BioMedR (version 1.2.1)

plotStructure: Plots compound structure(s) for molecules stored in SDF and SDFset containers

Description

Plots compound structure(s) for molecules stored in SDF and SDFset containers.

Usage

plotStructure(sdf, atomcex = 1.2, atomnum = FALSE,
  no_print_atoms = c("C"), noHbonds = TRUE, bondspacer = 0.12,
  colbonds = NULL, bondcol = "red", ...)

Arguments

sdf

Object of class SDF

atomcex

Font size for atom labels

atomnum

If TRUE, then the atom numbers are included in the plot. They are the position numbers of each atom in the atom block of an SDF.

no_print_atoms

Excludes specified atoms from being plotted.

noHbonds

If TRUE, then the C-hydrogens and their bonds - explicitly defined in an SDF - are excluded from the plot.

bondspacer

Numeric value specifying the plotting distance for double/triple bonds.

colbonds

Highlighting of subgraphs in main structure by providing a numeric vector of atom numbers, here position index in atom block. The bonds of connected atoms will be plotted in the color provided under bondcol.

bondcol

A character or numeric vector of length one to specify the color to use for substructure highlighting under colbonds.

...

Arguments to be passed to/from other methods.

Value

Prints summary of SDF/SDFset to screen and plots their structures to graphics device.

Details

The function plotStructure depicts a single 2D compound structure based on the XY-coordinates specified in the atom block of an SDF. The functions depend on the availability of the XY-coordinates in the source SD file and only 2D (not 3D) representations are plotted correctly.

References

...

Examples

# NOT RUN {
data(sdfbcl)
plotStructure(sdfbcl[[1]])
plotStructure(sdf = sdfbcl[[2]], atomcex = 1.2, atomnum = FALSE, 
              no_print_atoms = c("C"), noHbonds = TRUE, bondspacer = 0.08)
# }