plotStruc {ChemmineR} | R Documentation

## Plot compound structures

### Description

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

### Usage

    ## Convenience plot method
    # plot(x, griddim, print_cid=cid(x), print=TRUE, ...)

    ## Less important for user
    plotStruc(sdf, atomcex = 1.2, atomnum = FALSE, no_print_atoms = c("C"),
              noHbonds = TRUE, bondspacer = 0.12, colbonds=NULL, bondcol="red",
    			 regenCoords=FALSE, ...)

### 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`.
`regenCoords` | If ChemmineOB is installed and this option is TRUE, then Open Babel will be used to re-generate the 2D coords for each compound before plotting it. This often results in a nicer layout. If you want to save the results of the coord re-generation, call the `regenerateCoords` function first yourself and save the result.
`...` | Arguments to be passed to/from other methods.

### Details

The function `plotStruc` depicts a single 2D compound structure based on the XY-coordinates specified in the atom block of an SDF. The generic method `plot` can be used as a convenient shorthand to plot one or many structures at once. Both functions depend on the availability of the XY-coordinates in the source SD file and only 2D (not 3D) representations are plotted correctly.

Additional arguments that can only be passed on to the `plot` function when supplied with an SDFset object:

`griddim`: numeric vector of length two to define the dimensions for arranging several structures in one plot.

`print_cid`: character vector for printing custom compound labels. Default is `print_cid=cid(sdfset)`.

`print`: if `print=TRUE`, then a summary of the SDF content for each supplied compound is printed to the screen. This behavior is turned off with `print=TRUE`.

### Value

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

### Note

The compound depictions created by this function are not as pretty as the structure representations generated with the `sdf.visualize` function. This will be improved in the future.

### Author(s)

Thomas Girke

### References

...

### See Also

`sdf.visualize`

### Examples

    ## Import SDFset sample set
    data(sdfsample)
    (sdfset <- sdfsample)

    ## Plot single compound structure
    plotStruc(sdfset[[1]])

    ## Plot several compounds structures
    plot(sdfset[1:4])

    ## Highlighting substructures (here all rings)
    myrings <- as.numeric(gsub(".*_", "", unique(unlist(rings(sdfset[1])))))
    plot(sdfset[1], colbonds=myrings)

    ## Customize plot
    plot(sdfset[1:4], griddim=c(2,2), print_cid=letters[1:4], print=FALSE, noHbonds=FALSE)

[Package ChemmineR version 3.40.0 Index]