m_add_cylinder: Add Cylinder Between Points

In r3dmol: Create Interactive 3D Visualizations of Molecular Data

Description

Add cynliders between the given points. Will match starting point/s with ending point/s to create a line between each point. Styling options can be supplied as one option, or a vector of length equal to the number of lines.

Usage

m_add_cylinder(
  id,
  start,
  end,
  radius = 0.1,
  fromCap = 1,
  toCap = 1,
  dashed = FALSE,
  color = "black",
  alpha = FALSE,
  wireframe = FALSE,
  hidden = FALSE,
  spec = m_shape_spec()
)

Arguments

id	R3dmol id or a r3dmol object (the output from r3dmol()).
start	Starting position (or list() of positions) of line. Can be a single position or list() of positions. Format either m_sel() or m_vector3().
end	Ending position (or list() of positions) of line. Can be a single position or list() of positions. Format either m_sel() or m_vector3().
radius	Radius of cylinder.
fromCap	Cap at start of cylinder. 0 for none, 1 for flat, 2 for rounded.
toCap	Cap at end of cylinder. 0 for none, 1 for flat, 2 for rounded.
dashed	Boolean, dashed style cylinder instead of solid.
color	Color value for cylinders. Either 1 or vector of colors equal in length to start.
alpha	Alpha value for transparency.
wireframe	Logical, display as wireframe.
hidden	Logical, whether or not to hide the cylinder.
spec	Additional shape specifications defined with m_shape_spec().

Examples

## Add a cylinder between residue 1 & 2 of Chain "A"
r3dmol() %>%
  m_add_model(pdb_6zsl) %>%
  m_zoom_to(sel = m_sel(resi = 1)) %>%
  m_add_cylinder(
    start = m_sel(resi = 1, chain = "A"),
    end = m_sel(resi = 2, chain = "A"),
    dashed = TRUE,
    radius = 0.1
  )

# Add two cylinders.
# Blue cylinder is between residues 1 & 2
# Green cylinder is between residues 3 & 4
r3dmol() %>%
  m_add_model(pdb_6zsl) %>%
  m_zoom_to(sel = m_sel(resi = 1:4, chain = "A")) %>%
  m_add_cylinder(
    start = list(
      m_sel(resi = 1, chain = "A"),
      m_sel(resi = 3, chain = "A")
    ),
    end = list(
      m_sel(resi = 2, chain = "A"),
      m_sel(resi = 4, chain = "A")
    ),
    dashed = TRUE,
    radius = 0.1,
    color = c("blue", "green")
  ) %>%
  m_add_res_labels(m_sel(resi = 1:4, chain = "A"))

# The same scene achieved with m_multi_resi_sel()
r3dmol() %>%
  m_add_model(pdb_6zsl) %>%
  m_zoom_to(sel = m_sel(resi = 1:4, chain = "A")) %>%
  m_add_cylinder(
    start = m_multi_resi_sel(resi = c(1, 3), chain = "A"),
    end = list(
      m_sel(resi = 2, chain = "A"),
      m_sel(resi = 4, chain = "A")
    ),
    dashed = TRUE,
    radius = 0.1,
    color = c("blue", "green")
  ) %>%
  m_add_res_labels(m_sel(resi = 1:4, chain = "A"))

r3dmol documentation built on March 14, 2021, 5:08 p.m.