Source Code for Module Bio.PDB.Selection

 1  # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk) 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5   
 6  """Selection of atoms, residues, etc.""" 
 7   
 8  import itertools 
 9   
10  from Bio.PDB.Atom import Atom 
11  from Bio.PDB.Entity import Entity 
12  from Bio.PDB.PDBExceptions import PDBException 
13   
14   
15  entity_levels = ["A", "R", "C", "M", "S"] 
16   
17   
18 -def uniqueify(items): 
19      """Return a list of the unique items in the given iterable. 
20   
21      Order is NOT preserved. 
22      """ 
23      return list(set(items)) 
24   
25   
26 -def get_unique_parents(entity_list): 
27      """Translate a list of entities to a list of their (unique) parents.""" 
28      unique_parents = set(entity.get_parent() for entity in entity_list) 
29      return list(unique_parents) 
30   
31   
32 -def unfold_entities(entity_list, target_level): 
33      """Unfold entities list to a child level (e.g. residues in chain). 
34   
35      Unfold a list of entities to a list of entities of another 
36      level.  E.g.: 
37   
38      list of atoms -> list of residues 
39      list of modules -> list of atoms 
40      list of residues -> list of chains 
41   
42      o entity_list - list of entities or a single entity 
43      o target_level - char (A, R, C, M, S) 
44   
45      Note that if entity_list is an empty list, you get an empty list back: 
46   
47      >>> unfold_entities([], "A") 
48      [] 
49   
50      """ 
51      if not target_level in entity_levels: 
52          raise PDBException("%s: Not an entity level." % target_level) 
53      if entity_list == []: 
54          return [] 
55      if isinstance(entity_list, Entity) or isinstance(entity_list, Atom): 
56          entity_list = [entity_list] 
57   
58      level = entity_list[0].get_level() 
59      if not all(entity.get_level() == level for entity in entity_list): 
60          raise PDBException("Entity list is not homogeneous.") 
61   
62      target_index = entity_levels.index(target_level) 
63      level_index = entity_levels.index(level) 
64   
65      if level_index == target_index:  # already right level 
66          return entity_list 
67   
68      if level_index > target_index:  # we're going down, e.g. S->A 
69          for i in range(target_index, level_index): 
70              #entity_list = itertools.chain.from_iterable(entity_list)  # 2.6+ 
71              entity_list = itertools.chain(*entity_list) 
72      else:  # we're going up, e.g. A->S 
73          for i in range(level_index, target_index): 
74              # find unique parents 
75              entity_list = set(entity.get_parent() for entity in entity_list) 
76      return list(entity_list) 
77   
78   
79 -def _test(): 
80      """Run the Bio.PDB.Selection module's doctests (PRIVATE).""" 
81      import doctest 
82      print "Running doctests ..." 
83      doctest.testmod() 
84      print "Done" 
85   
86   
87  if __name__ == "__main__": 
88      _test() 
89