paramagpy.fit.DensityMap

class paramagpy.fit.DensityMap(origin, size, density)

A class to help with calculations on a grid. The grid can be setup by specifying the origin (centre) edge size and density. Arguments are given in Angstrom, but stored in metres The grid positions are available for calculations The density can be written out as a .ccp4 electron density map Use this class for any contour plots to view in PyMol

__init__(origin, size, density)

Make a density map over a cubic grid of coordinates

Parameters

• origin (np.ndarray of floats) – [x,y,z] position in Angstrom defining the centre of the cubic grid

• size (float) – the grid edge size in Angstrom

• density (float) – grid density defined as points per angstrom

Methods

__init__(origin, size, density)	Make a density map over a cubic grid of coordinates
boundary_min()	Does the minimum value lie on the boundary of the grid?
boundary_positions_below_density(cutoffValue)	Do any positions below <cutoffValue> lie on the grid boundary?
get_positions_below_density(cutoffValue)	Returns all positions in the grid that are below the argument <cutoffValue>
minpos()	Fetch the grid point position with minimum density value
write(fileName)	Write density values to file in .ccp4 format Headers are accounted for from the given geometry of the grid

Attributes

CCP4_HEADER_DTYPE