rgyr.Rd
Calculate the radius of gyration of coordinate sets.
rgyr(xyz, mass=NULL, ncore=1, nseg.scale=1)
xyz | a numeric vector, matrix or list object with an |
---|---|
mass | a numeric vector of atomic masses (unit a.m.u.),
or a PDB object with masses stored in the "B-factor" column.
If |
ncore | number of CPU cores used to do the calculation.
|
nseg.scale | split input data into specified number of segments
prior to running multiple core calculation. See |
Radius of gyration is a standard measure of overall structural change of macromolecules.
Returns a numeric vector of radius of gyration.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
Xin-Qiu Yao & Pete Kekenes-Huskey
# \donttest{ # PDB server connection required - testing excluded # -- Calculate Rog of single structure pdb <- read.pdb("1bg2")#> Note: Accessing on-line PDB file#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/1bg2.pdb exists. Skipping downloadmass <- rep(12, length(pdb$xyz)/3) mass[substr(pdb$atom[,"elety"], 1, 1) == "N"] <- 14 mass[substr(pdb$atom[,"elety"], 1, 1) == "H"] <- 1 mass[substr(pdb$atom[,"elety"], 1, 1) == "O"] <- 16 mass[substr(pdb$atom[,"elety"], 1, 1) == "S"] <- 32 rgyr(pdb, mass)#> [1] 19.8667# } if (FALSE) { # -- Calculate Rog of a trajectory xyz <- read.dcd(system.file("examples/hivp.dcd", package="bio3d")) rg <- rgyr(xyz) rg[1:10] }