load_clusters {MDplot} | R Documentation |
Loading cluster information
Description
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()
.
Usage
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: |
Value
Returns a n
xm
-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.
Author(s)
Christian Margreitter
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" )