Title:	Create Interactive 3D Visualizations of Molecular Data
Version:	0.1.2
Maintainer:	Wei Su <swsoyee@gmail.com>
Description:	Create rich and fully interactive 3D visualizations of molecular data. Visualizations can be included in Shiny apps and R markdown documents, or viewed from the R console and 'RStudio' Viewer. 'r3dmol' includes an extensive API to manipulate the visualization after creation, and supports getting data out of the visualization into R. Based on the '3dmol.js' and the 'htmlwidgets' R package.
License:	BSD_3_clause + file LICENSE
Encoding:	UTF-8
LazyData:	true
RoxygenNote:	7.1.1
Imports:	htmlwidgets, magrittr, methods, bio3d
Suggests:	knitr, rmarkdown, shiny, colourpicker, covr, testthat
VignetteBuilder:	knitr
Depends:	R (≥ 2.10)
URL:	https://github.com/swsoyee/r3dmol
BugReports:	https://github.com/swsoyee/r3dmol/issues
NeedsCompilation:	no
Packaged:	2021-03-13 15:36:34 UTC; suwei
Author:	Wei Su [aut, cre], Brady Johnston [aut]
Repository:	CRAN
Date/Publication:	2021-03-14 15:10:02 UTC

List of multiple start/stop locations.

Description

For use in addition of lines, arrows, cylinders, when multiple locations are specified in a single call.

Usage

.m_multi_spec(starts, ends)

Arguments

Cif file example

Description

Cif file example

Usage

cif_254385

Format

cif format

Source

https://github.com/3dmol/3Dmol.js/blob/master/tests/auto/data/254385.cif

Gaussian cube file example

Description

Gaussian cube file example

Usage

cube_benzene_homo

Format

Gaussian cube format

Source

https://github.com/3dmol/3Dmol.js/blob/master/tests/test_structs/benzene-homo.cube

Initialise a WebGL-based viewer

Description

Create and initialize an appropriate viewer at supplied HTML element using specification in config

Usage

r3dmol(
  id = NULL,
  viewer_spec = m_viewer_spec(),
  ...,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_zoom_to()

# Viewer configs setting
r3dmol(
  backgroundColor = "black",
  lowerZoomLimit = 1,
  upperZoomLimit = 350
) %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_zoom_to()

Add arrow shape

Description

Add an arrow from start to end, additional customisation through m_shape_spec().

Usage

m_add_arrow(
  id,
  start,
  end,
  radius = 0.2,
  radiusRatio = 1.62,
  mid = 0.62,
  spec = m_shape_spec(),
  hidden = FALSE
)

Arguments

Examples

## Not run: 
r3dmol() %>%
  m_add_model(data = m_fetch_pdb("1bna")) %>%
  m_zoom_to(sel = m_sel(resi = 1)) %>%
  m_add_arrow(
    start = m_sel(resi = 1),
    end = m_sel(resi = 3),
    spec = m_shape_spec(color = "green")
  )

## End(Not run)

Create and add model to viewer

Description

Given multimodel file and its format, all atoms are added to one model

Usage

m_add_as_one_molecule(id, data, format)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Create and add shape

Description

Create and add shape

Usage

m_add_box(id, spec = list())

m_add_curve(id, spec = list())

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

# Add arrow
r3dmol() %>%
  m_add_arrow(
    start = m_vector3(-10, 0, 0),
    end = m_vector3(0, -10, 0),
    radius = 1,
    radiusRatio = 1,
    mid = 1,
    spec = m_shape_spec(
      clickable = TRUE,
      callback =
        "function() {
            this.color.setHex(0xFF0000FF);
            viewer.render()
          }"
    )
  )

# Add curve
r3dmol() %>%
  m_add_curve(
    spec = list(
      points = list(
        m_vector3(0, 0, 0),
        m_vector3(5, 3, 0),
        m_vector3(5, 7, 0),
        m_vector3(0, 10, 0)
      ),
      radius = 0.5,
      smooth = 10,
      fromArrow = FALSE,
      toArrow = TRUE,
      color = "orange"
    )
  )

