Add Cylinder Between Points — m_add

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.

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"))