def asa_xtra(entities, mode='internal', xtra_key=None, **asa_kwargs):
"""Calculates accessible surface areas (ASA) and puts the results into the
xtra dictionaries of entities.
Arguments:
- entities: an entity or sequence of entities
- mode(str): 'internal' for calculations using the built-in cython code
or 'stride' if the stride binary should be called to do the job.
- xtra_key(str): Key in the xtra dictionary to hold the result for each
entity
Additional keyworded arguments are passed to the ``_prepare_asa`` and
``_run_asa`` functions.
"""
xtra_key = xtra_key or 'ASA'
structures = einput(entities, 'S')
if len(structures.values()) > 1:
raise ValueError(
'Entities from multiple structures are not supported.')
if mode == 'internal':
_prepare_entities(entities) # mask waters
result = _prepare_asa(entities, **asa_kwargs) # calculate ASA
_postpare_entities(entities) # unmask waters
result = dict([(id, {xtra_key: v}) for id, v in result.iteritems()])
xtradata(result, structures)
elif mode == 'stride':
models = einput(entities, 'M')
stride_app = Stride()
result = stride_app(entities)['StdOut'].readlines()
result = stride_parser(result)
xtradata(result, structures.values()[0][(0, )])
else:
raise ValueError('Not a valid mode: "%s"' % mode)
return result
def test_stdout_input_from_path(self):
"""Test Stride when input is an entity"""
s = Stride(InputHandler='_input_as_path')
res = s(self.input_file)
self.assertEqual(res['ExitStatus'], 0)
assert res['StdOut'] is not None
self.assertTrue(res['StdOut'].readline().endswith('--------- 2E12\n'))
self.assertEqual(len(res['StdOut'].readlines()), 267)
res.cleanUp()
def test_get_result_path(self):
"""Tests stride result path"""
s = Stride()
fd, name = tempfile.mkstemp()
os.close(fd)
s.Parameters['-f'].on(name)
res = s(self.input_structure)
self.assertEqual(res['ExitStatus'], 0)
self.assertEqualItems(res.keys(), ['StdOut', 'StdErr', 'ExitStatus', 'File'])
self.assertTrue(res['File'].readline().endswith('--------- 2E12\n'))
self.assertEquals(len(res['File'].readlines()), 267)
res.cleanUp()
self.assertFalse(os.path.exists(name))
def setUp(self):
input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(input_file))
stride_app = Stride()
res = stride_app(self.input_structure)
self.lines = res['StdOut'].readlines()