StructureAtom

class sknano.core.atoms.StructureAtom(*args, **kwargs)[source] [edit on github][source]

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.