Radius of Gyration

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.

Examples

# PDB server connection required - testing excluded

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

  Note: Accessing on-line PDB file

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)

[1] 19.8667



# -- Calculate Rog of a trajectory
xyz <- 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%

rg <- rgyr(xyz)
rg[1:10]

 [1] 17.50097 17.38617 17.45981 17.40144 17.32908 17.37739 17.46936 17.62601
 [9] 17.45649 17.47451

See also

Author