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quantized.atom Module

This module contains the atom class

Classes

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Atom

Atom(element, x, y, z)

Atom class containing coordinates, basis and mass. The atom will generally not be used in isolation, but will likely be part of a molecule. This is expected to be used as a structured container for atomic information, but it does contain logic to transform atoms in space.

Fields

element (Element) The element

x (float) The x coordinate of the atom

y (float) The y coordinate of the atom

z (float) The z coordinate of the atom

Methods

angle_to_xy_plane

Atom.angle_to_xy_plane(self) -> float

Angle, in radians, between this atom's coordinate vector and the xy plane

angle_to_xz_plane

Atom.angle_to_xz_plane(self) -> float

Angle, in radians, between this atom's coordinate vector and the xz plane

angle_to_yz_plane

Atom.angle_to_yz_plane(self) -> float

Angle, in radians, between this atom's coordinate vector and the yz plane

distance

Atom.distance(self, other: 'Atom') -> float

Determine the distance between this atom and another atom.

flipped_x

Atom.flipped_x(self) -> Atom

Return an equivalent atom, but the x coordinate is the opposite

rotated

Atom.rotated(self, r: 'np.ndarray') -> Atom

Return an equivalent atom rotated by the given rotation matrix

The matrix must have shape (3, 3)

rotated_about_x

Atom.rotated_about_x(self, angle: 'float') -> 'Atom'

Return an equivalent atom, rotated by angle radians about the x axis

rotated_about_y

Atom.rotated_about_y(self, angle: 'float') -> 'Atom'

Return an equivalent atom, rotated by angle radians about the y axis

rotated_about_z

Atom.rotated_about_z(self, angle: 'float') -> 'Atom'

Return an equivalent atom, rotated by angle radians about the z axis

rotation_matrix_to

Atom.rotation_matrix_to(self, x: 'float', y: 'float', z: 'float') -> np.ndarray

Get a matrix that would rotate this atom to align with the given coordinates

https://math.stackexchange.com/questions/180418/calculate-rotation-matrix-to-align-vector-a-to-vector-b-in-3d

scaled

Atom.scaled(self, factor: 'float') -> Atom

Return an equivalent atom with all coordinates scaled by some factor

translated

Atom.translated(self, x=0.0, y=0.0, z=0.0) -> Atom

Return an equivalent atom translated in the direction given

with_coords

Atom.with_coords(self, x: 'float', y: 'float', z: 'float') -> 'Atom'

Return an equivalent atom at these coordinates

Properties

coords

Three dimensional array of coordinates, [x, y, z]

mass

The mass of the atom

normalized_coords

Return a unit vector pointing towards the atom

Dunder Methods

__eq__

Atom.__eq__(self, other: "'Atom'") -> bool

Return True if the other atom is the same element, and very close