# Add cylinder
r3dmol() %>%
  m_add_cylinder(
    start = list(x = 0.0, y = 0.0, z = 0.0),
    end = list(x = 10.0, y = 0.0, z = 0.0),
    radius = 1.0,
    fromCap = 1,
    toCap = 2,
    spec = m_shape_spec(
      color = "red",
      hoverable = TRUE,
      clickable = TRUE,
      callback = "
        function() {
          this.color.setHex(0x00FFFF00);
          viewer.render();
        }",
      hover_callback = "
        function() {
          viewer.render();
        }",
      unhover_callback = "
        function() {
          this.color.setHex(0xFF000000);
          viewer.render();
        }"
    )
  )

# Add line
r3dmol() %>%
  m_add_line(
    dashed = TRUE,
    start = m_vector3(0, 0, 0),
    end = m_vector3(30, 30, 30)
  )

# Add box
r3dmol() %>%
  m_add_box(spec = list(
    center = m_vector3(0, 5, 0),
    demensions = list(w = 3, h = 4, d = 2),
    color = "magenta"
  ))

# Add sphere
r3dmol() %>%
  m_add_sphere(
    center = m_vector3(0, 0, 0),
    radius = 10,
    spec = m_shape_spec(color = "red")
  )

Add custom shape component from user supplied function

Description

Add custom shape component from user supplied function

Usage

m_add_custom(id, spec)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r <- 20

vertices <- list(
  m_vector3(0, 0, 0),
  m_vector3(r, 0, 0),
  m_vector3(0, r, 0)
)

normals <- list(
  m_vector3(0, 0, 1),
  m_vector3(0, 0, 1),
  m_vector3(0, 0, 1)
)

colors <- list(
  list(r = 1, g = 0, b = 0),
  list(r = 0, g = 1, b = 0),
  list(r = 0, g = 0, b = 1)
)

faces <- 0:2

r3dmol() %>%
  m_add_custom(spec = list(
    vertexArr = vertices,
    normalArr = normals,
    faceArr = faces,
    color = colors
  ))

Add Cylinder Between Points

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

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"))

Construct isosurface from volumetric data in gaussian cube format

Description

Construct isosurface from volumetric data in gaussian cube format

Usage

m_add_isosurface(id, data, isoSpec)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_isosurface(
    data = cube_benzene_homo,
    isoSpec = list(
      isoval = -0.01,
      color = "red",
      opacity = 0.95
    )
  ) %>%
  m_zoom_to()

Add label to viewer

Description

Add label to viewer

Usage

m_add_label(id, text, style = m_style_label(), sel = m_sel(), noshow = TRUE)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_add_label(
    text = "Label",
    sel = m_vector3(-6.89, 0.75, 0.35),
    style = m_style_label(
      backgroundColor = "#666666",
      backgroundOpacity = 0.9
    )
  ) %>%
  m_zoom_to()

Add Lines Between Points

Description

Add lines 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_line(
  id,
  start,
  end,
  dashed = TRUE,
  color = "black",
  opacity = 1,
  hidden = FALSE
)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl) %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_zoom_to() %>%
  m_add_style(
    sel = m_sel(resi = 1:10),
    style = c(
      m_style_stick(),
      m_style_sphere(scale = 0.3)
    )
  ) %>%
  m_add_line(
    start = list(
      m_sel(resi = 1, chain = "A"),
      m_sel(resi = 1, chain = "A")
    ),
    end = list(
      m_sel(resi = 10, chain = "A"),
      m_sel(resi = 10, chain = "B")
    ),
    dashed = TRUE
  )

Create and add model to viewer

Description

Create and add model to viewer, given molecular data and its format. If multi-model file is provided, use m_add_models adding atom data to the viewer as separate models.

