def addNewAtom(self, *args, **kwargs):
"""Add new Atom instance to the end of this Structure.
All arguments are forwarded to Atom constructor.
No return value.
"""
kwargs['lattice'] = self.lattice
a = QEAtom(*args, **kwargs)
list.append(self, a)
self._uncache('labels')
def append(self, a, copy=True):
"""Append atom to a structure and update its lattice attribute.
a -- instance of QEAtom
copy -- flag for appending a copy of a.
When False, append a and update a.owner.
No return value.
"""
self._uncache('labels')
adup = copy and QEAtom(a) or a
adup.lattice = self.lattice
list.append(self, adup)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def __setitem__(self, idx, a, copy=True):
"""Set idx-th atom to a.
idx -- index of atom in this Structure
a -- instance of QEAtom
copy -- flag for setting to a copy of a.
When False, set to a and update a.lattice.
No return value.
"""
self._uncache('labels')
adup = copy and QEAtom(a) or a
adup.lattice = self.lattice
list.__setitem__(self, idx, adup)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def insert(self, idx, a, copy=True):
"""Insert atom a before position idx in this Structure.
idx -- position in atom list
a -- instance of QEAtom
copy -- flag for inserting a copy of a.
When False, append a and update a.lattice.
No return value.
"""
self._uncache('labels')
adup = copy and QEAtom(a) or a
adup.lattice = self.lattice
list.insert(self, idx, adup)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def extend(self, atoms, copy=True):
"""Extend Structure by appending copies from a list of atoms.
atoms -- list of QEAtom instances
copy -- flag for extending with copies of QEAtom instances.
When False extend with atoms and update their lattice
attributes.
No return value.
"""
self._uncache('labels')
if copy: adups = [QEAtom(a) for a in atoms]
else: adups = atoms
for a in adups:
a.lattice = self.lattice
list.extend(self, adups)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def __setslice__(self, lo, hi, atoms, copy=True):
"""Set Structure slice from lo to hi-1 to the sequence of atoms.
lo -- low index for the slice
hi -- high index of the slice
atoms -- sequence of Atom instances
copy -- flag for using copies of Atom instances. When False, set
to existing instances and update their lattice attributes.
No return value.
"""
self._uncache('labels')
if copy: adups = [QEAtom(a) for a in atoms]
else: adups = atoms
for a in adups:
a.lattice = self.lattice
list.__setslice__(self, lo, hi, adups)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return