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, ...)
Value
Returns the similarity coefficient(s).
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.
Author
Lars Skjaerven
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.
See Also
Other similarity measures:
covsoverlap, bhattacharyya,
rmsip.