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.