Calculate the correlation between two atomic fluctuation vectors.
Usage
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.
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
Skjaerven, L. et al. (2014) BMC Bioinformatics15, 399.
Grant, B.J. et al. (2006) Bioinformatics22, 2695--2696.
Fuglebakk, E. et al. (2013) JCTC9, 5618--5628.
# NOT RUN {pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
a <- nma(pdb)
b <- nma(pdb, ff="anm")
sip(a$fluctuations, b$fluctuations)
# }