Module rotor

Representations of a mechanical rotor.

Functions

rotor_pdb(structure=None, rotor_angle=None, axis=None, axis_pt=True, centre=None, span=2e-09, blade_length=5e-10, model=None, staggered=False)
Create a PDB representation of a rotor motional model.

rotor_propellers(mol=None, rotor_angle=None, centre=None, axis=None, blade_length=5.0, staggered=False)
Create a PDB representation of a rotor motional model.

Variables

__package__ = 'lib.structure.represent'

Imports: pi, array, cross, dot, float64, transpose, zeros, norm, closest_point_ax, axis_angle_to_R

Function Details

rotor_pdb(structure=None, rotor_angle=None, axis=None, axis_pt=True, centre=None, span=2e-09, blade_length=5e-10, model=None, staggered=False)

Create a PDB representation of a rotor motional model.

Parameters:

• structure (lib.structure.internal.object.Internal instance) - The internal structural object instance to add the rotor to as a molecule.
• rotor_angle (float) - The angle of the rotor motion in radian.
• axis (numpy rank-1, 3D array) - The vector defining the rotor axis.
• axis_pt (numpy rank-1, 3D array) - A point lying anywhere on the rotor axis. This is used to define the position of the axis in 3D space.
• centre (numpy rank-1, 3D array) - The central point of the representation. If this point is not on the rotor axis, then the closest point on the axis will be used for the centre.
• span (float) - The distance from the central point to the rotor blades (meters).
• blade_length (float) - The length of the representative rotor blades.
• model (int or None) - The structural model number to add the rotor to. If not supplied, the same rotor structure will be added to all models.
• staggered (bool) - A flag which if True will cause the rotor blades to be staggered. This is used to avoid blade overlap.

rotor_propellers(mol=None, rotor_angle=None, centre=None, axis=None, blade_length=5.0, staggered=False)

Create a PDB representation of a rotor motional model.

Parameters:

• mol (MolContainer instance) - The internal structural object molecule container to add the atoms to.
• rotor_angle (float) - The angle of the rotor motion in radians.
• centre (numpy rank-1, 3D array) - The central point of the propeller.
• axis (numpy rank-1, 3D array) - The vector defining the rotor axis.
• blade_length (float) - The length of the representative rotor blades in Angstrom.
• staggered (bool) - A flag which if True will cause the rotor blades to be staggered. This is used to avoid blade overlap.