Usage

m_add_model(
  id,
  data,
  format = c("pdb", "sdf", "xyz", "pqr", "mol2", "cif"),
  keepH = FALSE,
  options = list()
)

m_add_models(id, data, format = c("pdb", "sdf", "xyz", "pqr", "mol2", "cif"))

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

# Single-model file with m_add_model() function
r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb")

# Multi-model file with m_add_models() function
r3dmol() %>%
  m_add_models(data = sdf_multiple, "sdf") %>%
  m_zoom_to()

# Multi-model file with m_add_model() function
r3dmol() %>%
  m_add_model(data = sdf_multiple, "sdf") %>%
  m_zoom_to()

# Add model and keep hydrogens.
## Not run: 
r3dmol() %>%
  m_add_model(m_fetch_pdb("5D8V"), keepH = TRUE) %>%
  m_set_style(m_style_sphere()) %>%
  m_zoom_to() %>%
  m_spin()

## End(Not run)

Create and add model to viewer

Description

Create and add model to viewer. Given multimodel file and its format, different atomlists are stored in model's frame property and model's atoms are set to the 0th frame

Usage

m_add_models_as_frames(id, data, format)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_models_as_frames(data = xyz_multiple, format = "xyz") %>%
  m_animate(options = list(loop = "forward", reps = 1)) %>%
  m_set_style(style = m_style_stick(colorScheme = "magentaCarbon")) %>%
  m_zoom_to()

Add colored outline to all objects in scene.

Description

Adds a colored outline to all objects in the scene, helping the viewer to distinguish depth in often complex molecular scenes.

Usage

m_add_outline(id, width = 0.1, color = "black")

Arguments

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_1j72) %>%
  m_set_style(style = m_style_stick()) %>%
  m_add_outline()

Add property labels

Description

This will generate one label per a selected atom at the atom's coordinates with the property value as the label text.

Usage

m_add_property_labels(id, prop, sel = m_sel(), style = m_style_label())

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = "data-raw/Conformer3D_CID_5291.sdf", format = "sdf") %>%
  m_set_style(style = m_style_stick(radius = 2)) %>%
  m_zoom_to() %>%
  m_add_property_labels(
    prop = "index",
    sel = list(not = list(elem = "H")),
    style = m_style_label(
      fontColor = "black",
      font = "sans-serif",
      fontSize = 28,
      showBackground = FALSE,
      alignment = "center"
    )
  )

Add Residue Labels

Description

Add residue labels. This will generate one label per a residue within the selected atoms. The label will be at the centroid of the atoms and styled according to the passed style. The label text will be resnresi

Usage

m_add_res_labels(id, sel = m_sel(), style = m_style_label(), byframe)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(
    style = c(
      m_style_stick(radius = 0.15),
      m_style_cartoon()
    )
  ) %>%
  m_add_res_labels(
    sel = m_sel(resn = "GLY"),
    style = m_style_label(
      font = "Arial",
      fontColor = "white",
      backgroundColor = "black",
      showBackground = TRUE
    )
  ) %>%
  m_zoom_to()

Add shape object to viewer

Description

Add shape object to viewer

Usage

m_add_shape(id, shapeSpec = list())

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Add Sphere Shape

Description

Adds sphere at given location, with given radius.

Usage

m_add_sphere(id, center, radius = 1, spec = m_shape_spec(), ...)

Arguments

Examples

r3dmol() %>%
  m_add_model(data = m_fetch_pdb("1bna")) %>%
  m_add_sphere(
    center = m_sel(resi = 1),
    spec = m_shape_spec(color = "green", wireframe = TRUE)
  ) %>%
  m_zoom_to(sel = m_sel(resi = 1))

Overwrite Previous Style

Description

Takes a selection and overwrites previous styling with given styles.

Usage

m_add_style(id, style = m_style_cartoon(), sel = m_sel())

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

# Add style to model
r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_add_style(style = m_style_cartoon()) %>%
  m_zoom_to()

# Set style to model
r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_set_style(
    sel = m_sel(chain = "A"),
    style = m_style_stick(
      radius = 0.5,
      colorScheme = "magentaCarbon"
    )
  ) %>%
  m_zoom_to()

Add surface representation to atoms

Description

Add surface representation to atoms

Usage

m_add_surface(
  id,
  type,
  style = m_style_surface(),
  atomsel = m_sel(),
  allsel,
  focus,
  surfacecallback
)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Unit cell visualization

Description

Use m_add_unit_cell to create and add unit cell visualization, and m_remove_unit_cell to remove it from model. Use m_replicate_unit_cell to replicate atoms in model to form a super cell of the specified dimensions. Original cell will be centered as much as possible.

