MDplot (version 1.0.1)

load_xrmsd: Loading function for xrmsd()

Description

Loads matrix information from the specified file.

Usage

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

Arguments

path

Specifies the input file.

factor

In case the RMSD values are given in $$nm * factor$$, 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".

Value

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" )