m_sel: Selection Function for r3dmol

In r3dmol: Create Interactive 3D Visualizations of Molecular Data

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

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))

## End(Not run)

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