Usage

m_add_unit_cell(id, model, spec)

m_replicate_unit_cell(id, a, b, c, model)

m_remove_unit_cell(id, model)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

# Create model
mol <- r3dmol() %>%
  m_add_model(
    data = cif_254385,
    "cif",
    options = list(doAssembly = TRUE, normalizeAssembly = TRUE)
  ) %>%
  m_set_style(style = c(
    m_style_sphere(colorScheme = "Jmol", scale = 0.25),
    m_style_stick(colorScheme = "Jmol")
  )) %>%
  m_add_unit_cell(spec = list(
    alabel = "x",
    blabel = "y",
    clabel = "z",
    box = list(hidden = TRUE)
  )) %>%
  m_zoom_to()

# Render model
mol

# Remove unit cell
mol %>%
  m_remove_unit_cell()

# Replicate atoms in model to form a super cell
r3dmol() %>%
  m_add_model(data = cif_254385, format = "cif") %>%
  m_set_style(style = m_style_sphere(scale = 0.25)) %>%
  m_add_unit_cell() %>%
  m_zoom_to() %>%
  m_replicate_unit_cell(a = 3, b = 2, c = 1)

Animate all models in viewer from their respective frames

Description

Animate all models in viewer from their respective frames

Usage

m_animate(id, options)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

xyz <- "4
* (null), Energy   -1000.0000000
N     0.000005    0.019779   -0.000003   -0.157114    0.000052   -0.012746
H     0.931955   -0.364989    0.000003    1.507100   -0.601158   -0.004108
H    -0.465975   -0.364992    0.807088    0.283368    0.257996   -0.583024
H    -0.465979   -0.364991   -0.807088    0.392764    0.342436    0.764260
"

r3dmol(
  width = 400,
  height = 400,
  backgroundColor = "0xeeeeee"
) %>%
  m_add_model(
    data = xyz,
    format = "xyz",
    options = list(vibrate = list(frames = 10, amplitude = 1))
  ) %>%
  m_set_style(style = m_style_stick()) %>%
  m_animate(list(loop = "backAndForth")) %>%
  m_zoom_to()

Load structure from package bio3d

Description

Function to take bio3d structure and use in the r3dmol app.

Usage

m_bio3d(pdb)

Arguments

Examples

library(bio3d)
library(r3dmol)

# create bio3d object
pdb <- read.pdb("1bna")

# inspect bio3d object
pdb

# load bio3d object into r3dmol
r3dmol() %>%
  m_add_model(data = m_bio3d(pdb)) %>%
  m_zoom_to()

Add button into viewer

Description

Add additional buttons to the viewer and pass in JavaScript functions to enable additional actions to be done when the button is clicked (such as styling changes to the model). You can also use css flex layout to control the layout of all added buttons.

Usage

m_button(
  id,
  name,
  label,
  func,
  align_items = "flex-start",
  justify_content = "flex-start"
)

Arguments

Details

If more than one button is set, only the layout (justify-content and align-items) of the first button will be used.

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_zoom_to() %>%
  m_button(
    name = "cartoon",
    label = "Cartoon",
    align_items = "flex-end",
    justify_content = "center",
    func = "
      function() {
        viewer.setStyle({cartoon:{}});
        viewer.render();
      }
    "
  ) %>%
  m_button(
    name = "stick",
    label = "Stick",
    func = "
      function() {
        viewer.setStyle({stick:{}});
        viewer.render();
      }
    "
  )

Re-center the viewer around the provided selection

Description

Re-center the viewer around the provided selection (unlike zoomTo, does not zoom).

Usage

m_center(id, sel, animationDuration, fixedPath)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_center(animationDuration = 1000)

Clear scene of all objects

Description

Clear scene of all objects

Usage

m_clear(id)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Create a new model from atoms specified by sel

Description

Create a new model from atoms specified by sel. If extract, removes selected atoms from existing models.

Usage

m_create_model_from(id, sel, extract)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Enable/disable fog for content far from the camera

Description

Enable/disable fog for content far from the camera

Usage

m_enable_fog(id, fog = TRUE)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_enable_fog(fog = FALSE)

Fetch Structure from PDB

Description

Using specified pdb id, retrieved .pdb file using bio3d::get.pdb() function. Will always query the only PDB for structure, and not store on local drive. May take some time to fetch information, every time it is run.

