Reads an SDF file and extracts the 3D molecule model
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
# \donttest{
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")
# }