Demo - Caffeine Molecule

library(rgl)
library(devout)
library(devoutrgl)
library(ggrgl)
library(ggplot2)
library(dplyr)
library(raymolecule)

Caffeine Molecule with geom_sphere_3d

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# remotes::install_github("tylermorganwall/raymolecule")
# Get the caffeine molecule
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sdf <- raymolecule::get_example_molecule("caffeine") %>% read_sdf()

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# de-noramlise the bonds into actual coordinate endpoints
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bonds <- sdf$bonds %>% select(from, to)
bonds <- bonds %>% 
  left_join(sdf$atoms, by = c(to = 'index')) 

bonds <- bonds %>%
  dplyr::rename(xend = x, yend = y, zend = z) %>%
  select(-type) %>%
  left_join(sdf$atoms, by = c(from = 'index'))

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create a plot with `geom_sphere_3d`
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p <- ggplot() +
  geom_sphere_3d(data = sdf$atoms, aes(x=x, y=y, z=z, colour = type, size = type)) +
  geom_segment_3d(data = bonds, aes(x=x, y=y, z=z, xend=xend, yend=yend, zend=zend), 
                  alpha = 0.5) +
  theme_ggrgl() + 
  labs(
    title = "ggrgl::geom_sphere_3d()",
    subtitle = "with {devoutrgl}"
  ) +
  scale_size_manual(values = c(3, 6, 9, 12)) + 
  coord_equal() 


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Render with a 3d backend - devoutrgl
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
devoutrgl::rgldev(fov = 30, view_angle = -30)
p
invisible(dev.off())

Use your mouse, mouse buttons and scrollwheel to manipulate the 3d plot

Raymolecule

Thanks to Tyler Morgan Wall for the RayMolecule package.