Usage

m_fetch_pdb(pdb, save.pdb = FALSE, path = NULL)

Arguments

Examples

library(r3dmol)
## Not run: 
r3dmol() %>%
  m_add_model(data = m_fetch_pdb("1bna")) %>%
  m_set_style(style = c(m_style_cartoon(), m_style_stick())) %>%
  m_zoom_to()

## End(Not run)

Return specified model

Description

Return specified model

Usage

m_get_model(id, modelId)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Quickly View Given Structure

Description

Creates a scene with a number of simple defaults in order to quickly view the structure without having to write multiple lines of code.

Usage

m_glimpse(
  model,
  highlight = m_sel(),
  zoom = TRUE,
  spin = FALSE,
  nomouse = FALSE,
  ribbon = FALSE,
  outline = TRUE,
  backgroundColor = "white"
)

Arguments

Examples

library(r3dmol)

# write/read demo structure as {bio3d} object
tmp <- tempfile()
write(pdb_6zsl, tmp)
pdb <- bio3d::read.pdb(tmp)

# quickly preview structure
pdb %>%
  m_glimpse()

# preview structure, highlighting particular region.
pdb %>%
  m_glimpse(m_sel(resi = 1:10, chain = "A"), spin = 0.2)
## Not run: 

# Fetch given PDB string and quickly preview structure
"4ozs" %>%
  m_glimpse(spin = TRUE)

## End(Not run)

Create a grid of viewers that share a WebGL canvas

Description

Create a grid of viewers that share a WebGL canvas

Usage

m_grid(
  viewer,
  element_id,
  rows = NULL,
  cols = NULL,
  control_all = TRUE,
  viewer_config = m_viewer_spec(),
  width = NULL,
  height = NULL
)

Arguments

Value

An r3dmol object (the output from r3dmol()).

Examples

library(r3dmol)

m1 <- r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_zoom_to()

m2 <- m1 %>%
  m_set_style(style = m_style_cartoon(color = "spectrum"))

m3 <- m1 %>%
  m_set_style(style = m_style_stick())

m4 <- m1 %>%
  m_set_style(style = m_style_sphere())

m_grid(
  viewer = list(m1, m2, m3, m4),
  control_all = TRUE,
  viewer_config = m_viewer_spec(
    backgroundColor = "black"
  )
)

Get viewer animate status

Description

Return true if viewer is currently being animated, false otherwise

Usage

m_is_animated(id)

Arguments

Value

logical

Selection Across Multiple Residues

Description

Behaves just like the m_sel(), but returns a new selection for each residue specified with resi.

Usage

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

Arguments

Details

The m_sel(resi = 1:10) returns a selection of all 10 residues. The m_multi_resi_sel(resi = 1:10) returns 10 individual selections, each containing only 1 of the residues.

Value

sel list() for selecting atoms.

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl) %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_zoom_to() %>%
  m_add_style(
    sel = m_sel(resi = 1:10),
    style = c(
      m_style_stick(),
      m_style_sphere(scale = 0.3)
    )
  ) %>%
  m_add_line(
    start = m_multi_resi_sel(resi = rep(1, 9), chain = "A"),
    end = m_multi_resi_sel(
      resi = 2:10,
      chain = "B"
    )
  )

Convert widgets to PNG image

Description

Convert widgets to PNG image

Usage

m_png(id, width, height)

Arguments

Value

Base64 encoded png image wrapped by <img> tag.

