| 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 |