12.2.9. Fast QCP RMSD structure alignment — MDAnalysis.lib.qcprot

Author:Joshua L. Adelman, University of Pittsburgh
Author:Robert R. Delgado, Cornell University and Arizona State University
Contact:jla65@pitt.edu
Year:2011, 2016
Licence:BSD

PyQCPROT is a python/cython implementation of Douglas Theobald’s QCP method for calculating the minimum RMSD between two structures [Theobald2005] and determining the optimal least-squares rotation matrix [Liu2010].

A full description of the method, along with the original C implementation can be found at http://theobald.brandeis.edu/qcp/

See also

MDAnalysis.analysis.align
Align structures using CalcRMSDRotationalMatrix()
MDAnalysis.analysis.rms.rmsd
Calculate the RMSD between two structures using CalcRMSDRotationalMatrix()

Changed in version 0.16.0: Call signatures were changed to directly interface with MDAnalysis coordinate arrays: shape (N, 3)

References

If you use this QCP rotation calculation method in a publication, please reference:

[Theobald2005]Douglas L. Theobald (2005) “Rapid calculation of RMSD using a quaternion-based characteristic polynomial.” Acta Crystallographica A 61(4):478-480.
[Liu2010]Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2010) “Fast determination of the optimal rotational matrix for macromolecular superpositions.” J. Comput. Chem. 31, 1561-1563.

12.2.9.1. Functions

Users will typically use the CalcRMSDRotationalMatrix() function.

MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix()

Calculate the RMSD & rotational matrix.

Parameters:
  • ref (ndarray, np.float64_t) – reference structure coordinates
  • conf (ndarray, np.float64_t) – condidate structure coordinates
  • N (int) – size of the system
  • rot (ndarray, np.float64_t) – array to store rotation matrix. Must be flat
  • weights (ndarray, npfloat64_t (optional)) – weights for each component
Returns:

  • rmsd (float) – RMSD value
  • .. versionchanged:: 0.16.0 – Array size changed from 3xN to Nx3.

MDAnalysis.lib.qcprot.InnerProduct()

Calculate the inner product of two structures.

Parameters:
  • A (ndarray np.float64_t) – result inner product array, modified in place
  • coords1 (ndarray np.float64_t) – reference structure
  • coord2 (ndarray np.float64_t) – candidate structure
  • N (int) – size of system
  • weights (ndarray np.float64_t (optional)) – use to calculate weighted inner product
Returns:

Notes

  1. You MUST center the structures, coords1 and coords2, before calling this function.
  2. Coordinates are stored as Nx3 arrays (as everywhere else in MDAnalysis).

Changed in version 0.16.0: Array size changed from 3xN to Nx3.

MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation()

Calculate the RMSD, and/or the optimal rotation matrix.

Parameters:
  • rot (ndarray np.float64_t) – result rotation matrix, modified inplace
  • A (ndarray np.float64_t) – the inner product of two structures
  • E0 (float64) – 0.5 * (G1 + G2)
  • N (int) – size of the system
Returns:

rmsd – RMSD value for two structures

Return type:

float

Changed in version 0.16.0: Array sized changed from 3xN to Nx3.