Coordinate transformations

The following utility functions provide mechanisms for spatial transformations for mbuild compounds:

mbuild.coordinate_transform.force_overlap(move_this, from_positions, to_positions, add_bond=True)

Computes an affine transformation that maps the from_positions to the respective to_positions, and applies this transformation to the compound.

Parameters:

move_this : mb.Compound

The Compound to be moved.

from_positions : np.ndarray, shape=(n, 3), dtype=float

Original positions.

to_positions : np.ndarray, shape=(n, 3), dtype=float

New positions.

add_bond : bool, optional, default=True

If from_positions and to_positions are Ports, create a bond between the two anchor atoms.

mbuild.coordinate_transform.translate(*args, **kwargs)

mbuild.coordinate_transform.translate_to(*args, **kwargs)

mbuild.coordinate_transform.rotate(*args, **kwargs)

mbuild.coordinate_transform.spin(*args, **kwargs)

mbuild.coordinate_transform.x_axis_transform(compound, new_origin=None, point_on_x_axis=None, point_on_xy_plane=None)

Move a compound such that the x-axis lies on specified points.

Parameters:

compound : mb.Compound

The compound to move.

new_origin : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 0.0]

Where to place the new origin of the coordinate system.

point_on_x_axis : mb.Compound or list-like of size 3, optional, default=[1.0, 0.0, 0.0]

A point on the new x-axis.

point_on_xy_plane : mb.Compound, or list-like of size 3, optional, default=[1.0, 0.0, 0.0]

A point on the new xy-plane.

mbuild.coordinate_transform.y_axis_transform(compound, new_origin=None, point_on_y_axis=None, point_on_xy_plane=None)

Move a compound such that the y-axis lies on specified points.

Parameters:

compound : mb.Compound

The compound to move.

new_origin : mb.Compound or like-like of size 3, optional, default=[0.0, 0.0, 0.0]

Where to place the new origin of the coordinate system.

point_on_y_axis : mb.Compound or list-like of size 3, optional, default=[0.0, 1.0, 0.0]

A point on the new y-axis.

point_on_xy_plane : mb.Compound or list-like of size 3, optional, default=[0.0, 1.0, 0.0]

A point on the new xy-plane.

mbuild.coordinate_transform.z_axis_transform(compound, new_origin=None, point_on_z_axis=None, point_on_zx_plane=None)

Move a compound such that the z-axis lies on specified points.

Parameters:

compound : mb.Compound

The compound to move.

new_origin : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 0.0]

Where to place the new origin of the coordinate system.

point_on_z_axis : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 1.0]

A point on the new z-axis.

point_on_zx_plane : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 1.0]

A point on the new xz-plane.