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_zoom_to() %>%
  m_png(width = 600)

Remove all labels from viewer

Description

Remove all labels from viewer

Usage

m_remove_all_labels(id)

Arguments

Value

id R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

mol <- r3dmol() %>%
  m_add_model(data = "data-raw/Conformer3D_CID_5291.sdf", format = "sdf") %>%
  m_set_style(style = m_style_stick(radius = 2)) %>%
  m_zoom_to() %>%
  m_add_property_labels(
    prop = "index",
    sel = list(not = list(elem = "H")),
    style = m_style_label(
      fontColor = "black",
      font = "sans-serif",
      fontSize = 28,
      showBackground = FALSE,
      alignment = "center"
    )
  )

# Render model with labels
mol

# Remove all labels
mol %>%
  m_remove_all_labels()

Delete all existing models

Description

Delete all existing models

Usage

m_remove_all_models(id)

Arguments

Value

id R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

mol <- r3dmol() %>%
  m_add_model(data = "data-raw/Conformer3D_CID_5291.sdf", format = "sdf")

# Render model
mol

# Remove all labels
mol %>%
  m_remove_all_models()

Remove all shape objects from viewer

Description

Remove all shape objects from viewer

Usage

m_remove_all_shapes(id)

Arguments

Value

id R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

mol <- r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_add_sphere(
    center = list(x = 0, y = 0, z = 0),
    radius = 10.0,
    color = "red"
  )

# Render model with shape
mol

# Remove shape
mol %>%
  m_remove_all_shapes()

Remove all labels from viewer

Description

Remove all labels from viewer

Usage

m_remove_all_surfaces(id)

Arguments

Value

id R3dmol id or a r3dmol object (the output from r3dmol())

Remove label from viewer

Description

Remove label from viewer

Usage

m_remove_label(id, label)

Arguments

Value

id R3dmol id or a r3dmol object (the output from r3dmol())

Render current state of viewer

Description

Render current state of viewer, after adding/removing models, applying styles, etc. In most cases, the model will render automatically, only call it when manual rendering is required.

Usage

m_render(id)

Arguments

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_render()

Rotate scene by angle degrees around axis

Description

Rotate scene by angle degrees around axis

Usage

m_rotate(id, angle, axis = "v", animationDuration = 0, fixedPath)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)
r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_rotate(angle = 90, axis = "y", animationDuration = 1000)

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

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)

Set color by element

Description

Set color by element

Usage

m_set_color_by_element(id, sel, colors)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Set the default cartoon quality for newly created models

Description

Set the default cartoon quality for newly created models. Default is 5. Current models are not affected.

Usage

m_set_default_cartoon_quality(id, quality)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_set_default_cartoon_quality(20) %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_zoom_to()

Set the duration of the hover delay

Description

Set the duration of the hover delay

Usage

m_set_hover_duration(id, hoverDuration)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Set the distance between the model and the camera

Description

Essentially zooming. Useful while stereo rendering.

Usage

m_set_preceived_distance(id, dist)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_set_preceived_distance(dist = 200)

Set view projection scheme

Description

Set view projection scheme

Usage

m_set_projection(id, scheme = c("perspective", "orthographic"))

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_set_projection(scheme = "orthographic")

Set slab of view

Description

Set slab of view (contents outside of slab are clipped).

Usage

m_set_slab(id, near, far)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_zoom_to() %>%
  m_set_slab(near = -90, far = 0)

Add Style to Selection

Description

Takes a selection and adds additional styling to selection.

Usage

m_set_style(id, style = m_style_cartoon(), sel = m_sel())

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

# Add style to model
r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_add_style(style = m_style_cartoon()) %>%
  m_zoom_to()

Sets the view to the specified translation, zoom, rotation and style

Description

Sets the view to the specified translation, zoom, rotation and style

Usage

m_set_view(id, arg, style)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_set_style(style = m_style_cartoon()) %>%
  m_set_view(arg = c(20, -20, 10, -200, 0, 1, 0, 0)) %>%
  m_add_outline(color = "blue")

Set viewer properties

Description

Functions of setting viewer properties, such as width, height, background color, etc. The viewer size can be adjusted automatically under normal circumstances.

Usage

m_set_width(id, width)

m_set_height(id, height)

m_set_background_color(id, hex, alpha)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_zoom_to() %>%
  m_set_width(300) %>%
  m_set_background_color("#666666", alpha = 0.9)

Set lower and upper limit stops for zoom

Description

Set lower and upper limit stops for zoom

Usage

m_set_zoom_limits(id, lower = 0, upper = Inf)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Specify Styling for Generic Shapes

Description

Styling options for the various shapes. Used inside m_add_sphere(), m_add_arrow(), m_add_cylinder() etc.

