Draw Molecule by {rcdk} Defined by SMILES or SDF

Drawing a molecular structure based on rcdk package and using SMILES or SDF input data. This function is inspired by the Edgardo Rivera-Delgado article.

Usage

draw_molecule_by_rcdk(
  molecule,
  type = "smiles",
  mol.label = NULL,
  mol.label.color = "black",
  mol.label.xy.posit = c(8.2, 1.2),
  sma = NULL,
  annotate = "off",
  style = "cow",
  abbr = "off",
  suppressh = TRUE,
  ...
)

Arguments

molecule

Character input string => either SMILES strings (in case of type = "smiles"/type = "SMILES") or file path strings pointing to ".sdf" file.

type

Character string referred to the original molecular type input => either type = "smiles"/type = "SMILES" or type = "sdf"/type = "SDF". Default: type = "smiles".

mol.label

Character string, pointing to name of the molecule/compound, e.g. mol.label = c("acetone") or mol.label = c("PBN"). If mol.label = NULL (default) a character string "mol. structure viewer" with the gray color is shown.

mol.label.color

Character string, pointing to displayed font color of the chemical structure label. Default: mol.label.color = "black".

mol.label.xy.posit

Numeric vector of two values, matching the \(x,y\)-position of the mol.label within the image having the total size of (1,1,10,10) => see rasterImage. Default: mol.label.xy.posit = c(8.2,1,2) => the label is positioned at the bottom right corner.

sma

Character string, allowing to highlight sub-structures using SMARTS (SMILES ARbitrary Target Specification) to highlight the common substructures in a set of molecules, such as sma = "C=O".

annotate

Character string, whether to display (annotate = "number") or do not display (annotate = "off") the atomic numbers/indexes. Default: annotate = "off".

style

Character string, denoting the plotting style like =>

Plotting Style	Style Text String
"color on black"	style = "cob"
"color on white"	style = "cow"
"black on white"	style = "bow"
"white on black"	style = "wob"
"neon on black"	style = "nob"

Default: style = "cow".

abbr

Character string, which controls how the structure is displayed. Following options can be set => abbr = "off" (default), pointing to present structure as is; abbr = "groups", creating an abbreviation for groups; abbr = "reagents", creating an abbreviation for reagents or abbr = "on" to abbreviate both. The abbr = "groups" WORKS ONLY IF annotate = "off"!

suppressh

Logical, denoting whether to suppress displaying of the hydrogen atoms. The SMILES or SDF STRUCTURE MUST CONTAIN H ATOMS! Default: supressh = TRUE.

...

additional options/arguments for the get.depictor.

Value

Graphics/Figure object with molecular structure.

See also

Other Visualizations and Graphics: plot_EPR_Specs(), plot_EPR_Specs2D_interact(), plot_EPR_Specs3D_interact(), plot_EPR_Specs_integ(), plot_EPR_present_interact(), plot_labels_xyz(), plot_layout2D_interact(), plot_theme_In_ticks(), plot_theme_NoY_ticks(), plot_theme_Out_ticks(), present_EPR_Sim_Spec()

Examples

## draw N,N,N',N'-tetramethyl-p-phenylenediamine based
## on the `smiles` code character with highlighting
## the "C(aromatic)--N" bond
draw_molecule_by_rcdk("CN(C)C1=C([H])C([H])=C(N(C)C)C([H])=C1[H]",
                      type = "smiles",
                      sma = "cN")

#
## draw N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) radical
## cation based on the `smiles` code character, with hydrogen atoms
## and molecule name label = "TMPD^(+.)"
draw_molecule_by_rcdk("CN(C)[C+]1C([H])=C([H])[C.]([N](C)C)C([H])=C1[H]",
                      type = "smiles",
                      mol.label = expression(TMPD^+.),
                      mol.label.color = "blue",
                      suppressh = FALSE)

#
## draw N,N,N',N'-tetramethyl-p-phenylenediamine based
## on the `sdf` file path ("TMPD.sdf") with "color on black"
## style + atom numbering
draw_molecule_by_rcdk(molecule = load_data_example("TMPD.sdf"),
                      type = "sdf",
                      annotate = "number",
                      style = "cob")