def __init__(self, title='Unnamed'):
self._title = str(title)
self._n_atoms = 0
self._coords = None
self._hv = None
self._sn2i = None
self._timestamps = None
self._kdtrees = None
self._bmap = None
self._bonds = None
self._cslabels = []
self._acsi = None
self._n_csets = 0
self._data = dict([(field.var, None)
for field in ATOMIC_DATA_FIELDS.itervalues()])
def __init__(cls, name, bases, dict):
for field in ATOMIC_DATA_FIELDS.values():
meth = field.meth
getMeth = 'get' + meth
setMeth = 'set' + meth
# Define public method for retrieving a copy of data array
if field.call:
def getData(self, var=field.var, call=field.call):
for meth in call:
getattr(self._ag, meth)()
array = self._ag._data[var]
return array[self._index]
else:
def getData(self, var=field.var):
array = self._ag._data[var]
if array is None:
return None
return array[self._index]
getData = wrapGetMethod(getData)
getData.__name__ = getMeth
getData.__doc__ = field.getDocstr('set', False)
setattr(cls, getMeth, getData)
setattr(cls, '_' + getMeth, getData)
if field.readonly:
continue
# Define public method for setting values in data array
def setData(self, value, var=field.var, none=field.none):
array = self._ag._data[var]
if array is None:
raise AttributeError('attribute of the AtomGroup is '
'not set')
array[self._index] = value
if None:
self._ag.__setattr__('_' + none, None)
setData = wrapSetMethod(setData)
setData.__name__ = setMeth
setData.__doc__ = field.getDocstr('set', False)
setattr(cls, setMeth, setData)
def __init__(cls, name, bases, dict):
for field in ATOMIC_DATA_FIELDS.values():
meth = field.meth_pl
getMeth = 'get' + meth
if field.call:
def getData(self, var=field.var, call=field.call,
dtype=field.dtype):
for meth in call:
getattr(self._ag, meth)()
data = self._ag._data[var][self._indices]
result = np.zeros((self._len,) + data.shape[1:], dtype)
result[self._mapping] = data
return result
else:
def getData(self, var=field.var, dtype=field.dtype):
array = self._ag._data[var]
if array is None:
return None
data = self._ag._data[var][self._indices]
result = np.zeros((self._len,) + data.shape[1:], dtype)
result[self._mapping] = data
return result
getData = wrapGetMethod(getData)
getData.__name__ = getMeth
if field.dtype in (int, float):
zero = '0'
elif field.dtype == bool:
zero = 'True'
else:
zero = '""'
getData.__doc__ = field.getDocstr('get', selex=False) + \
'Entries for dummy atoms will be ``{0:s}``.'.format(zero)
setattr(cls, getMeth, getData)
setattr(cls, '_' + getMeth, getData)
def __init__(cls, name, bases, dict):
for field in ATOMIC_DATA_FIELDS.values():
meth = field.meth_pl
getMeth = 'get' + meth
setMeth = 'set' + meth
# Define public method for retrieving a copy of data array
if field.call:
def getData(self, var=field.var, call=field.call):
for meth in call:
getattr(self, meth)()
array = self._data[var]
return array.copy()
else:
def getData(self, var=field.var):
array = self._data[var]
if array is None:
return None
return array.copy()
getData = wrapGetMethod(getData)
getData.__name__ = getMeth
getData.__doc__ = field.getDocstr('get')
setattr(cls, getMeth, getData)
# Define private method for retrieving actual data array
def _getData(self, var=field.var):
return self._data[var]
_getData = wrapGetMethod(_getData)
_getData.__name__ = '_' + getMeth
_getData.__doc__ = field.getDocstr('_get')
setattr(cls, '_' + getMeth, _getData)
if field.readonly:
continue
# Define public method for setting values in data array
def setData(self, array, var=field.var, dtype=field.dtype,
ndim=field.ndim, none=field.none):
if self._n_atoms == 0:
self._n_atoms = len(array)
elif len(array) != self._n_atoms:
raise ValueError('length of array must match numAtoms')
if isinstance(array, list):
array = np.array(array, dtype)
elif not isinstance(array, np.ndarray):
raise TypeError('array must be an ndarray or a list')
elif array.ndim != ndim:
raise ValueError('array must be {0:d} dimensional'
.format(ndim))
elif array.dtype != dtype:
try:
array = array.astype(dtype)
except ValueError:
raise ValueError('array cannot be assigned type '
'{0:s}'.format(dtype))
self._data[var] = array
if none:
self.__setattr__('_'+none, None)
setData = wrapSetMethod(setData)
setData.__name__ = setMeth
setData.__doc__ = field.getDocstr('set')
setattr(cls, setMeth, setData)
