Square Inner Product

Calculate the correlation between two atomic fluctuation vectors.

sip(...)

# S3 method for nma
sip(a, b, ...)

# S3 method for enma
sip(enma, ncore=NULL, ...)

# S3 method for default
sip(v, w, ...)

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	an ‘nma’ object as object from function nma to be compared to b.
b	an ‘nma’ object as object from function nma to be compared to a.
v	a numeric vector containing the atomic fluctuation values.
w	a numeric vector containing the atomic fluctuation values.
...	arguments passed to associated functions.

Details

SIP is a measure for the similarity of atomic fluctuations of two proteins, e.g. experimental b-factors, theroetical RMSF values, or atomic fluctuations 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. Fuglebakk, E. et al. (2013) JCTC 9, 5618--5628.

Author

Lars Skjaerven

See also

Other similarity measures: covsoverlap, bhattacharyya, rmsip.

Examples

pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
a <- nma(pdb)
#>  Building Hessian...		Done in 0.011 seconds.
#>  Diagonalizing Hessian...	Done in 0.08 seconds.
b <- nma(pdb, ff="anm")
#>  Building Hessian...		Done in 0.011 seconds.
#>  Diagonalizing Hessian...	Done in 0.082 seconds.

sip(a$fluctuations, b$fluctuations)
#> [1] 0.9281376