Builds a scene containing only bond geometry from a PDB or SDF model.
generate_bond_scene(
model,
x = 0,
y = 0,
z = 0,
scale = 1,
center = TRUE,
force_single_bonds = FALSE,
material = rayrender::glossy,
material_args = list(),
material_vertex = material_list(diffuse = "grey33", ambient = "grey33", type = "phong",
ambient_intensity = 0.3)
)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.
- force_single_bonds
Default `FALSE`. Whether to force all bonds to show as a single connection.
- material
Default `rayrender::glossy`. Optional rayrender material used to initialize the mesh material when `material_vertex` is not supplied. Must be either `glossy`, `diffuse`, or `dielectric`.
- material_args
Default `list()`. Named list of additional arguments passed to `material`. Arguments supplied by raymolecule for colors and textures override entries with the same names. For example, use `list(gloss = 0.35, reflectance = 0.12)` with `rayrender::glossy`, or `list(sigma = 0.4)` with `rayrender::diffuse`.
- material_vertex
Default `material_list(diffuse="grey33",ambient="grey33",type="phong", ambient_intensity=0.3)`. Mesh material to use for the bonds.
Value
Raymesh scene containing only the connections between atoms in a molecule/protein.
Examples
bond_model = read_sdf(get_example_molecule("benzene"))
# Start with a centered bond scene using the molecule's recorded bond
# orders and default bond material.
bond_model |>
generate_bond_scene() |>
render_model(
pathtrace = FALSE,
width = 800,
height = 800,
background = "grey10"
)
# This version reduces the spacing, forces every connection to a single
# bond, and lights the ligand from above and below while pathtracing.
bond_model |>
generate_bond_scene(
x = 0,
y = 0,
z = 0,
scale = 0.7,
center = TRUE,
force_single_bonds = TRUE,
material = rayrender::glossy,
material_args = list(gloss = 0.35)
) |>
render_model(
pathtrace = TRUE,
lights = "both",
width = 800,
height = 800,
samples = 32
)
# A custom rayvertex material changes the raster bond color and ambient
# contribution while keeping the same geometry.
bond_material = rayvertex::material_list(
diffuse = "grey85",
ambient = "grey25",
type = "phong",
ambient_intensity = 0.4
)
cinnemaldehyde_model = read_sdf(get_example_molecule("cinnemaldehyde"))
cinnemaldehyde_model |>
generate_bond_scene(
material_vertex = bond_material
) |>
render_model(
pathtrace = FALSE,
width = 800,
height = 800,
background = "grey10"
)
