Package schrodinger :: Package application :: Package bioluminate :: Module escomp :: Class PotGrid

Class PotGrid

The container that holds the potential grid from APBS calculation. The potential has the unit of kT/e.

Instance Methods

__init__(self, **kwargs)
There are two ways to initialize the object: read from a DX file, or copy from an existing object with the option of using another 3D potential map.

_read(self, dx_file)
Read the potential from a DX file and store the data.

_new(self, pg, pots=None)
Create a new object from an existing object

1D Numpy array (N)

getSurfacePotential(self, vertex_coords)
Interpolate the potential from the grid to the surface.

Method Details

[hide private]

_read(self, dx_file)

Read the potential from a DX file and store the data.

Parameters:

dx_file (String) - the DX file from APBS calculation

_new(self, pg, pots=None)

Create a new object from an existing object

Parameters:

pg (PotGrid object) - the existing PotGrid object
pots (3D Numpy array) - the potential map on the grid

getSurfacePotential(self, vertex_coords)

Interpolate the potential from the grid to the surface.

Parameters:

vertex_coords (2D Numpy array (N x 3)) - list of coordinates of surface vertex points

Returns: 1D Numpy array (N)

list of potential values on surface points