Remove atoms with CDK

[xdomingoal]

How can you remove a specific atom from a molecule (IAtomContainer) using CDK in R?

[zachcp]

Hi, here is an example.

# devtools::install_github("CDK-R/depict")

library(rcdk)
library(depict)

mol <- depict::parse_smiles("C1CCCCC1")

depiction() %>%
  depict(mol) %>%
  get_image() %>%
  grid::grid.raster()

# use rJava `as.list` method to view the Java iterator as a list
list_of_atoms <- as.list(mol$atoms())

# delete the atom of interest
mol$removeAtom(list_of_atoms[[1]])

depiction() %>%
  depict(mol) %>%
  get_image() %>%
  grid::grid.raster()