Visualizing Molecular Dynamics Analyses

Documentation for package ‘MDplot’ version 0.3

clusters	Cluster bar plot
clusters_ts	Cluster timeseries plot
dssp_summary	DSSP summary 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_summary	Load DSSP information
load_dssp_ts	Load DSSP timeseries
load_hbond	Loading hydrogen bonds
load_hbond_ts	Loading hydrogen bonds timeseries
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
ramachandran	Ramachandran plot for two dihedral angles
rmsd	Root-mean-square-deviation plot
rmsf	Root-mean-square-fluctuation 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