Usage

m_shape_spec(
  color = NULL,
  opacity = 1,
  wireframe = FALSE,
  hidden = FALSE,
  frame = NULL,
  clickable = FALSE,
  callback = NULL,
  hoverable = FALSE,
  hover_callback = NULL,
  unhover_callback = NULL
)

Arguments

Examples

library(r3dmol)
## Not run: 
r3dmol() %>%
  m_add_model(data = m_fetch_pdb("1bna")) %>%
  m_add_sphere(
    center = m_sel(resi = 1),
    spec = m_shape_spec(color = "green", wireframe = TRUE)
  ) %>%
  m_zoom_to(sel = m_sel(resi = 1))

## End(Not run)

Run examples of using r3dmol in a Shiny app

Description

Run examples of using r3dmol in a Shiny app

Usage

m_shiny_demo()

Examples

if (interactive()) {
  m_shiny_demo()
}

Continuously rotate a scene around the specified axis

Description

Continuously rotate a scene around the specified axis

Usage

m_spin(id, axis = "y", speed = 1)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)
model <- r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_set_style(style = m_style_cartoon(color = "spectrum")) %>%
  m_zoom_to()

# spin the model
model %>% m_spin()

# reverses the direction of spin
model %>% m_spin(speed = -0.5)

Stop animation of all models in viewer

Description

Stop animation of all models in viewer

Usage

m_stop_animate(id)

Arguments

Specify Styling for Cartoon

Description

Styling options for the cartoon representation. Used inside m_add_style() and m_set_style().

Usage

m_style_cartoon(
  color = NULL,
  style = "rectangle",
  ribbon = FALSE,
  arrows = TRUE,
  tubes = FALSE,
  thickness = 0.4,
  width = NULL,
  opacity = 1,
  colorfunc = NULL
)

Arguments

Examples

r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = m_style_cartoon(color = "spectrum")) %>%
  m_zoom_to()

Specify Styling for Labels

Description

Styling options for the labels. Used inside m_add_label(), m_add_res_labels() and m_add_property_labels().

Usage

m_style_label(
  font = "sans-serif",
  fontSize = 18,
  fontColor = "white",
  fontOpacity = 1,
  backgroundColor = "black",
  backgroundOpacity = 1,
  borderOpacity = 1,
  borderThickness = 0,
  borderColor = backgroundColor,
  inFront = TRUE,
  showBackground = TRUE,
  fixed = FALSE,
  alignment = c("topLeft", "topCenter", "topRight", "centerLeft", "center",
    "centerRight", "bottomLeft", "bottomCenter", "bottomRight"),
  position = NULL,
  frame = NULL
)

Arguments

Examples

r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = m_style_stick()) %>%
  m_add_res_labels(style = m_style_label(
    fontSize = 14,
    backgroundColor = "green"
  )) %>%
  m_zoom_to()

Specify Styling for Lines

Description

Styling options for the line representation. Used inside m_add_style() and m_set_style(). Can also be used for styling when adding individual lines with m_add_line().

Usage

m_style_line(
  colorScheme = "default",
  color = NULL,
  opacity = 1,
  hidden = FALSE
)

Arguments

Examples

r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = m_style_line(color = "blue")) %>%
  m_zoom_to()

Specify Styling for Sphere

Description

Styling options for the sphere representation. Used inside m_add_style() and m_set_style().

Usage

m_style_sphere(
  scale = 1,
  colorScheme = "default",
  color = NULL,
  radius = NULL,
  hidden = FALSE,
  opacity = 1
)

Arguments

Examples

r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = m_style_sphere(radius = 0.5)) %>%
  m_zoom_to()

Specify Styling for Stick

Description

Styling options for the stick representation. Used inside m_add_style() and m_set_style().

Usage

m_style_stick(
  radius = 0.3,
  singleBonds = FALSE,
  colorScheme = "default",
  color = NULL,
  opacity = 1,
  hidden = FALSE
)

Arguments

Examples

r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = m_style_stick(opacity = 0.4)) %>%
  m_zoom_to()

Specify Styling for Surface

Description

Styling options for the surface representation. Used inside m_add_surface().

