StructureAtom

class sknano.core.atoms.StructureAtom(*args, **kwargs)

Bases: sknano.core.atoms.mixins.AtomAdapterMixin, sknano.core.atoms.mixins.AtomTopologyMixin, sknano.core.atoms.mixins.AtomTransformationsMixin, sknano.core.atoms.mixins.POAVAtomMixin, sknano.core.atoms.mixins.RingAtomMixin, sknano.core.atoms.neighbor_atoms.NeighborAtom, sknano.core.atoms.image_atoms.ImageAtom, sknano.core.atoms.lattice_atoms.LatticeAtom, sknano.core.atoms.xyz_atoms.XYZAtom, sknano.core.atoms.charged_atoms.ChargedAtom, sknano.core.atoms.type_atoms.TypeAtom, sknano.core.atoms.id_atoms.IDAtom

An Atom class for structure analysis.

Attributes

CN	NeighborAtom coordination number.
NN	Nearest-neighbor Atoms.
Nneighbors	Number of neighbors.
POAV1	POAV1 instance.
POAV2	POAV2 instance.
POAVR	POAVR instance.
Z	Atomic number $Z$.
angles	Atom bond Angles.
atomID	Alias for id.
atomtype
bonds	Atom Bonds
dihedrals	Atom Dihedrals
dr	$x, y, z$ components of Atom displacement vector.
element	Element symbol.
first_neighbors	First nearest neighbors.
fmtstr	Format string.
i	$i_x, i_y, i_z$ image flags
id	id.
impropers	Atom Impropers
ix	$i_x$ image flag.
iy	$i_y$ image flag.
iz	$i_z$ image flag.
lattice	Crystal3DLattice.
m	An alias for mass.
mass	Atomic mass $m_a$ in atomic mass units.
mol	mol.
moleculeID	Alias for mol.
molid	An alias for mol.
neighbor_distances	Neighbor atom distances.
neighbor_map	Neighbor atoms.
neighbors	Neighbor atoms.
q	Charge $q$ as multiple of elementary charge $e$.
r	$x, y, z$ components of Atom position vector.
r0	$x, y, z$ components of Atom position vector at t=0.
rs	Scaled $x, y, z$ components of Atom position vector.
second_neighbors	Second nearest neighbors
serial	Alias for id.
symbol	Element symbol.
third_neighbors	Third nearest neighbors
type	type.
vmd_index	VMD atom index attribute.
x	$x$-coordinate in units of Angstroms.
xs	Scaled $x$-coordinate.
y	$y$-coordinate in units of Angstroms.
ys	Scaled $y$-coordinate.
z	$z$-coordinate in units of Angstroms.
zs	Scaled $z$-coordinate.

Methods

get_coords([asdict])	Return atom coords.
get_nth_nearest_neighbors(n[, exclusive])	Get the `n`th set of neighbors.
getattr(attr[, default, recursive])	Get atom attribute named attr.
reset_attrs(**kwargs)	Reset atom attributes.
rezero([epsilon])	Alias for Atom.rezero_xyz, but calls super class rezero method as well.
rezero_coords([epsilon])	Alias for Atom.rezero_xyz.
rezero_xyz([epsilon])	Re-zero position vector components.
rotate(**kwargs)	Rotate Atom position vector.
set_nth_nearest_neighbors(n, neighbors)	Set nth nearest neighbors
todict()	Return dict of constructor parameters.
translate(t[, fix_anchor_point, cartesian])	Translate Atom position vector by Vector t.
update_attrs(**kwargs)	Update atom attributes.