Square Inner Product

Usage

sip(...)


"sip"(a, b, ...)


"sip"(enma, ncore=NULL, ...)


"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.

Description

Calculate the correlation between two atomic fluctuation vectors.

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.

Examples


pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
a <- nma(pdb)



 Building Hessian...		Done in 0.053 seconds.
 Diagonalizing Hessian...	Done in 0.134 seconds.



b <- nma(pdb, ff="anm")



 Building Hessian...		Done in 0.046 seconds.
 Diagonalizing Hessian...	Done in 0.133 seconds.




sip(a$fluctuations, b$fluctuations)



[1] 0.9281376

See also

Other similarity measures: covsoverlap, bhattacharyya, rmsip.

Author

Lars Skjaerven