bio3d (version 2.1-2)

sip: 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, ...)
## S3 method for class '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.

Value

• Returns the similarity coefficient(s).

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.

References

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)