| rmsd {bio3d} | R Documentation |
Calculate the RMSD between coordinate sets.
rmsd(a, b=NULL, a.inds=NULL, b.inds=NULL, fit=FALSE)
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. |
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.
Returns a numeric vector of RMSD value(s).
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
fit.xyz, rot.lsq,
read.pdb, read.fasta.pdb
# -- Calculate RMSD between two or more structures
aln <- read.fasta(system.file("examples/kif1a.fa",package="bio3d"))
pdb.path = system.file("examples",package="bio3d")
pdbs <- read.fasta.pdb(aln, pdb.path = pdb.path, pdbext = ".ent")
# Indices
gaps <- unique( which(is.na(pdbs$xyz),arr.ind=TRUE)[,2] )
inds <- c(1:ncol(pdbs$xyz))[-gaps]
# RMSD between structure 1 and structure 2
rmsd(a=pdbs$xyz[1,], b=pdbs$xyz[2,], a.inds=inds, b.inds=inds)
rmsd(a=pdbs$xyz[1,], b=pdbs$xyz[2,], a.inds=inds, b.inds=inds, fit=TRUE)
## Not run:
# RMSD between structure 1 and structures 2 and 3
rmsd(a=pdbs$xyz[1,], b=pdbs$xyz[2:3,], a.inds=inds, b.inds=inds)
# RMSD between structure 1 and all structures in alignment
rmsd(a=pdbs$xyz[1,], b=pdbs, a.inds=inds, b.inds=inds, fit=TRUE)
# pairwise RMSD
rmsd(pdbs$xyz[,inds])
## End(Not run)