dist.trj: Atom distances from Molecular Dynamics Trajectories

In s-cosseddu/RMD: General function to analyse MD simulations

Description

Take trajectory and pdb objects, 2 selection and return time series of distances between the atom in selection1 and selection2 according to sub and subseqB. It is based on bio3d functions.

Usage

dist.trj(pdb, trj, sel_string1, sel_string2, pdb2 = NULL, trj2 = NULL,
  pdb2sel_string1 = sel_string1, pdb2sel_string2 = sel_string2,
  ref = "mean", sub = c("A", "B", "C", "D"), subseqB = c(1:3, 4:6, 7:9,
  10:12), stride = 1, start = 1, overall = FALSE)

Arguments

pdb	Structure object of class pdb as read by read.pdb() funcion of bio3d lib.
trj	(Optional) trajectory as read by read.dcd() funcion of bio3d lib.
sel_string1	First selection of atom for bio3d function atom.select(), refer to manual (es. "///71///CD/")
pdb2	pdb of a reference (optional, default NULL)
trj2	dcd of the reference (optional, default NULL)
ref	deprecated to delete
sub	when working on multible subunits, list of subunit, default c("A","B","C","D")
subseqB	sequence of subunits of the second atomselection, default c(1:3,4:6,7:9,10:12)
stride	time interval for ts()
start	starting time for ts()
overall	All the data are collected as a single vector, to get an overall description of the dataset
sel_string1	Second selection of atom for bio3d function atom.select()
pdb2sel_string1=sel_string1
pdb2sel_string2=sel_string2

Examples

pdb=protein.pdb
trj=protein.trj             #trajectory
sel_string1="///80///K/"    #selection
sel_string2="///81///K/"
pdb2 <- xrays.pdb[["Code1K4C"]]         #reference
stride=Stride
start=First_frame
trj2 <- NULL
pdb2sel_string1=sel_string1
pdb2sel_string2=sel_string2

ref="mean"
sub=c("A","B","C","D")
subseqB=c(1:3,4:6,7:9,10:12)
stride=1
start=1
overall=FALSE

s-cosseddu/RMD documentation built on May 28, 2019, 10:46 a.m.