Selection Function for r3dmol — m

Provides documentation for some basic useful selection criteria. For more advanced selection options, see the Official Documenation

m_sel(
  model = NULL,
  resi = NULL,
  resn = NULL,
  invert = NULL,
  chain = NULL,
  elem = NULL,
  atom = NULL,
  byres = NULL,
  b = NULL,
  expand = NULL,
  bonds = NULL,
  ss = NULL,
  clickable = NULL,
  callback = NULL
)

Arguments

model: a single model or list of models from which atoms should be selected. Can also specify by numerical creation order. Reverse indexing is allowed (-1 specifies last added model).
resi: Residue number/s. (vector)
resn: Parent residue name as 3-letter code (e.g. "ALA", "GLY", "CYS"...)
invert: Logical, if invert = TRUE, Inverts the selection criteria.
chain: String, chain this atom belongs to (e.g. 'A' for chain A)
elem: element abbreviation (e.g 'H', 'Ca', etc)
atom: Atom name, may be more specific than 'elem' (e.g. 'CA' for alpha carbon)
byres: Logical, if byres = TRUE, expands the selection to entire residues that include any selected atoms.
b: Atom b factor data
expand: Expand selection to include atoms within a specified distance from current selection. all atoms of any residue that has any atom already selected.
bonds: overloaded to select number of bonds, e.g. bonds = 0 will select all non-bonded atoms
ss: Secondary structure identifier. 'h' for helix, 's' for beta-sheet.
clickable: Set this flag to true to enable click selection handling for this atom
callback: Callback click handler function to be executed on this atom and its parent viewer.

Value

sel list() for selecting atoms.

Examples

library(r3dmol)
if (FALSE) {
r3dmol() %>%
  m_add_model(data = m_fetch_pdb("1bna")) %>%
  m_add_style(
    style = m_style_stick(),
    sel = m_sel(resi = 1:2)
  ) %>%
  m_zoom_to(sel = m_sel(resi = 1))

# Expand example
r3dmol() %>%
  m_add_model(data = m_fetch_pdb("1bna")) %>%
  m_add_style(
    style = m_style_stick(),
    sel = m_sel(
      resi = 1,
      expand = 10,
      byres = TRUE
    )
  ) %>%
  m_zoom_to(sel = m_sel(resi = 1))
}