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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() | |