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MDplot (version 0.2)

Visualizing Molecular Dynamics Analysis

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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Version

Install

install.packages('MDplot')

Monthly Downloads

33

Version

0.2

License

GPL-3

Maintainer

Christian Margreitter

Last Published

February 11th, 2016

Functions in MDplot (0.2)

MDplot_argument-class

Arguments for bash script interface
MDplot-internal

Internal functions for MDplot
rmsd

Root-mean-square-deviation plot
clusters_ts

Cluster timeseries plot
rmsf

Root-mean-square-fluctuation plot
xrmsd

XRMSD plot in heatmap style
load_dssp_summary

Load DSSP information
load_TIcurve

Loading function for thermodynamic integration function TIcurve
load_xrmsd

Loading function for MDplot::xrmsd()
load_dssp_ts

Load DSSP timeseries
load_hbond_ts

Loading hydrogen bonds timeseries
load_hbond

Loading hydrogen bonds
load_ramachandran

Load dihedral information (Ramachandran plot input)
translate_aminoacids

Function to translate between canonical and GROMOS amino acid abbreviations
hbond_ts

Plot hydrogen bond timeseries
load_clusters_ts

Loading time-series cluster information
load_clusters

Loading cluster information
dssp_summary

DSSP summary plot for secondary structure elements (proteins)
load_rmsd

Loading function for MDplot::rmsd()
clusters

Cluster bar plot
TIcurve

Thermodynamic integration plot
ramachandran

Ramachandran plot for two dihedral angles
load_rmsf

Loading function for MDplot::rmsf()
dssp_ts

DSSP timeseries plot for secondary structure elements (proteins)
hbond

Plot hydrogen bond summary