA2+
HETATM    7 CA   ION B   2      30.822  10.665  17.190  1.00 36.87
t   use_scale_matrix_if_availablet   fs€   Number of scatterers: 7
At special positions: 0
Unit cell: (61.41, 54.829, 43.543, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
s×  Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
pdb=" N   GLN A   3 " N      4 ( 0.5748  0.2020  0.4380) 1.00 0.4672 [ - ]
pdb=" CA  GLN A   3 " C      4 ( 0.5615  0.1811  0.4316) 0.63 [ - ] 0.4797
     u_cart =  0.779  0.322  0.338 -0.123  0.106  0.260
pdb=" Q   GLN A   3 " C      4 ( 0.5721  0.1620  0.4103) 0.84 [ - ] 0.4752
     u_cart =  0.788  0.304  0.334 -0.098  0.073  0.266
pdb=" O   GLN A   3 " segid="STUV" O      4 ( 0.5626  0.1426  0.4070) 1.00 0.4881 [ - ]
pdb="1CB AGLN A   3 " C      4 ( 0.5370  0.1865  0.4242) 1.00 0.4787 [ - ]
pdb="CA  AION B   1 " Ca2+   4 ( 0.5270  0.2023  0.3975) 0.92 0.4554 [ - ]
pdb="CA   ION B   2 " Ca     4 ( 0.5019  0.1945  0.3948) 1.00 0.4670 [ - ]
t   unit_cube_pseudo_crystalsj   Number of scatterers: 7
At special positions: 0
Unit cell: (1, 1, 1, 90, 90, 90)
Space group: P 1 (No. 1)
s×  Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
pdb=" N   GLN A   3 " N      1 (35.2990 11.0750 19.0700) 1.00 0.4672 [ - ]
pdb=" CA  GLN A   3 " C      1 (34.4820  9.9270 18.7940) 0.63 [ - ] 0.4797
     u_cart =  0.779  0.322  0.338 -0.123  0.106  0.260
pdb=" Q   GLN A   3 " C      1 (35.1300  8.8800 17.8640) 0.84 [ - ] 0.4752
     u_cart =  0.788  0.304  0.334 -0.098  0.073  0.266
pdb=" O   GLN A   3 " segid="STUV" O      1 (34.5480  7.8190 17.7240) 1.00 0.4881 [ - ]
pdb="1CB AGLN A   3 " C      1 (32.9790 10.2230 18.4690) 1.00 0.4787 [ - ]
pdb="CA  AION B   1 " Ca2+   1 (32.3600 11.0920 17.3080) 0.92 0.4554 [ - ]
pdb="CA   ION B   2 " Ca     1 (30.8220 10.6650 17.1900) 1.00 0.4670 [ - ]
sO   ATOM      1  N   GLN A   3      35.299  11.075  99.070  1.00 36.89      STUV A
t   enable_scattering_type_unknowni    t   unknownsÅ   Unknown chemical element type:
  "ATOM      1  N   GLN A   3 .*.STUV A  "
  To resolve this problem, specify a chemical element type in
  columns 77-78 of the PDB file, right justified (e.g. " C").sC   ATOM      1 1A   GLN A   3      35.299  11.075  99.070  1.00 36.89
sÅ   Unknown chemical element type:
  "ATOM      1 1A   GLN A   3 .*.        "
  To resolve this problem, specify a chemical element type in
  columns 77-78 of the PDB file, right justified (e.g. " C").sQ   ATOM      1  N   GLN A   3      35.299  11.075  99.070  1.00 36.89           Bx5
sd   Unknown charge:
  "ATOM      1  N   GLN A   3 .*.     Bx5"
                                       ^^sQ   ATOM      1  N   GLN A   3      35.299  11.075  99.070  1.00 36.89          Cs3-
t   Cst   scattering_type_exactt   outsž   Number of scattering types: 1
  Type     Number    sf(0)   Gaussians
   unknown     1      None      None
  sf(0) = scattering factor at diffraction angle 0.
