sknano.core.atoms.VanDerWaalsAtoms

class sknano.core.atoms.VanDerWaalsAtoms(atoms=None, casttype=True, **kwargs)[source][source]

An Atoms sub-class for VanDerWaalsAtoms.

A container class for VanDerWaalsAtom objects.

Parameters:

atoms : {None, sequence, ChargedAtoms}, optional

if not None, then a list of ChargedAtom instance objects or an existing ChargedAtoms instance object.

Attributes

M Total mass of Atoms.
Natoms Number of atoms in Atoms.
elements ndarray of Atom.elements in Atoms.
fmtstr
masses ndarray of Atom.masss in Atoms.
r_vdw Return array of VanDerWaalsAtom van der Waals radii.
symbols ndarray of Atom.symbols in Atoms.

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]) Return list of Atoms.
getatomattr(attr) Get ndarray of atom attributes attr.
index(item, *args)
insert(i, item)
mapatomattr([from_attr, to_attr, attrmap]) Set/update atom attribute from another atom attribute with dict.
pop([i])
remove(item)
reverse()
rezero([epsilon]) Set values with absolute value less than epsilon to zero.
rotate(**kwargs) Rotate Atom vectors.
sort([key, reverse])
todict()
translate(t[, fix_anchor_points]) Translate Atom vectors by Vector t.