IDAtoms

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

Bases: sknano.core.atoms.atoms.Atoms

An Atoms sub-class for IDAtoms.

Sub-class of Atoms class, and a container class for lists of IDAtom instances.

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

Attributes

M	Total mass of Atoms.
Natoms	Number of atoms in Atoms.
atom_ids	Alias for ids.
elements	ndarray of Atom.elements.
fmtstr	Format string.
ids	Return array of IDAtom.ids.
indices	Return array of IDAtom.indexs.
masses	ndarray of Atom.masss.
mol_ids	Alias for mols.
molecule_ids	Alias for mols.
mols	Return array of IDAtom.mols.
serials	Alias for ids.
symbols	ndarray of Atom.symbols.

Methods

append(atom)
assign_unique_ids([starting_id])	Assign unique IDAtom.id to each IDAtom in IDAtoms.
clear()
copy()
count(item)
extend(other)
filter(condition[, invert])	Filter Atoms by condition.
filter_ids(atom_ids[, invert])	Filter Atoms by IDAtoms.ids in atom_ids.
filtered(condition[, invert])	Return new list of Atoms filtered by condition.
filtered_ids(atom_ids[, invert])	Return new Atoms object filtered by atom_ids.
get_atom(id)	Get IDAtom with Xatom.id == id.
get_atoms([ids])	Overrides parent class Atoms.get_atoms.
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.