# Visualising Molecular Dynamics Analyses

## 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