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# Copyright (C) 2002, Thomas Hamelryck ([email protected])
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Selection of atoms, residues, etc."""
import itertools
from Bio.PDB.Atom import Atom
from Bio.PDB.Entity import Entity
from Bio.PDB.PDBExceptions import PDBException
entity_levels = ["A", "R", "C", "M", "S"]
def uniqueify(items):
"""Return a list of the unique items in the given iterable.
Order is NOT preserved.
"""
return list(set(items))
def get_unique_parents(entity_list):
"""Translate a list of entities to a list of their (unique) parents."""
unique_parents = {entity.get_parent() for entity in entity_list}
return list(unique_parents)
def unfold_entities(entity_list, target_level):
"""Unfold entities list to a child level (e.g. residues in chain).
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
- entity_list - list of entities or a single entity
- target_level - char (A, R, C, M, S)
Note that if entity_list is an empty list, you get an empty list back:
>>> unfold_entities([], "A")
[]
"""
if target_level not in entity_levels:
raise PDBException(f"{target_level}: Not an entity level.")
if entity_list == []:
return []
if isinstance(entity_list, (Entity, Atom)):
entity_list = [entity_list]
level = entity_list[0].get_level()
if not all(entity.get_level() == level for entity in entity_list):
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
entities = entity_list
if level_index > target_index: # we're going down, e.g. S->A
for i in range(target_index, level_index):
entities = itertools.chain.from_iterable(entities)
else: # we're going up, e.g. A->S
for i in range(level_index, target_index):
# get unique parents by removing duplicates while preserving order
entities = {entity.get_parent(): None for entity in entities}
return list(entities)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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