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MDplot (version 0.3.1)

Visualising Molecular Dynamics Analyses

Description

Provides automatization for plot generation succeeding common molecular dynamics analyses. This includes straightforward plots, such as RMSD (Root-Mean-Square-Deviation) and RMSF (Root-Mean-Square-Fluctuation) but also more sophisticated ones such as dihedral angle maps, hydrogen bonds, cluster bar plots and DSSP (Definition of Secondary Structure of Proteins) analysis.

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Install

install.packages('MDplot')

Monthly Downloads

196

Version

0.3.1

License

GPL-3

Issues

Pull Requests

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Repository

https://github.com/MDplot/MDplot

Maintainer

Christian Margreitter

Last Published

April 28th, 2016

Functions in MDplot (0.3.1)

DSSP timeseries plot for secondary structure elements (proteins)

Plot hydrogen bond summary

MDplot-internal

Internal functions for MDplot

Loading function for xrmsd()

Root-mean-square-deviation plot

Loading function for thermodynamic integration function TIcurve()

Root-mean-square-fluctuation plot

translate_aminoacids

Function to translate between canonical and GROMOS amino acid abbreviations

Loading cluster information

load_clusters_ts

Loading timeseries cluster information

General timeseries plotting function

load_timeseries

Loading function for timeseries()

Loading function for rmsd()

Cluster bar plot

load_ramachandran

Load dihedral information (Ramachandran plot input)

load_dssp_summary

Load DSSP information

Load DSSP timeseries

DSSP summary plot for secondary structure elements (proteins)

Plot hydrogen bond timeseries

Loading hydrogen bonds timeseries

Loading hydrogen bonds

XRMSD plot in heatmap style

Thermodynamic integration plot

Ramachandran plot for two dihedral angles

MDplot_argument-class

Arguments for bash script interface

Loading function for rmsf()

Cluster timeseries plot