load_clusters_ts {MDplot}

Loading timeseries cluster information

Description

This function loads the timeseries information for clusters from a plain text file and stores them in a list. The trajectories can be named by the user.

Usage

load_clusters_ts( path,
                  lengths,  
                  names = NA,
                  mdEngine = "GROMOS" )

Arguments

path

Specifies the path of the text input file.

lengths

Mandatory vector holding the number of snapshots for the respective trajectories (e.g. when three trajectories of 3000 snapshots each have been analysed together: lengths = c(3000,3000,300)).

names

Optional vector of trajectory names. If provided, needs to be of the same length as the number of clusters to be plotted.

mdEngine

Argument distinguishes between input formats based on the molecular dynamics engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".

Value

Returns a list of name-cluster lists, which consist of:

[1]

Trajectory name.

[2]

Vector of cluster numbers, where 0 indicates a structure not belonging to a cluster specified.

Author(s)

Christian Margreitter

Examples

# GROMOS
load_clusters_ts( system.file( "extdata/clusters_ts_example.txt.gz", package = "MDplot" ),
                  lengths = c( 4000, 4000, 4000, 4000, 4000, 4000 ) )

# GROMACS
load_clusters_ts( system.file( "extdata/clusters_example_GROMACS.txt.gz", package = "MDplot" ),
                  mdEngine = "GROMACS", lengths = c( 1001, 1001 ) )

# AMBER
load_clusters_ts( system.file( "extdata/clusters_ts_example_AMBER.txt.gz", package = "MDplot" ),
                  mdEngine = "AMBER", lengths = c( 50, 50 ) )