1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
|
from types import ListType
from PDBExceptions import PDBException
__doc__="Selection of atoms, residues, etc."
entity_levels=["A", "R", "C", "M", "S"]
def uniqueify(l):
"Return unique items in list l."
d={}
for i in l:
if not d.has_key(i):
d[i]=None
return d.keys()
def get_unique_parents(entity_list):
"""
Translate a list of entities to a list of their
(unique) parents.
"""
l=[]
for entity in entity_list:
parent=entity.get_parent()
l.append(parent)
return uniqueify(l)
def unfold_entities(entity_list, target_level):
"""
Unfold a list of entities to a list of entities of another
level. E.g.:
list of atoms -> list of residues
list of modules -> list of atoms
list of residues -> list of chains
o entity_list - list of entities or a single entity
o target_level - char (A, R, C, M, S)
"""
if not target_level in entity_levels:
raise PDBException, "%s: Not an entity level." % target_level
if type(entity_list)!=ListType:
# single entity
entity_list=[entity_list]
# level of entity list
level=entity_list[0].get_level()
for entity in entity_list:
if not (entity.get_level()==level):
raise PDBException, "Entity list is not homogeneous."
target_index=entity_levels.index(target_level)
level_index=entity_levels.index(level)
if level_index==target_index:
# already right level
return entity_list
if level_index>target_index:
# we're going down, e.g. S->A
for i in range(target_index, level_index):
new_entity_list=[]
for entity in entity_list:
new_entity_list=new_entity_list+entity.get_list()
entity_list=new_entity_list
else:
# we're going up, e.g. A->S
for i in range(level_index, target_index):
new_entity_list=[]
for entity in entity_list:
parent=entity.get_parent()
new_entity_list.append(parent)
# find unique parents
entity_list=uniqueify(new_entity_list)
return entity_list
|
