13.2.9. 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.

13.2.9.1. Functions

Users will typically use the CalcRMSDRotationalMatrix() function.

MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix(ref, conf, N, rot, weights)

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(A, coords1, coords2, N, weight)

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(rot, A, E0, N)

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.