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 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_stride_parser(self):
"""tests if output is parsed fully"""
id_xtra = stride_parser(self.lines)
assert len(id_xtra) < len(self.input_structure[(0,)][('A',)]) + \
len(self.input_structure[(0,)][('B',)])
self.input_structure[(0, )][('A', )].remove_hetero()
self.input_structure[(0, )][('B', )].remove_hetero()
assert len(id_xtra) == len(self.input_structure[(0,)][('A',)]) + \
len(self.input_structure[(0,)][('B',)])
def test_stride_parser(self):
"""tests if output is parsed fully"""
id_xtra = stride_parser(self.lines)
assert len(id_xtra) < len(self.input_structure[(0,)][('A',)]) + \
len(self.input_structure[(0,)][('B',)])
self.input_structure[(0,)][('A',)].remove_hetero()
self.input_structure[(0,)][('B',)].remove_hetero()
assert len(id_xtra) == len(self.input_structure[(0,)][('A',)]) + \
len(self.input_structure[(0,)][('B',)])
def stride_xtra(entities, **kwargs):
"""Runs the stride application and maps the result on the residue xtra
dictionaries.
"""
structures = einput(entities, 'S')
if len(structures.values()) > 1:
raise ValueError('Entities from multiple structures are not supported.')
stride_app = Stride(**kwargs)
result = stride_app(entities)['StdOut'].readlines()
result = stride_parser(result)
xtradata(result, structures.values()[0][(0,)])
return result
def stride_xtra(entities, **kwargs):
"""Runs the stride application and maps the result on the residue xtra
dictionaries.
"""
structures = einput(entities, 'S')
if len(structures.values()) > 1:
raise ValueError('Entities from multiple structures are not supported.')
stride_app = Stride(**kwargs)
result = stride_app(entities)['StdOut'].readlines()
result = stride_parser(result)
xtradata(result, structures.values()[0][(0,)])
return result