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)[source]
Move a Compound such that a position overlaps with another.
Computes an affine transformation that maps the from_positions to the respective to_positions, and applies this transformation to the compound.
- Parameters
- move_thismb.Compound
The Compound to be moved.
- from_positionsnp.ndarray, shape=(n, 3), dtype=float
Original positions.
- to_positionsnp.ndarray, shape=(n, 3), dtype=float
New positions.
- add_bondbool, optional, default=True
If from_positions and to_positions are Ports, create a bond between the two anchor atoms.
- mbuild.coordinate_transform.translate(compound, pos)[source]
Translate a compound by a vector.
- Parameters
- compoundmb.Compound
The compound being translated.
- posnp.ndarray, shape=(3,), dtype=float
The vector to translate the compound by.
- mbuild.coordinate_transform.translate_to(compound, pos)[source]
Translate a compound to a coordinate.
- Parameters
- compoundmb.Compound
The compound being translated.
- posnp.ndarray, shape=(3,), dtype=float
The coordinate to translate the compound to.
- mbuild.coordinate_transform.rotate(compound, theta, around)[source]
Rotate a compound around an arbitrary vector.
- Parameters
- compoundmb.Compound
The compound being rotated.
- thetafloat
The angle by which to rotate the compound, in radians.
- aroundnp.ndarray, shape=(3,), dtype=float
The vector about which to rotate the compound.
- mbuild.coordinate_transform.spin(compound, theta, around)[source]
Rotate a compound in place around an arbitrary vector.
- Parameters
- compoundmb.Compound
The compound being rotated.
- thetafloat
The angle by which to rotate the compound, in radians.
- aroundnp.ndarray, shape=(3,), dtype=float
The axis about which to spin the compound.
- mbuild.coordinate_transform.x_axis_transform(compound, new_origin=None, point_on_x_axis=None, point_on_xy_plane=None)[source]
Move a compound such that the x-axis lies on specified points.
- Parameters
- compoundmb.Compound
The compound to move.
- new_originmb.Compound or list-like of size 3, default=[0.0, 0.0, 0.0]
Where to place the new origin of the coordinate system.
- point_on_x_axismb.Compound or list-like of size 3, default=[1, 0, 0]
A point on the new x-axis.
- point_on_xy_planemb.Compound or list-like of size 3, default=[1, 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)[source]
Move a compound such that the y-axis lies on specified points.
- Parameters
- compoundmb.Compound
The compound to move.
- new_originmb.Compound or like-like of size 3, default=[0, 0, 0]
Where to place the new origin of the coordinate system.
- point_on_y_axismb.Compound or list-like of size 3, default=[0, 1, 0]
A point on the new y-axis.
- point_on_xy_planemb.Compound or list-like of size 3, default=[0, 1, 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)[source]
Move a compound such that the z-axis lies on specified points.
- Parameters
- compoundmb.Compound
The compound to move.
- new_originmb.Compound or list-like of size 3, default=[0, 0, 0]
Where to place the new origin of the coordinate system.
- point_on_z_axismb.Compound or list-like of size 3, default=[0, 0, 1]
A point on the new z-axis.
- point_on_zx_planemb.Compound or list-like of size 3, default=[0, 0, 1]
A point on the new xz-plane.