def __init__(self, ag, indices, acsi, **kwargs):
AtomPointer.__init__(self, ag, acsi)
if not isinstance(indices, np.ndarray):
indices = np.array(indices, int)
elif not indices.dtype == int:
indices = indices.astype(int)
if kwargs.get('unique'):
self._indices = indices
else:
self._indices = np.unique(indices)
self._selstr = kwargs.get('selstr')
def __init__(self, ag, indices, mapping, dummies, title='Unnamed',
acsi=None, **kwargs):
"""Instantiate an atom map.
:arg ag: AtomGroup instance from which atoms are mapped
:arg indices: indices of mapped atoms
:arg mapping: mapping of the atoms
:arg dummies: list of indices for dummy atoms
:arg title: title of the instance, default is 'Unnamed'
:arg acsi: active coordinate set index, defaults is that of *ag*
Length of *mapping* must be equal to length of *indices*. Number of
atoms (including dummy atoms) are determined from the total lengths
of *mapping* and *dummies* arrays.
Following built-in functions are customized for this class:
* :func:`len` returns the number of atoms in the instance.
* :func:`iter` yields :class:`~.Atom` instances.
* Indexing is not available."""
AtomPointer.__init__(self, ag, acsi)
if not isinstance(indices, np.ndarray):
self._indices = np.array(indices, int)
elif not indices.dtype == int:
self._indices = indices.astype(int)
else:
self._indices = indices
if not isinstance(mapping, np.ndarray):
self._mapping = np.array(mapping, int)
elif not mapping.dtype == int:
self._mapping = mapping.astype(int)
else:
self._mapping = mapping
if not isinstance(dummies, np.ndarray):
self._dummies = np.array(dummies, int)
elif not dummies.dtype == int:
self._dummies = dummies.astype(int)
else:
self._dummies = dummies
self._title = str(title)
self._len = len(self._dummies) + len(self._mapping)
def __init__(self, ag, indices, acsi=None, **kwargs):
"""Instantiate an atom map.
:arg ag: AtomGroup instance from which atoms are mapped
:arg indices: indices of mapped atoms
:arg acsi: active coordinate set index, defaults is that of *ag*
:arg mapping: mapping of atom *indices*
:arg dummies: dummy atom indices
:arg title: title of the instance, default is 'Unknown'
*mapping* and *dummies* arrays must be provided together. Length of
*mapping* must be equal to length of *indices*. Elements of *mapping*
must be an ordered in ascending order. When dummy atoms are present,
number of atoms is the sum of lengths of *mapping* and *dummies*.
Following built-in functions are customized for this class:
* :func:`len` returns the number of atoms in the instance.
* :func:`iter` yields :class:`.Atom` instances.
* Indexing returns an :class:`.Atom` or an :class:`.AtomMap` instance
depending on the type and value of the index."""
AtomPointer.__init__(self, ag, acsi)
self._dummies = self._mapping = None
mapping = kwargs.get('mapping', None)
dummies = kwargs.get('dummies', False)
if mapping is None:
if not kwargs.get('intarrays'):
indices = array(indices, int)
try:
len(dummies)
except TypeError:
pass
else:
raise TypeError('mapping and dummies must be provided '
'together')
self._len = len(indices)
if dummies:
dummies = (indices == DUMMY).nonzero()[0]
if len(dummies):
self._dummies = dummies
self._mapping = (indices < DUMMY).nonzero()[0]
self._indices = indices[self._mapping]
self._idarray = indices
else:
self._indices = self._idarray = indices
else:
self._indices = self._idarray = indices
else:
if dummies is None:
raise TypeError('mapping and dummies must be provided '
'together')
if len(mapping) != len(indices):
raise ValueError('indices and mapping arrays must have the '
'same length')
if not kwargs.get('intarrays'):
indices = array(indices, int)
mapping = array(mapping, int)
dummies = array(dummies, int)
if any(mapping[1:] - mapping[:-1] < 0):
raise ValueError('mapping must be an ordered array')
self._len = len(indices)
if len(dummies):
self._indices = indices
self._mapping = mapping
self._dummies = dummies
self._len += len(dummies)
self._idarray = idarray = zeros(self._len, int)
idarray[self._mapping] = self._indices
idarray[self._dummies] = DUMMY
else:
self._indices = self._idarray = indices[mapping]
self._title = str(kwargs.get('title', 'Unknown'))
def __init__(self, ag, index, acsi):
AtomPointer.__init__(self, ag, acsi)
self._index = int(index)
