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MDplot (version 1.0.1)

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. Currently able to load GROMOS, GROMACS and AMBER formats, respectively.

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Install

install.packages('MDplot')

Monthly Downloads

194

Version

1.0.1

License

GPL-3

Issues

1

Pull Requests

0

Stars

27

Forks

11

Maintainer

Christian Margreitter

Last Published

July 4th, 2017

Functions in MDplot (1.0.1)

clusters_ts

Cluster timeseries plot
dssp

DSSP plot for secondary structure elements (proteins)
load_rmsd

Loading function for rmsd()
load_rmsf

Loading function for rmsf()
MDplot-internal

Internal functions for MDplot
MDplot_argument-class

Arguments for bash script interface
load_clusters

Loading cluster information
load_clusters_ts

Loading timeseries cluster information
noe

Plot NOE violations
ramachandran

Ramachandran plot for two dihedral angles
TIcurve

Thermodynamic integration plot
clusters

Cluster bar plot
load_dssp

Load DSSP information
load_dssp_ts

Load DSSP timeseries
rmsf

Root-mean-square-fluctuation (RMSF) plot
timeseries

General timeseries plotting function
hbond_ts

Plot hydrogen bond timeseries
load_TIcurve

Loading function for thermodynamic integration function TIcurve()
load_noe

Loading NOE violations
load_ramachandran

Load dihedral information (Ramachandran plot input)
rmsd

Root-mean-square-deviation (RMSD) plot
rmsd_average

Root-mean-square-deviation (RMSD) average plot
dssp_ts

DSSP timeseries plot for secondary structure elements (proteins)
hbond

Plot hydrogen bond summary
load_hbond

Loading hydrogen bond data
load_hbond_ts

Loading hydrogen bonds timeseries
translate_aminoacids

Function to translate between canonical and GROMOS amino acid abbreviations
xrmsd

XRMSD plot in heatmap style
load_timeseries

Loading function for timeseries()
load_xrmsd

Loading function for xrmsd()