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

In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

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.

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.

Value

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

Author(s)

Min-feng Zhu <[e-mail]>

References

...

Examples

data(sdfbcl)
plotStructure(sdfbcl[[1]])
plotStructure(sdf = sdfbcl[[2]], atomcex = 1.2, atomnum = FALSE, 
              no_print_atoms = c("C"), noHbonds = TRUE, bondspacer = 0.08)

wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.