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Geometry of chains

Measure the shape of a chain of points, such as a polymer or a protein backbone, frame by frame. ShapeAnalysis reads frames by points by dimensions, from an array or a trajectory.

import numpy as np

from skcomplex.core.analysis import ShapeAnalysis

chain = np.array([[[0.0, 0.0, 0.0], [3.0, 4.0, 0.0]]])
assert ShapeAnalysis('end-to-end').prepare(chain).run().values_.tolist() == [5.0]
ShapeAnalysis('end-to-end').prepare(chain).run().values_

array([5.])

ShapeAnalysis(kind, group=None, reference=None) takes one of three kinds.

  • 'gyration' gives the radius of gyration per frame.
  • 'end-to-end' gives the distance between the first and the last point.
  • 'rmsd' gives the root mean square deviation from reference after optimal superposition.