load_xrmsd function

Loading function for xrmsd()

Loads matrix information from the specified file.

load_xrmsd(  path,
             factor = 1,
             removeLowerHalf = TRUE,
             mdEngine = "GROMOS"  )

Arguments

• path: Specifies the input file.
• factor: In case the RMSD values are given in

, the factor can be specified. If the unit is already nanometers, 1 is the appropriate value.

• removeLowerHalf: If TRUE, the lower half of the plot will be white.
• mdEngine: Argument distinguishes between input formats based on the molecular dynamics engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".

Returns

Returns a nx3-matrix, with the first two columns holding the position (x- and y-axis) and the third the respective RMSD value.

Examples

# GROMOS
load_xrmsd( system.file( "extdata/xrmsd_example.txt.gz",
                         package = "MDplot" ),
            factor = 10000 )

# GROMACS
load_xrmsd( system.file( "extdata/xrmsd_example_GROMACS.xpm.gz",
                         package = "MDplot" ),
            mdEngine = "GROMACS" )

# AMBER
load_xrmsd( system.file( "extdata/xrmsd_example_AMBER.txt.gz",
                         package = "MDplot" ),
            mdEngine = "AMBER" )

Author(s)

Christian Margreitter