load_clusters_ts function

Loading timeseries cluster information

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.

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".

Returns

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.

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 ) )

Author(s)

Christian Margreitter