MDplot (version 1.0.1)

load_ramachandran: Load dihedral information (Ramachandran plot input)

Description

Loads a textfile with dihedral angles, which are to be stored in a matrix. By default, the first column is phi and the second psi. Angles can be shifted by a constant value (in order to transform them from 0 to 360 to the usually used -180 to 180).

Usage

load_ramachandran( path,
                   angleColumns = c(1,2),
                   shiftAngles = NA,
                   mdEngine = "GROMOS" )

Arguments

path

Path to input file. At least two columns of the same length are expected.

angleColumns

If more columns are present, the angle columns can be chosen by this vector.

shiftAngles

In order to shift the values by a constant factor (e.g. -180).

mdEngine

Argument distinguishes between input formats based on the molecular dynamics engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".

Value

A nx2-matrix with phi and psi angles in the respective columns.

Examples

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

# GROMACS
load_ramachandran( system.file( "extdata/ramachandran_example_GROMACS.txt.gz",
                   package = "MDplot" ), mdEngine = "GROMACS" )

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