rmsd {bio3d}

Root Mean Square Deviation

Description

Calculate the RMSD between coordinate sets.

Usage

rmsd(a, b=NULL, a.inds=NULL, b.inds=NULL, fit=FALSE, ncore=1, nseg.scale=1)

Arguments

a

a numeric vector containing the reference coordinate set for comparison with the coordinates in b. Alternatively, if b=NULL then a can be a matrix or list object containing multiple coordinates for pairwise comparison.

b

a numeric vector, matrix or list object with an xyz component, containing one or more coordinate sets to be compared with a.

a.inds

a vector of indices that selects the elements of a upon which the calculation should be based.

b.inds

a vector of indices that selects the elements of b upon which the calculation should be based.

fit

logical, if TRUE coordinate superposition is performed prior to RMSD calculation.

ncore

number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.

nseg.scale

split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.

Details

RMSD is a standard measure of structural distance between coordinate sets.

Structure a[a.inds] and b[b.inds] should have the same length.

A least-squares fit is performed prior to RMSD calculation by setting fit=TRUE. See the function fit.xyz for more details of the fitting process.

Value

Returns a numeric vector of RMSD value(s).

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

fit.xyz, rot.lsq, read.pdb, read.fasta.pdb

Examples

# Redundant testing excluded

# -- Calculate RMSD between two or more structures
aln <- read.fasta(system.file("examples/kif1a.fa",package="bio3d"))
pdbs <- read.fasta.pdb(aln)

# Gap positions
inds <- gap.inspect(pdbs$xyz)

# Superposition before pairwise RMSD 
rmsd(pdbs$xyz, fit=TRUE)

# RMSD between structure 1 and structures 2 and 3
rmsd(a=pdbs$xyz[1,], b=pdbs$xyz[2:3,], a.inds=inds$f.inds, b.inds=inds$f.inds, fit=TRUE)

# RMSD between structure 1 and all structures in alignment
rmsd(a=pdbs$xyz[1,], b=pdbs, a.inds=inds$f.inds, b.inds=inds$f.inds, fit=TRUE)

# RMSD without superposition
rmsd(pdbs$xyz)