def residues(self, **kwargs):
"""Get residues from this structure. The keyword arguments work as
described by EntitySelector.
:kwargs: Keywords for filtering and ordering
:returns: The requested residues.
"""
if 'polymeric' not in kwargs:
kwargs['polymeric'] = True
if kwargs.get('polymeric', False) is None:
kwargs.pop('polymeric')
return EntitySelector(self._residues, **kwargs)
def atoms(self, **kwargs):
"""Get, filter and sort the atoms in this component. Access is as
described by EntitySelector.
:kwargs: The keyword arguments to filter and sort by.
:returns: A list of the requested atoms.
"""
name = kwargs.get('name')
if isinstance(name, basestring):
definition = self.centers.definition(name)
if definition:
kwargs['name'] = definition
return EntitySelector(self._atoms, **kwargs)
def test_can_filter_by_method_to_find_several(self):
ids = ['1S72|1|A|C|1', '1S72|1|A|C|3']
val = sorted(EntitySelector(self.atoms, component_unit_id=ids),
key=lambda a: a.name)
self.assertEquals([self.atoms[0], self.atoms[2]], val)
def test_can_filter_by_method_to_find_one(self):
comp_id = '1S72|1|A|C|1'
val = list(EntitySelector(self.atoms, component_unit_id=comp_id))
self.assertEquals([self.atoms[2]], val)
def test_it_does_not_fail_if_missing_attribute_used(self):
val = sorted(EntitySelector(self.atoms, name3=('a1', 'c2'), type='N'),
key=lambda a: a.name)
self.assertEquals([], val)
def test_can_filter_by_several(self):
val = sorted(EntitySelector(self.atoms, name=('a1', 'c2'), type='N'),
key=lambda a: a.name)
self.assertEquals([self.atoms[3]], val)
def test_can_filter_by_function_using_object(self):
val = sorted(EntitySelector(self.atoms, _=lambda a: a.x >= 2),
key=lambda a: a.name)
self.assertEquals([self.atoms[1], self.atoms[2]], val)
def test_can_select_with_set_of_names(self):
val = sorted(EntitySelector(self.atoms, name=set(['a1', 'c2'])),
key=lambda a: a.name)
self.assertEquals([self.atoms[0], self.atoms[3]], val)
def test_can_select_by_one_name(self):
val = list(EntitySelector(self.atoms, name='a1'))
self.assertEquals([self.atoms[0]], val)
def test_gives_nothing_if_no_match(self):
val = list(EntitySelector(self.atoms, name='bob'))
self.assertEquals([], val)
def test_matches_everything_with_empty_filter(self):
filter = {}
val = len(list(EntitySelector(self.atoms), **filter))
self.assertEquals(4, val)
def test_can_iterate_over_all(self):
val = len(list(EntitySelector(self.atoms)))
self.assertEquals(4, val)
def test_can_filter_using_method_and_lambda(self):
comp_id = '1S72|1|A|C|1'
val = list(
EntitySelector(self.atoms,
component_unit_id=lambda t: t == comp_id))
assert [self.atoms[2]] == val
def test_can_filter_using_op(self):
val = list(EntitySelector(self.atoms, type=ft.partial(op.eq, 'C')))
assert [self.atoms[0], self.atoms[1]] == val