load_ramchandran function

Load dihedral information (Ramachandran plot input)

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).

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".

Returns

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" )

Author(s)

Christian Margreitter