Package generic_fns :: Package structure :: Module api_base :: Class Displacements
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Class Displacements

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

Instance Methods [hide private]
 
__init__(self)
Initialise the storage objects.
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_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.
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from_xml(self, str_node, dir=None, id=None, file_version=1)
Recreate the structural object from the XML structural object node.
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to_xml(self, doc, element)
Create XML elements for each model.
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Method Details [hide private]

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

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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, file_version=1)

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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.
  • file_version (int) - The relax XML version of the XML file.

to_xml(self, doc, element)

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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.