Visualising Molecular Dynamics Analyses

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Documentation for package ‘MDplot’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

clusters	Cluster bar plot
clusters_ts	Cluster timeseries plot
dssp	DSSP plot for secondary structure elements (proteins)
dssp_ts	DSSP timeseries plot for secondary structure elements (proteins)
hbond	Plot hydrogen bond summary
hbond_ts	Plot hydrogen bond timeseries
load_clusters	Loading cluster information
load_clusters_ts	Loading timeseries cluster information
load_dssp	Load DSSP information
load_dssp_ts	Load DSSP timeseries
load_hbond	Loading hydrogen bond data
load_hbond_ts	Loading hydrogen bonds timeseries
load_noe	Loading NOE violations
load_ramachandran	Load dihedral information (Ramachandran plot input)
load_rmsd	Loading function for 'rmsd()'
load_rmsf	Loading function for 'rmsf()'
load_TIcurve	Loading function for thermodynamic integration function 'TIcurve()'
load_timeseries	Loading function for 'timeseries()'
load_xrmsd	Loading function for 'xrmsd()'
MDplot_argument	Arguments for bash script interface
MDplot_argument-class	Arguments for bash script interface
noe	Plot NOE violations
ramachandran	Ramachandran plot for two dihedral angles
rmsd	Root-mean-square-deviation (RMSD) plot
rmsd_average	Root-mean-square-deviation (RMSD) average plot
rmsf	Root-mean-square-fluctuation (RMSF) plot
TIcurve	Thermodynamic integration plot
timeseries	General timeseries plotting function
translate_aminoacids	Function to translate between canonical and GROMOS amino acid abbreviations
xrmsd	XRMSD plot in heatmap style