generate_full_scene: Build Scene (bonds + atoms)

In raymolecule: Parse and Render Molecular Structures in 3D

Build Scene (bonds + atoms)

Description

Reads an SDF file and extracts the 3D molecule model

Usage

generate_full_scene(
  model,
  x = 0,
  y = 0,
  z = 0,
  scale = 1,
  center = TRUE,
  pathtrace = TRUE,
  force_single_bonds = FALSE,
  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 interatom 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.
force_single_bonds	Default 'FALSE'. Whether to force all bonds to show as a single connection.
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

Examples

# Generate a scene with caffeine molecule

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

#Generate a rayvertex scene with a custom material
get_example_molecule("caffeine") %>%
  read_sdf() %>%
  generate_full_scene(pathtrace=FALSE, material_vertex=rayvertex::material_list(type="phong")) %>%
  render_model(background="grey33")

#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_full_scene(pathtrace=FALSE, material_vertex=shiny_toon_material) %>%
  render_model(background="grey66")

# Generate a scene with morphine, increasing the inter-atom spacing
get_example_molecule("tubocurarine_chloride") %>%
  read_sdf() %>%
  generate_full_scene(scale=1.5) %>%
  render_model(samples=256,sample_method="sobol_blue")


# Force bonds to appear as a single link (to focus purely on the shape of the molecule)
get_example_molecule("tubocurarine_chloride") %>%
  read_sdf() %>%
  generate_full_scene(force_single_bonds = TRUE) %>%
  render_model(samples=256,sample_method="sobol_blue")

raymolecule documentation built on May 29, 2024, 1:13 a.m.