load_dssp_ts {MDplot}

Load DSSP timeseries

Description

Loads DSSP output files from a specified directory (GROMOS) or a specified file (GROMACS, AMBER) and combines it into a list suited as input for dssp_ts().

Usage

load_dssp_ts( folder,
              filenames = NA,
              stride = 1,
              mdEngine = "GROMOS" )

Arguments

folder

Folder, in which the DSSP output files are located.

filenames

Vector with filenames. GROMOS: default file names are "3-Helix.out", "4-Helix.out", "5-Helix.out", "Bend.out", "Beta-Bridge.out", "Beta-Strand.out" and "Turn.out". Files not present are ignored. GROMACS and AMBER: just give the appropriate filename (see examples below).

stride

Allows to use only every xth snapshot.

mdEngine

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

Value

Returns a list, where every element represents a secondary structure motif holding the following information:

name

The name of the secondary structure motif.

values

Holds one vector each for the x and y axis:

• x Snapshots, at which the respective motif has been identified.

• y Residues, for which the respective motif has been identified.

Author(s)

Christian Margreitter

Examples

# GROMOS
load_dssp_ts( system.file( "extdata/dssp_ts_example", package = "MDplot" ) )

# GROMACS
load_dssp_ts( folder = system.file( "extdata", package = "MDplot" ),
              filenames = "dssp_example_GROMACS.txt.gz",
              mdEngine = "GROMACS" )

# AMBER
load_dssp_ts( folder = system.file( "extdata", package = "MDplot" ),
              filenames = "dssp_ts_example_AMBER.txt.gz",
              mdEngine = "AMBER" )