fit.trj: Coordinate superposition

In SOMMD: Self Organising Maps for the Analysis of Molecular Dynamics Data

Coordinate superposition

Description

Coordinate superposition with the Kabsch algorithm. This function make use of the bio3d fit.xyz function to align a SOMMD trj object. If ref is not specified, the trj object is aligned to the first frame of the simulation, otherwise it is aligned to the reference input object.

Usage

fit.trj(trj, ref = NULL, trj.inds = NULL, ref.inds = NULL)

Arguments

trj	an object with class trj
ref	a struct object read with read.struct() to be used as reference
trj.inds	a vector of indices that selects the trj atoms upon which fitting should be based. If not specified all atoms will be used.
ref.inds	a vector of indices that selects the ref atoms upon which fitting should be based. If not specified all atoms will be used.

Value

A trj object aligned

Author(s)

Stefano Motta [e-mail]

Examples

#Read trajectory
trj <- read.trj(trjfile = system.file("extdata", "HIF2a-MD.xtc", package = "SOMMD"),
  topfile = system.file("extdata", "HIF2a.gro", package = "SOMMD"))
# Fit a trajectory to the first frame based on alpha carbons:
ca.inds <- which(trj$top$elety=="CA")
trj.fit <- fit.trj(trj, trj.inds=ca.inds)

SOMMD documentation built on Oct. 2, 2024, 5:07 p.m.