generate_atom_scene {raymolecule}

Build Scene (atoms only)

Description

Reads an SDF file and extracts the 3D molecule model

Usage

generate_atom_scene(
  model,
  x = 0,
  y = 0,
  z = 0,
  scale = 1,
  center = TRUE,
  pathtrace = TRUE,
  material = rayrender::glossy,
  material_vertex = material_list(type = "phong")
)

Arguments

model

Model extracted from a PDB or SDF file.

x

Default '0'. X offset, applied after centering.

y

Default '0'. Y offset, applied after centering.

z

Default '0'. Z offset, applied after centering.

scale

Default '1'. Amount to scale the inter-atom spacing.

center

Default 'TRUE'. Centers the bounding box of the model.

pathtrace

Default 'TRUE'. If 'FALSE', the 'rayvertex' package will be used to render the scene.

material

Default 'rayrender::glossy'. Rayrender material to use when 'pathtrace = TRUE'. Must be either 'glossy', 'diffuse', or 'dielectric'.

material_vertex

Default 'rayvertex::material_list()'. Material to use when 'pathtrace = FALSE'. 'diffuse'/'ambient' colors and 'ambient_intensity' are determined automatically, but all other material properties can be changed.

Value

Rayrender/rayvertex scene containing only the atoms in a molecule/protein.

Examples

#Generate a scene with caffeine molecule with just the atoms

get_example_molecule("caffeine") %>%
  read_sdf() %>%
  generate_atom_scene() %>%
  render_model(samples=256,sample_method="sobol_blue")

#Generate a rayvertex scene, using toon shading
shiny_toon_material = rayvertex::material_list(type="toon_phong",
                                               toon_levels=3,
                                               toon_outline_width=0.1)
get_example_molecule("caffeine") %>%
  read_sdf() %>%
  generate_atom_scene(pathtrace=FALSE, material_vertex = shiny_toon_material) %>%
  render_model(background="white")

#Generate a scene with caffeine, reducing the inter-atom spacing
get_example_molecule("caffeine") %>%
  read_sdf() %>%
  generate_atom_scene(scale=0.5) %>%
  render_model(samples=256,sample_method="sobol_blue")