Calculate the covariance overlap obtained from NMA.

covsoverlap(...)
# S3 method for enma
covsoverlap(enma, ncore=NULL, ...)
# S3 method for nma
covsoverlap(a, b, subset=NULL, ...)

## Arguments

enma |
an object of class `"enma"` obtained from function
`nma.pdbs` . |

ncore |
number of CPU cores used to do the calculation.
`ncore>1` requires package ‘parallel’ installed. |

a |
a list object with elements ‘U’ and ‘L’
(e.g. as obtained from function `nma` ) containing the
eigenvectors and eigenvalues, respectively, to be
compared with `b` . |

b |
a list object with elements ‘U’ and ‘L’
(e.g. as obtained from function `nma` ) containing the
eigenvectors and eigenvalues, respectively, to be
compared with `a` . |

subset |
the number of modes to consider. |

... |
arguments passed to associated functions. |

## Details

Covariance overlap is a measure for the similarity between two
covariance matrices, e.g. obtained from NMA.

## Value

Returns the similarity coefficient(s).

## References

Skjaerven, L. et al. (2014) *BMC Bioinformatics* **15**, 399.
Grant, B.J. et al. (2006) *Bioinformatics* **22**, 2695--2696.
Romo, T.D. et al. (2011) *Proteins* **79**, 23--34.

## Author

Lars Skjaerven

## See also