read.trj: Read trj file

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

Read trj file

Description

Function to read a trajectory file

Usage

read.trj(trjfile, topfile)

Arguments

trjfile	contains the name and the path to the reference file (pdb or gro files are accepted)
topfile	contains the name and the path to the trajectory file (xtc or dcd files are accepted)

Value

Returns a list of class "trj" with the following components:

topfile	the input topology file.
topformat	the format of the input topology.
trjfile	the input trajectory file.
trjformat	the format of the input trajectory.
coord	a three dimensional array containing atomic coordinates for all the frames. Dimensions are: Natoms:3:Nframes.
top	a data.frame containing topological informations with a row per atom and a column per record type (resno, resid, elety, eleno, chain).
start	a vector with the first frame of the simulation. When multiple simulations are concatenated with cat.trj the vector indicates the first frame of each simulation.
end	a vector with the last frame of the simulation. When multiple simulations are concatenated with cat.trj the vector indicates the last frame of each simulation.
call	the matched call.

Author(s)

Alessandro Pandini

Examples

#Read trajectory
trj <- read.trj(trjfile = system.file("extdata", "HIF2a-MD.xtc", package = "SOMMD"),
  topfile = system.file("extdata", "HIF2a.gro", package = "SOMMD"))

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