Class Displacements

A special object for representing rotational and translational displacements between models.

Instance Methods

__init__(self)
Initialise the storage objects.

_calculate(self, model_from=None, model_to=None, coord_from=None, coord_to=None, centroid=None)
Calculate the rotational and translational displacements using the given coordinate sets.

from_xml(self, str_node, dir=None, id=None)
Recreate the structural object from the XML structural object node.

to_xml(self, doc, element)
Create XML elements for each model.

Method Details

_calculate(self, model_from=None, model_to=None, coord_from=None, coord_to=None, centroid=None)

Calculate the rotational and translational displacements using the given coordinate sets.

This uses the Kabsch algorithm (http://en.wikipedia.org/wiki/Kabsch_algorithm).

Parameters:

• model_from (int) - The model number of the starting structure.
• model_to (int) - The model number of the ending structure.
• coord_from (numpy rank-2, Nx3 array) - The list of atomic coordinates for the starting structure.
• coord_to (numpy rank-2, Nx3 array) - The list of atomic coordinates for the ending structure.
• centroid (list of float or numpy rank-1, 3D array) - An alternative position of the centroid, used for studying pivoted systems.

from_xml(self, str_node, dir=None, id=None)

Recreate the structural object from the XML structural object node.

Parameters:

• str_node (xml.dom.minicompat.Element instance) - The structural object XML node.
• dir (str) - The name of the directory containing the results file.
• id (str) - The specific structural object ID string. This can be 'scientific', 'internal', etc.

to_xml(self, doc, element)

Create XML elements for each model.

Parameters:

• doc (xml.dom.minidom.Document instance) - The XML document object.
• element (XML element object) - The element to add the displacement XML elements to.