Source Code for Module Biskit.ModelList

  1  ## 
  2  ## Biskit, a toolkit for the manipulation of macromolecular structures 
  3  ## Copyright (C) 2004-2005 Raik Gruenberg & Johan Leckner 
  4  ## 
  5  ## This program is free software; you can redistribute it and/or 
  6  ## modify it under the terms of the GNU General Public License as 
  7  ## published by the Free Software Foundation; either version 2 of the 
  8  ## License, or any later version. 
  9  ## 
 10  ## This program is distributed in the hope that it will be useful, 
 11  ## but WITHOUT ANY WARRANTY; without even the implied warranty of 
 12  ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 
 13  ## General Public License for more details. 
 14  ## 
 15  ## You find a copy of the GNU General Public License in the file 
 16  ## license.txt along with this program; if not, write to the Free 
 17  ## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. 
 18  ## 
 19  ## 
 20   
 21  ## last $Author: leckner $ 
 22  ## last $Date: 2006/09/06 13:59:10 $ 
 23  ## $Revision: 2.5 $ 
 24   
 25  """ 
 26  organise, sort, and filter list of PDBModels 
 27  """ 
 28  from DictList import DictList 
 29  from PDBModel import PDBModel 
 30  import Biskit.tools as T 
 31   
 32 -class ModelList( DictList ): 
 33      """ 
 34      A list of diverse PDBModels. Special support is given to access and use 
 35      entries in the info dictionaries for filtering and sorting. 
 36      Some care is taken to avoid the adding of non-PDBModel objects (but 
 37      somehow it is, certainly, still possible). 
 38   
 39      See DictList for a complete description of all methods! 
 40   
 41      Comparison to Trajectory: 
 42   
 43      In contrast to Trajectory, ModelList does not require structures 
 44      with identical atom content. This makes it of course less efficient and 
 45      less powerful, in many respects. On the other hand, models are kept as 
 46      seperate PDBModel instances with individual residue/atom profiles and 
 47      info dictionaries. 
 48      """ 
 49   
 50 -    def __init__( self, lst=[], item_type=PDBModel ): 
 51          """ 
 52          @param lst: list 
 53          @type  lst: [ dict ] 
 54          @param item_type: type, class of allowed items [ dict ] 
 55          @type  item_type: [ dict ] 
 56           
 57          @raise DictListError: if list contains non-item_type item. 
 58          """ 
 59          DictList.__init__( self, lst, item_type ) 
 60   
 61   
 62 -    def version( self ): 
 63          """ 
 64          Version of class. 
 65           
 66          @return: class version number 
 67          @rtype: str 
 68          """ 
 69          return DictList.version( self ) + '; ModelList $Revision: 2.5 $' 
 70   
 71   
 72 -    def getItemValue( self, item, key, default=None ): 
 73          """ 
 74          Get a value from a given item (dictionary). Overrides DictList method. 
 75           
 76          @param item: possible entry of this list 
 77          @type  item: dict 
 78          @param key: dictionary key 
 79          @type  key: any 
 80          @param default: return value if key is not found (default: None) 
 81          @type  default: any 
 82   
 83          @return: any 
 84          @rtype: any 
 85          """ 
 86          return item.info.get( key, default ) 
 87   
 88   
 89 -    def file2model( self, file_or_model ): 
 90          """ 
 91          Load PDBModel from file if necessary. 
 92           
 93          @param file_or_model: file name or existing model 
 94          @type  file_or_model: str OR PDBModel 
 95           
 96          @return: existing model or model loaded from file 
 97          @rtype: PDBModel 
 98          """ 
 99          if isinstance( file_or_model, PDBModel ): 
100              return file_or_model 
101   
102          return PDBModel( file_or_model ) 
103   
104   
105 -    def _processNewItem( self, v, i ): 
106          """ 
107          Called before an item is added to the list. Override but call. 
108           
109          @param i: index 
110          @type  i: int 
111          @param v: value 
112          @type  v: dict 
113   
114          @return: value 
115          @rtype: dict         
116          """ 
117          v = self.file2model( v ) 
118   
119          return DictList._processNewItem( self, v, i ) 
120   
121   
122  ############# 
123  ##  TESTING         
124  ############# 
125           
126 -class Test: 
127      """ 
128      Test class 
129      """ 
130       
131   
132 -    def run( self, local=0 ): 
133          """ 
134          run function test 
135           
136          @param local: transfer local variables to global and perform 
137                        other tasks only when run locally 
138          @type  local: 1|0 
139           
140          @return: list with sequences of models 
141          @rtype: [str] 
142          """ 
143          import random 
144           
145          f_lst = [ T.testRoot() + '/rec/1A2P.pdb', 
146                    T.testRoot() + '/lig/1A19.pdb', 
147                    T.testRoot() + '/com/1BGS.pdb' ] 
148   
149          ## Loading PDBs... 
150          self.l = ModelList( f_lst ) 
151   
152          seq = [] 
153          for m in self.l: 
154              m.info['score'] = random.random() 
155              seq += [ m.compress( m.maskProtein() ).sequence() ] 
156   
157          p = self.l.plot( 'score' ) 
158   
159          if local: 
160              print self.l.valuesOf('score') 
161              p.show() 
162              globals().update( locals() ) 
163               
164          return seq 
165   
166   
167   
168 -    def expected_result( self ): 
169          """ 
170          Precalculated result to check for consistent performance. 
171   
172          @return: list with sequences of models 
173          @rtype:  [str] 
174          """ 
175          return ['VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR', 'KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGADITIILS', 'AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIRKKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGADITIILS'] 
176       
177           
178   
179  if __name__ == '__main__': 
180   
181      test = Test() 
182   
183      assert test.run( local=1 ) == test.expected_result() 
184