load_clusters function

Loading cluster information

This function loads clusters from a plain text file and stores them in a matrix. The trajectories can be named by the user. The output of this function can be used as input of function clusters().

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

Arguments

• path: Specifies the path of the text input file.
• names: Optional vector of trajectory names. If provided, needs to be of the same length as the number of clusters to be plotted.
• lengths: When GROMACS input needs to be parsed, the lengths of the respective trajectories have to be given. This holds also in the case, that only one is used.
• mdEngine: Argument distinguishes between input formats based on the molecular dynamics engine used. Currently available: "GROMOS", "GROMACS" and "AMBER". Note, that two different kinds of AMBER output may be loaded (see example input files).

Returns

Returns a nxm-matrix with n being the number of input trajectories and m the number of different clusters. Each element in the matrix holds the number of snapshots, the respective cluster occured in the respective trajectory.

Examples

# GROMOS
load_clusters( system.file( "extdata/clusters_example.txt.gz", package = "MDplot" ) )

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

# AMBER (first)
load_clusters( system.file( "extdata/clusters_example_1_AMBER.txt.gz", package = "MDplot" ),
               mdEngine = "AMBER" )

# AMBER (second)
load_clusters( system.file( "extdata/clusters_example_2_AMBER.txt.gz", package = "MDplot" ),
               mdEngine = "AMBER" )

Author(s)

Christian Margreitter