r3dmol (version 0.1.2)

m_sel: Selection Function for r3dmol

Description

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

Usage

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

# NOT RUN {
library(r3dmol)
# }
# NOT RUN {
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))
# }