Atoms

class sknano.core.atoms.Atoms(atoms=None, update_item_class=True, **kwargs)

Bases: sknano.core.strings.TabulateMixin, sknano.core.collections.UserList

Base class for collection of Atom objects.

Parameters:atoms ({None, sequence, Atoms}, optional) – if not None, then a list of Atom instance objects or an existing Atoms instance object.

Attributes

M	Total mass of Atoms.
Natoms	Number of atoms in Atoms.
elements	ndarray of Atom.elements.
fmtstr	Format string.
masses	ndarray of Atom.masss.
symbols	ndarray of Atom.symbols.

Methods

append(atom)
clear()
copy()
count(item)
extend(other)
filter(condition[, invert])	Filter Atoms by condition.
filtered(condition[, invert])	Return new list of Atoms filtered by condition.
get_atoms([asarray, aslist])	Return Atoms either as list (default) or numpy array or self.
getattr(attr[, default, recursive])	Get ndarray of atom attributes attr.
index(item, *args)
insert(i, atom)
mapatomattr([from_attr, to_attr, attrmap])	Set/update atom attribute from another atom attribute with dict.
pop([i])
remove(item)
reset_attrs(**kwargs)	Call corresponding reset_attrs method on each atom
reverse()
rezero([epsilon])	Set values with absolute value less than epsilon to zero.
select([selstr, selstrlist, verbose])	Return Atom or Atoms from selection command.
sort([key, reverse])
todict()	Return dict of constructor parameters.
update_attrs(**kwargs)	Call update_attrs method on each atom.