def test_xtradata(self):
"""tests if an full_id's in the data dict are correctly parsed."""
structure = einput(self.input_structure, 'S')[('2E12',)]
model = einput(self.input_structure, 'M')[('2E12', 0)]
chain = einput(self.input_structure, 'C')[('2E12', 0, 'B')]
residue = einput(self.input_structure, 'R')[('2E12', 0, 'B', ('LEU', 24, ' '))]
atom = einput(self.input_structure, 'A')[('2E12', 0, 'B', ('LEU', 24, ' '), ('CD1', ' '))]
data_model = {(None, 0):{'model':1}}
xtradata(data_model, structure)
self.assertEquals(model.xtra, {'model': 1})
data_chain = {(None, None, 'B'):{'chain':1}}
xtradata(data_chain, model)
self.assertEquals(chain.xtra, {'chain': 1})
data_chain = {(None, 0, 'B'):{'chain': 2}}
xtradata(data_chain, structure)
self.assertEquals(chain.xtra['chain'], 2)
data_residue = {(None, None, 'B', ('LEU', 24, ' ')):{'residue':1}}
xtradata(data_residue, model)
self.assertEquals(residue.xtra, {'residue': 1})
data_residue = {(None, 0, 'B', ('LEU', 24, ' ')):{'residue':2}}
xtradata(data_residue, structure)
self.assertEquals(residue.xtra, {'residue': 2})
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 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
def contacts_xtra(query, xtra_key=None, **cnt_kwargs):
"""Finds distance contacts between entities. This function searches for
contacts for query entities (query) either within the asymmetric unit,
biological molecule, unit-cell or crystal.
Arguments:
- query (entitie[s]): query entity or sequence entities
- xtra_key (str): name of the key
Additional keyworded arguments are passed to the ``_prepare_contacts``
functon.
"""
xtra_key = xtra_key or 'CONTACTS'
structures = einput(query, 'S')
if len(structures.values()) > 1:
raise ValueError('Entities from multiple structures are not supported.')
result = _prepare_contacts(query, **cnt_kwargs) # calculate CONTACTS
result = dict([(id, {xtra_key:v}) for id, v in result.iteritems()])
xtradata(result, structures)
return result
def contacts_xtra(query, xtra_key=None, **cnt_kwargs):
"""Finds distance contacts between entities. This function searches for
contacts for query entities (query) either within the asymmetric unit,
biological molecule, unit-cell or crystal.
Arguments:
- query (entitie[s]): query entity or sequence entities
- xtra_key (str): name of the key
Additional keyworded arguments are passed to the ``_prepare_contacts``
functon.
"""
xtra_key = xtra_key or 'CONTACTS'
structures = einput(query, 'S')
if len(list(structures.values())) > 1:
raise ValueError('Entities from multiple structures are not supported.')
result = _prepare_contacts(query, **cnt_kwargs) # calculate CONTACTS
result = dict([(id, {xtra_key:v}) for id, v in result.items()])
xtradata(result, structures)
return result