sip {bio3d}

Square Inner Product

Description

Calculate the correlation between two atomic fluctuation vectors.

Usage

sip(...)

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

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

## Default S3 method:
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).

Author(s)

Lars Skjaerven

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.

See Also

Other similarity measures: covsoverlap, bhattacharyya, rmsip.

Examples

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

sip(a$fluctuations, b$fluctuations)