/usr/lib/python2.7/dist-packages/cogent/struct/selection.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 | """Contains functions to select and group structural entities."""
from cogent.core.entity import StructureHolder, ModelHolder, ChainHolder, \
ResidueHolder, AtomHolder, HIERARCHY
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
def select(entities, level, *args, **kwargs):
"""Shorthand for ``einput`` and subsequent ``selectChildren``. Returns
Returns a ``Holder`` instance. The "name" can be specified.
Additional arguments and keyworded arguments are passed to the
``selectChildren`` method of the holder instance.
"""
try:
name = kwargs.pop('name')
except KeyError:
name = 'select'
holder = einput(entities, level)
selection = holder.selectChildren(*args, **kwargs)
try:
holder = einput(selection.values(), level, name)
except ValueError:
raise ValueError('No entities have been selected')
return holder
def einput(entities, level, name=None):
"""Creates a ``XyzHolder`` instance of entities at the specified level. Where
Xyz is 'Structure', 'Model', 'Chain', Residue' or 'Atom'.
Arguments:
- entities: ``Entity`` instance or sequence of entities.
- level: one of 'H', 'S', 'M', 'C', 'R', 'A'
- name: optional name of the ``XyzHolder`` instance.
"""
# Keep it bug-free
all = {}
index = HIERARCHY.index(level)
for entity in entities: # __iter__ override in Entity
if index > HIERARCHY.index(entity.level): # call for children
all.update(get_children(entity, level))
elif index < HIERARCHY.index(entity.level): # call for parents
all.update(get_parent(entity, level))
else:
all.update({entity.getFull_id():entity}) # call for self
higher_level = HIERARCHY[index - 1] # one up;)
if all:
name = name or higher_level
if higher_level == 'C':
holder = ResidueHolder(name, all)
elif higher_level == 'R':
holder = AtomHolder(name, all)
elif higher_level == 'M':
holder = ChainHolder(name, all)
elif higher_level == 'S':
holder = ModelHolder(name, all)
elif higher_level == 'H':
holder = StructureHolder(name, all)
else:
raise ValueError, "einput got no input entites."
holder.setSort_tuple()
return holder
def get_children(entity, level):
"""Return unique entities of lower or equal level
Arguments:
- entity: any ``Entity`` instance.
- level: one of 'H', 'S', 'M', 'C', 'R', 'A'
"""
entity.setTable()
return entity.table[level]
def get_parent(entity, level):
"""Returns unique entities of higher level.
Arguments:
- entity: any ``Entity`` instance.
- level: one of 'H', 'S', 'M', 'C', 'R', 'A'
"""
parent = entity.getParent(level) # get the correct parent
return {parent.getFull_id(): parent}
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