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 [ᶜTheobald2005] and determining the optimal least-squares rotation matrix [ᶜLiu2010].

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:

[ᶜTheobald2005]

Douglas L. Theobald. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A, 61(4):478–480, Jul 2005. doi:10.1107/S0108767305015266.

[ᶜLiu2010]

Pu Liu, Dimitris K. Agrafiotis, and Douglas L. Theobald. Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7):1561–1563, 2010. doi:10.1002/jcc.21439.

13.2.9.1. 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.