Root Mean Square Inner Product

Usage

rmsip(...)
"rmsip"(enma, ncore=NULL, subset=10, ...)
"rmsip"(modes.a, modes.b, subset=10, row.name="a", col.name="b", ...)

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.

subset

the number of modes to consider.

modes.a

an object of class "pca" or "nma" as obtained from functions pca.xyz or nma.

modes.b

an object of class "pca" or "nma" as obtained from functions pca.xyz or nma.

row.name

prefix name for the rows.

col.name

prefix name for the columns.

...

arguments passed to associated functions.

Examples

# Load data for HIV example
trj <- read.dcd(system.file("examples/hivp.dcd", package="bio3d"))

 NATOM = 198 
 NFRAME= 117 
 ISTART= 0 
 last  = 117 
 nstep = 117 
 nfile = 117 
 NSAVE = 1 
 NDEGF = 0 
 version 24 
Reading (x100)
  |======================================================================| 100%

pdb <- read.pdb(system.file("examples/hivp.pdb", package="bio3d"))

# Do PCA on simulation data
xyz.md <- fit.xyz(pdb$xyz, trj, fixed.inds=1:ncol(trj))
pc.sim <- pca.xyz(xyz.md)

# NMA 
modes <- nma(pdb)

Warning message:
Possible multi-chain structure or missing in-structure residue(s) present
  Fluctuations at neighboring positions may be affected.
 Building Hessian...		Done in 0.079 seconds.
 Diagonalizing Hessian...	Done in 0.464 seconds.


# Calculate the RMSIP between the MD-PCs and the NMA-MODEs
r <- rmsip(modes, pc.sim, subset=10, row.name="NMA", col.name="PCA")

# Plot pairwise overlap values
plot(r, xlab="NMA", ylab="PCA")

See also

Author