class HasCathIDMixin(object):
"""
Mixin for classes that contain a :class:`cathpy.core.models.CathID`
Usage:
.. code:: python
class MyClass(HasCathIDMixin, object):
def __init__(self, *, cath_id, **kwargs):
super(MyClass, self).super(cath_id=cath_id)
Provides:
.. code:: python
self.cath_id
self.cath_id_depth
self.sfam_id
self.cath_id_to_depth(n)
"""
def __init__(self, *, cath_id, **kwargs):
super().__init__(**kwargs)
self._cath_id = CathID(cath_id)
@property
def cath_id(self):
"""
Returns the full CATH ID
"""
return self._cath_id.cath_id
@property
def cath_id_depth(self):
"""
Returns the depth of the CATH ID (eg '1.10.8' = 3)
"""
return self._cath_id.depth
@property
def sfam_id(self):
"""
Returns the Superfamily ID of the CATH ID
"""
return self._cath_id.cath_id_to_depth(4)
def cath_id_to_depth(self, depth):
"""
Returns the CATH ID to a given depth
"""
return self._cath_id.cath_id_to_depth(depth)
def __lt__(self, other):
if isinstance(other, str):
other = CathID(other)
return self._cath_id < other._cath_id
def filter_cath_id(self, cath_id):
"""
Returns a new container after filtering to only include entries within a given CATH ID
"""
if not isinstance(cath_id, CathID):
cath_id = CathID(cath_id)
depth = cath_id.depth
filtered_entries = [
c for c in self.entries if c.cath_id_to_depth(depth) == cath_id]
return self.__class__(entries=filtered_entries)
def test_cath_id(self):
self.assertEqual(str(CathID("1")), "1")
self.assertEqual(str(CathID("1.10.8")), "1.10.8")
self.assertEqual(str(CathID("1.10.8.10.1.1.1.2.3")),
"1.10.8.10.1.1.1.2.3")
self.assertEqual(CathID("1.10.8.10").sfam_id, "1.10.8.10")
self.assertEqual(CathID("1.10.8.10.1").sfam_id, "1.10.8.10")
with self.assertRaises(OutOfBoundsError) as err:
cath_id = CathID("1.10.8").sfam_id
self.assertRegex(err.exception, r'require depth',
'sfam_id fails when depth < 4')
def __lt__(self, other):
if isinstance(other, str):
other = CathID(other)
return self._cath_id < other._cath_id
def __init__(self, *, cath_id, **kwargs):
super().__init__(**kwargs)
self._cath_id = CathID(cath_id)