Package Bio :: Package PDB :: Module Selection
[hide private]
[frames] | no frames]

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  from Bio.PDB.Entity import Entity 
 9  from Bio.PDB.PDBExceptions import PDBException 
10   
11   
12  entity_levels=["A", "R", "C", "M", "S"] 
13   
14   
15 -def uniqueify(items):
16 """Return a list of the unique items in the given iterable. 17 18 Order is NOT preserved. 19 """ 20 return list(set(items))
21 22
23 -def get_unique_parents(entity_list):
24 """Translate a list of entities to a list of their (unique) parents.""" 25 parents = [entity.get_parent() for entity in entity_list] 26 return uniqueify(parents)
27 28
29 -def unfold_entities(entity_list, target_level):
30 """ 31 Unfold a list of entities to a list of entities of another 32 level. E.g.: 33 34 list of atoms -> list of residues 35 list of modules -> list of atoms 36 list of residues -> list of chains 37 38 o entity_list - list of entities or a single entity 39 o target_level - char (A, R, C, M, S) 40 """ 41 if not target_level in entity_levels: 42 raise PDBException("%s: Not an entity level." % target_level) 43 if isinstance(entity_list, Entity): 44 # single entity 45 entity_list=[entity_list] 46 # level of entity list 47 level=entity_list[0].get_level() 48 for entity in entity_list: 49 if not (entity.get_level()==level): 50 raise PDBException("Entity list is not homogeneous.") 51 target_index=entity_levels.index(target_level) 52 level_index=entity_levels.index(level) 53 if level_index==target_index: 54 # already right level 55 return entity_list 56 if level_index>target_index: 57 # we're going down, e.g. S->A 58 for i in range(target_index, level_index): 59 new_entity_list=[] 60 for entity in entity_list: 61 new_entity_list=new_entity_list+entity.get_list() 62 entity_list=new_entity_list 63 else: 64 # we're going up, e.g. A->S 65 for i in range(level_index, target_index): 66 new_entity_list=[] 67 for entity in entity_list: 68 parent=entity.get_parent() 69 new_entity_list.append(parent) 70 # find unique parents 71 entity_list=uniqueify(new_entity_list) 72 return entity_list
73