R: Radius of Gyration

rgyr {bio3d} | R Documentation

## Radius of Gyration

### Description

Calculate the radius of gyration of coordinate sets.

### Usage

    rgyr(xyz, mass=NULL, ncore=1, nseg.scale=1)

### Arguments

`xyz` | a numeric vector, matrix or list object with an `xyz` component, containing one or more coordinate sets.
`mass` | a numeric vector of atomic masses (unit a.m.u.), or a PDB object with masses stored in the "B-factor" column. If `mass==NULL`, all atoms are assumed carbon.
`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

Radius of gyration is a standard measure of overall structural change of macromolecules.

### Value

Returns a numeric vector of radius of gyration.

### Author(s)

Xin-Qiu Yao & Pete Kekenes-Huskey

### References

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

### See Also

`fit.xyz`, `rmsd`, `read.pdb`, `read.fasta.pdb`

### Examples

    # PDB server connection required - testing excluded

    # -- Calculate Rog of single structure
    pdb <- read.pdb("1bg2")
    mass <- 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)

    ## Not run:
    # -- Calculate Rog of a trajectory
    xyz <- read.dcd(system.file("examples/hivp.dcd", package="bio3d"))
    rg <- rgyr(xyz)
    rg[1:10]

    ## End(Not run)

[Package bio3d version 2.4-2 Index]