def parseEMDStream(stream, **kwargs):
""" Returns an :class:`.AtomGroup` containing EMD data parsed from a stream of EMD file.
:arg stream: Any object with the method ``readlines``
(e.g. :class:`file`, buffer, stdin)"""
cutoff = kwargs.get('cutoff', None)
if cutoff is not None:
cutoff = float(cutoff)
n_nodes = kwargs.get('n_nodes', 0)
num_iter = int(kwargs.get('num_iter', 20))
map = kwargs.get('map', False)
make_nodes = kwargs.get('make_nodes', False)
if n_nodes > 0:
make_nodes = True
n_nodes = int(n_nodes)
if map is False and make_nodes is False:
LOGGER.warn(
'At least one of map and make_nodes should be True. '
'Setting map to False was an intentional change from the default '
'behaviour so make_nodes has been set to True with n_nodes=1000.')
make_nodes = True
n_nodes = 1000
title_suffix = kwargs.get('title_suffix', '')
atomgroup = AtomGroup(str(kwargs.get('title', 'Unknown')) + title_suffix)
atomgroup._n_atoms = n_nodes
if make_nodes:
LOGGER.info(
'Building coordinates from electron density map. This may take a while.'
)
LOGGER.timeit()
if map:
emd, atomgroup = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \
num_iter=num_iter, map=map, make_nodes=make_nodes)
else:
atomgroup = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \
num_iter=num_iter, map=map, make_nodes=make_nodes)
LOGGER.report('{0} pseudoatoms were fitted in %.2fs.'.format(
atomgroup.numAtoms(), atomgroup.numCoordsets()))
else:
emd = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \
num_iter=num_iter, map=map, make_nodes=make_nodes)
if make_nodes:
if map:
return emd, atomgroup
else:
return atomgroup
else:
return emd
def parseEMDStream(stream, **kwargs):
""" Returns an :class:`.AtomGroup` containing EMD data parsed from a stream of EMD file.
:arg stream: Any object with the method ``readlines``
(e.g. :class:`file`, buffer, stdin)"""
cutoff = kwargs.get('cutoff', None)
if cutoff is not None:
cutoff = float(cutoff)
n_nodes = int(kwargs.get('n_nodes', 1000))
num_iter = int(kwargs.get('num_iter', 20))
map = kwargs.get('map',True)
make_nodes = kwargs.get('make_nodes',False)
if map is False and make_nodes is False:
LOGGER.warn('At least one of map and make_nodes should be True. '
'Setting map to False was an intentional change from the default '
'behaviour so make_nodes has been set to True.')
make_nodes = True
title_suffix = kwargs.get('title_suffix','')
atomgroup = AtomGroup(str(kwargs.get('title', 'Unknown')) + title_suffix)
atomgroup._n_atoms = n_nodes
if make_nodes:
LOGGER.info('Building coordinates from electron density map. This may take a while.')
LOGGER.timeit()
if map:
emd, atomgroup = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \
num_iter=num_iter, map=map, make_nodes=make_nodes)
else:
atomgroup = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \
num_iter=num_iter, map=map, make_nodes=make_nodes)
LOGGER.report('{0} atoms and {1} coordinate sets were '
'parsed in %.2fs.'.format(atomgroup.numAtoms(), atomgroup.numCoordsets()))
else:
emd = _parseEMDLines(atomgroup, stream, cutoff=cutoff, n_nodes=n_nodes, \
num_iter=num_iter, map=map, make_nodes=make_nodes)
if make_nodes:
if map:
return emd, atomgroup
else:
return atomgroup
else:
return emd
def parseEMDStream(stream, **kwargs):
"""Parse lines of data stream from an EMD/MRC2014 file and
optionally return an :class:`.AtomGroup` containing TRN
nodes based on it.
:arg stream: Any object with the method ``readlines``
(e.g. :class:`file`, buffer, stdin)
"""
cutoff = kwargs.get('cutoff', None)
min_cutoff = kwargs.get('min_cutoff', cutoff)
if min_cutoff is not None:
if isinstance(min_cutoff, Number):
min_cutoff = float(min_cutoff)
else:
raise TypeError('min_cutoff should be a number or None')
max_cutoff = kwargs.get('max_cutoff', None)
if max_cutoff is not None:
if isinstance(max_cutoff, Number):
max_cutoff = float(max_cutoff)
else:
raise TypeError('max_cutoff should be a number or None')
n_nodes = kwargs.get('n_nodes', 0)
num_iter = int(kwargs.get('num_iter', 20))
map = kwargs.get('map', False)
if not isinstance(n_nodes, int):
raise TypeError('n_nodes should be an integer')
if n_nodes > 0:
make_nodes = True
else:
make_nodes = False
map = True
LOGGER.info('As n_nodes is less than or equal to 0, no nodes will be'
' made and the raw map will be returned')
emd = EMDMAP(stream, min_cutoff, max_cutoff)
if make_nodes:
title_suffix = kwargs.get('title_suffix', '')
atomgroup = AtomGroup(
str(kwargs.get('title', 'Unknown')) + title_suffix)
atomgroup._n_atoms = n_nodes
coordinates = np.zeros((n_nodes, 3), dtype=float)
atomnames = np.zeros(n_nodes, dtype=ATOMIC_FIELDS['name'].dtype)
resnames = np.zeros(n_nodes, dtype=ATOMIC_FIELDS['resname'].dtype)
resnums = np.zeros(n_nodes, dtype=ATOMIC_FIELDS['resnum'].dtype)
chainids = np.zeros(n_nodes, dtype=ATOMIC_FIELDS['chain'].dtype)
trn = TRNET(n_nodes=n_nodes)
trn.inputMap(emd, sample='density')
trn.run(tmax=num_iter)
for i in range(n_nodes):
coordinates[i, :] = trn.W[i, :]
atomnames[i] = 'B'
resnames[i] = 'CGB'
resnums[i] = i + 1
chainids[i] = 'X'
atomgroup.setCoords(coordinates)
atomgroup.setNames(atomnames)
atomgroup.setResnames(resnames)
atomgroup.setResnums(resnums)
atomgroup.setChids(chainids)
if make_nodes:
if map:
return atomgroup, emd
else:
return atomgroup
else:
return emd
