molsysmt.thirds.nglview.add_arrows#

molsysmt.thirds.nglview.add_arrows(view, origin=None, end=None, vectors=None, color='#808080', radius='0.2 angstroms')[source]#

Adding arrows to a view.

A list of arrows can be added to an NGL view (NGLWidget).

Parameters:

view (nglview.NGLWidget) – A view of the molecular system as an nglview.NGLWidget native object.
coordinates (Quantity (value:numpy.ndarray, dimensionality:['L']=1)) – Positions of the points of origin for the set of arrows. A quantity with length dimensions is required ([‘L’]=1), the value must be a numpy ndarray with shape [n_arrows, 3] (n_arrows is the number of arrows to be added).
arrows (Quantity (value:numpy.ndarray, dimensionality:['L']=1)) – Vectors to be added as arrows. A quantity with length dimensions is required ([‘L’]=1), the value must be a numpy ndarray with shape [n_arrows, 3] (n_arrows is the number of arrows to be added).
color (list, tuple, string default='#808080') – HEX or RGB color code of the arrows.
radius (Quantity (value:float, dimensionality:['L']=1), default='0.2 angstroms') – Radius of the arrows.

Returns:

The method modifies an nglview.NGLWidget object to add a list of arrows.

Return type:

None

Examples

>>> import molsysmt as msm
>>> from molsysmt import pyunitwizard as puw
>>> import numpy as np
>>> molecular_system = msm.convert('181L', selection='molecule_type=="protein"')
>>> coordinates = msm.get(molecular_system, element='atom', selection='atom_name=="CA"', coordinates=True)
>>> vectors = puw.quantity(np.ones([coordinates.shape[0],3]), 'angstroms')
>>> view = msm.view(molecular_system)
>>> msm.thirds.add_arrows(view, origin=coordinates, vectors=arrows)
>>> view