sm   Unknown scattering type:
  "ATOM      1  N   GLN A   3 .*.    Cs3-"
               ^^^^                  ^^^^s8  MODEL        1
ATOM      1  N   GLN A   3      35.299  11.075  19.070  1.00 36.89
ATOM      2  CA  GLN A   3      34.482   9.927  18.794  0.63 37.88
ENDMDL
MODEL        2
ATOM      1  N   GLN A   3      25.299   1.075   9.070  0.54 26.89
ATOM      2  CA  GLN A   3      24.482  -1.927   8.794  1.00 27.88
ENDMDL
s­  Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
model="   1" pdb=" N   GLN A   3 " N      1 (35.2990 11.0750 19.0700) 1.00 0.4672 [ - ]
model="   1" pdb=" CA  GLN A   3 " C      1 (34.4820  9.9270 18.7940) 0.63 0.4798 [ - ]
model="   2" pdb=" N   GLN A   3 " N      1 (25.2990  1.0750  9.0700) 0.54 0.3406 [ - ]
model="   2" pdb=" CA  GLN A   3 " C      1 (24.4820 -1.9270  8.7940) 1.00 0.3531 [ - ]
i   sý   Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
model="   1" pdb=" N   GLN A   3 " N      1 (35.2990 11.0750 19.0700) 1.00 0.4672 [ - ]
model="   1" pdb=" CA  GLN A   3 " C      1 (34.4820  9.9270 18.7940) 0.63 0.4798 [ - ]
i   sý   Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
model="   2" pdb=" N   GLN A   3 " N      1 (25.2990  1.0750  9.0700) 0.54 0.3406 [ - ]
model="   2" pdb=" CA  GLN A   3 " C      1 (24.4820 -1.9270  8.7940) 1.00 0.3531 [ - ]
sš   ATOM    369 PEAK PEAK    1      61.114  12.134   8.619  1.00 20.00      PEAK
ATOM    504 SITE SITE    2      67.707   2.505  14.951  1.00 20.00      SITE
t   constR(   s   MODEL        1
ENDMDL
s,   MODEL        1
ENDMDL
MODEL        2
ENDMDL
s}   MODEL        1
ATOM      1  N   GLN A   3      35.299  11.075  99.070  1.00 36.89           O-2
ENDMDL
MODEL        2
ENDMDL
s   O2-s}   MODEL        1
ENDMDL
MODEL        2
ATOM      1  N   GLN A   3      35.299  11.075  99.070  1.00 36.89          Fe+3
ENDMDL
s   Fe3+sƒ  ATOM      1  N   GLN A   3      35.299  11.075  19.070  1.00 36.89           N
ATOM      2  CA  GLN A   3      34.482   9.927  18.794  0.63 37.88           C0
ATOM      3  C   GLN A   3      35.130   8.880  17.864  0.84 37.52           C 0
ATOM      4  O   GLN A   3      34.548   7.819  17.724  1.00 38.54           O00
ATOM      5 1CB  GLN A   3      32.979  10.223  18.469  1.00 37.80           C 1
HETATM    6 CA   ION B   1      32.360  11.092  17.308  0.92 35.96           X
HETATM    7 CA   ION B   2      30.822  10.665  17.190  1.00 36.87          FE4+
ATOM      8  O   MET A   5       6.215  22.789  24.067  1.00  0.00            -2
t   NRŒ   t   OR¢   g�•C‹lç@gZd;ßO�@gú~j¼t“@iZ   t   space_group_symbolt   P1i
   i   i   iP   iU   i_   s   P-1sž   ATOM      1  N   GLN A   3      35.299  11.075  19.070  1.00 36.89           N
ATOM      2  CA  GLN A   3      34.482   9.927  18.794  0.63 37.88           C
R¡   sÕ   CRYST1   10.000   20.000   30.000  80.00  85.00  95.00
ATOM      1  N   GLN A   3      35.299  11.075  19.070  1.00 36.89           N
ATOM      2  CA  GLN A   3      34.482   9.927  18.794  0.63 37.88           C
sÚ   CRYST1                                                 P -1
ATOM      1  N   GLN A   3      35.299  11.075  19.070  1.00 36.89           N
ATOM      2  CA  GLN A   3      34.482   9.927  18.794  0.63 37.88           C
RÖ   sÚ   CRYST1   10.000   20.000   30.000  80.00  85.00  95.00 P -1
ATOM      1  N   GLN A   3      35.299  11.075  19.070  1.00 36.89           N
ATOM      2  CA  GLN A   3      34.482   9.927  18.794  0.63 37.88           C
(   g�•C‹lç@gZd;ßO�@gú~j¼t“@iZ   iZ   iZ   (   i
   i   i   iP   iU   i_   (!   R   RY   R=   R   RF   R-   R/   t   xray_structure_simpleR   t   show_summaryR   t   getvalueR   t   show_scattererst
   scattererst   scattering_typeR   R   R	   t   scattering_type_registryt   showt   xray_structures_simpleR.   t   type_index_pairs_as_dictR¾   t   unique_countsRª   R   RØ   R×   t   customized_copyR¢   RÖ   (   RÝ   Rÿ   t   xray_structureR  R$   t   xray_structurest   input_pdb_stringt	   scatterert   cs1t   cs2t   xs(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt   exercise_xray_structure_simple  sx   																						
					$	$	$	$	$""#	$""#
		'				!c          C   sž   t  j j d ƒ }  |  d  k r" d  Sg  } xW t j |  ƒ D]F } | j d ƒ pY | j d ƒ sb q8 n  | j t j j	 |  | ƒ ƒ q8 Wt
 | ƒ d k sš t ‚ | S(   Ns   phenix_regression/pdbs   .pdbs   .enti    (   t   libtbxt   envt   find_in_repositoriesR=   RJ   t   listdirt   endswitht   appendRK   R¿   R.   R   (   t   pdb_dirR1   t   node(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt$   get_phenix_regression_pdb_file_namesR  s       c         C   so   t  ƒ  } d |  k } xK t rb t ƒ  t ƒ  t d | ƒ t ƒ  t ƒ  t ƒ  t ƒ  | s Pq q Wt	 ƒ  GHd  S(   Ns	   --foreverRO   (
   R(  R/   R'   RC   RU   R[   Rì   Rþ   R  R   (   t   argst    phenix_regression_pdb_file_namest   forever(    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyR   \  s    		 t   __main__i   ('   t
   __future__R    t   iotbxR   t	   iotbx.pdbR   t   cctbxR   t   cctbx.array_familyR   t   libtbx.utilsR   R   R   R   t   libtbx.test_utilsR	   R
   R   t   libtbx.load_envR   t	   cStringIOR   Rð   Rí   t   sysRJ   R'   RC   RU   R[   R½   Rì   Rþ   R  R(  R   t   __name__t   argv(    (    (    s?   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/tst_ext.pyt   <module>   s2   "		'	2	¿	ÿ ¯		ÿ L	
	