In CDK-R/depict: Draw Beautiful Molecular Structures

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

knitr::opts_chunk$set(echo = TRUE)
suppressMessages(library(depict))


## Simple Depiction

A simple wrapper around cdk's excellent depict module.


```r
library(depict)

# load a smiles string
pen <- parse_smiles("CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)[O-])C penicillin")

# `depiction` is the base class; styles are applied to it
# `depict` applies the styles to the molecule
depiction() |>
  set_zoom(2) |>
  depict(pen) |>
  get_svg_string() |>
  cat()

Multiple Structure Depiction

Multiple Smiles

# load a few smiles as AtomContainers
atmcontainers <- lapply(
  c("CCCC", "CCCCCC", "CCCC1CCC1CC2CCCC2"),
  parse_smiles
)

# convert them into a java iterable
many_containers <- atomcontainer_list_to_jarray(atmcontainers)


depiction() |>
  set_zoom(2) |>
  depict(many_containers) |>
  get_svg_string() |>
  cat()

Use Colors, SMARTS, Highlighting

# you must supply java colors
color <- J("java.awt.Color")

# load in penicillin
pen <- parse_smiles("CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)[O-])C penicillin")
cav <- parse_smiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C")

# define the regions to highlight
# either all atoms/bonds
# or a SMARTS-defined subregion
atms <- pen$atoms()
bnds <- pen$bonds()
lactam <- match_smarts("C1(=O)NCC1", pen)

# use piping to change the behavior as desired
depiction() |>
  highlight_atoms(atms, color$LIGHT_GRAY) |>
  highlight_atoms(bnds, color$LIGHT_GRAY) |>
  highlight_atoms(lactam, color$RED) |>
  set_zoom(2) |>
  outerglow() |>
  add_title() |>
  depict(pen) |>
  get_svg_string() |>
  cat()

SMARTS for highlighting mutiple containers

small_highlight <- match_smarts("C1CCC1", many_containers)

depiction() |>
  highlight_atoms(small_highlight, color$RED) |>
  set_zoom(2) |>
  outerglow() |>
  add_title() |>
  depict(many_containers) |>
  get_svg_string() |>
  cat()

Multiple Colors

mol <- parse_smiles(paste("CC(n1c(C)ncc1c1ccnc(n1)Nc1ccc(cc1)S(=O)(=O)C)C",
  "CMGC:CDC2:6gu3:A:FB8",
  sep = " "
))

# imid      <- 'c1cnc[nH]1'  #1H-imidazole
highlight_imid <- match_smarts("c1cncn1", mol)
highlight_2 <- match_smarts("n1cccnc1Nc2ccccc2", mol)

color <- J("java.awt.Color")

depiction() |>
  highlight_atoms(highlight_imid, color$GREEN) |>
  highlight_atoms(highlight_2, color$RED) |>
  set_zoom(2) |>
  outerglow() |>
  add_title() |>
  depict(mol) |>
  get_svg_string() |>
  cat()

A Larger Example

# loading a molfile
insulinmol <- system.file("molfiles/ChEBI_5931.mol", package = "depict")
insulin <- read_mol(insulinmol)

cysteine <- match_smarts("C(=O)C(CS)N", insulin)
xlinks <- match_smarts("SS", insulin)

depiction() |>
  set_zoom(0.7) |>
  outerglow() |>
  highlight_atoms(cysteine, color$YELLOW) |>
  highlight_atoms(xlinks, color$YELLOW) |>
  depict(insulin) |>
  get_svg_string() |>
  cat()