hbond {MDplot}

Plot hydrogen bond summary

Description

This function plots the summary output of hydrogen bond calculations and allows selection of donor and acceptor residues and atoms. Occurrence over the whole trajectory is indicated by a colour scale. A legend indicating the colour scale can be printed. Note, that in case multiple hydrogen bond interactions between two particular residues take place, the one with prevalence will be used for colour-coding (and by default, this interaction is marked with a black circle, see below).

Usage

hbond( hbonds,
       plotMethod = "residue-wise",
       acceptorRange = NA,
       donorRange = NA,
       printLegend = TRUE,
       showMultipleInteractions = TRUE,
       barePlot = FALSE,
       ... )

Arguments

hbonds

Table containing the hydrogen bond information in its columns hbondID, resDonor, resDonorName, resAcceptor, resAcceptorName, atomDonor, atomDonorName, atomH, atomAcceptor, AtomAcceptorName, percentage. This kind of table is automatically generated by function load_hbond().

plotMethod

Allows to set the detail of hbond information displayed. Options are currently:

• residue-wise

acceptorRange

Vector, specifying which range of acceptor residues is used.

donorRange

Vector, specifying which range of donor residues is used.

printLegend

Boolean, used to print or hide the legend for the occurences.

showMultipleInteractions

If TRUE, this option causes multiple interactions between the same residues as being represented by a black circle around the coloured dot.

barePlot

Boolean, indicating whether the plot is to be made without any additional information.

...

Additional arguments (ellipsis).

Value

Returns a table containing the information used for the plot:

• resDonor Residue number (donor).

• resAcceptor Residue number (acceptor).

• percentage Percentage, that has been used for colour-coding.

• numberInteractions Number of hydrogen bond interactions taking place between the specified donor and acceptor residues.

Author(s)

Christian Margreitter

Examples

# GROMOS (see load_hbond() for other input possibilities)
hbond( load_hbond( system.file( "extdata/hbond_example.txt.gz",
                                package = "MDplot" ) ) )