Usage

m_style_surface(opacity = 1, colorScheme = "default", color = NULL)

Arguments

Examples

r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = m_style_stick()) %>%
  m_add_surface(style = m_style_surface(opacity = 0.4)) %>%
  m_zoom_to()

Translate current view or models by x,y screen coordinates

Description

m_translate() pans the camera rather than translating the model. m_translate_scene() translates the models relative to the current view. It does not change the center of rotation.

Usage

m_translate(id, x, y, animationDuration, fixedPath)

m_translate_scene(id, x, y, animationDuration, fixedPath)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

# Translate current view by x,y screen coordinates
r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = c(m_style_cartoon(), m_style_stick())) %>%
  m_translate(
    x = 200,
    y = 50,
    animationDuration = 1000
  ) %>%
  m_rotate(
    angle = 90,
    axis = "z",
    animationDuration = 1000
  ) %>%
  m_zoom_to()

# Translate current models by x,y screen coordinates
r3dmol() %>%
  m_add_model(data = pdb_1j72, format = "pdb") %>%
  m_set_style(style = c(m_style_cartoon(), m_style_stick())) %>%
  m_translate_scene(
    x = 200,
    y = 50,
    animationDuration = 1000
  ) %>%
  m_rotate(
    angle = 90,
    axis = "z",
    animationDuration = 1000
  ) %>%
  m_zoom_to()

Create a 3 dimensional vector

Description

Create a 3 dimensional vector

Usage

m_vector3(x = 0, y = 0, z = 0)

Arguments

Value

3 dimensional list object

Examples

library(r3dmol)
m_vector3(1, 2, 3)

Add model's vibration

Description

If atoms have dx, dy, dz properties (in some xyz files), vibrate populates each model's frame property based on parameters. Models can then be animated.

Usage

m_vibrate(id, numFrames, amplitude, bothWays, arrowSpec)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

xyz <- "4
* (null), Energy   -1000.0000000
N     0.000005    0.019779   -0.000003   -0.157114    0.000052   -0.012746
H     0.931955   -0.364989    0.000003    1.507100   -0.601158   -0.004108
H    -0.465975   -0.364992    0.807088    0.283368    0.257996   -0.583024
H    -0.465979   -0.364991   -0.807088    0.392764    0.342436    0.764260
"

r3dmol() %>%
  m_add_model(data = xyz, format = "xyz") %>%
  m_set_style(style = m_style_stick()) %>%
  m_vibrate(numFrames = 10, amplitude = 1) %>%
  m_animate(options = list(loop = "backAndForth", reps = 0)) %>%
  m_zoom_to()

Specifying setup options for viewer

Description

Returns a list for the setup r3dmol() function, to set overall settings for the viewer going forward.

Usage

m_viewer_spec(
  id = NULL,
  defaultcolors = NULL,
  cartoonQuality = 5,
  antialias = TRUE,
  nomouse = FALSE,
  backgroundColor = "white",
  lowerZoomLimit = 5,
  upperZoomLimit = 400,
  orthographic = FALSE,
  disableFog = FALSE
)

Arguments

Zoom current view by a constant factor

Description

Zoom current view by a constant factor

Usage

m_zoom(id, factor = 2, animationDuration, fixedPath)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_zoom_to() %>%
  m_zoom(factor = 2, animationDuration = 1000)

Zoom to center of atom selection

Description

Zoom to center of atom selection. The slab will be set appropriately for the selection, unless an empty selection is provided, in which case there will be no slab.

Usage

m_zoom_to(id, sel, animationDuration, fixedPath)

Arguments

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

r3dmol() %>%
  m_add_model(data = pdb_6zsl, format = "pdb") %>%
  m_zoom_to()

Crystal Structure of Mutant Macrophage Capping Protein (Cap G) with Actin-severing Activity in the Ca2+-Free Form in PDB format

Description

Crystal Structure of Mutant Macrophage Capping Protein (Cap G) with Actin-severing Activity in the Ca2+-Free Form in PDB format

Usage

pdb_1j72

Format

PDB Format.

Source

DOI: 10.2210/pdb1J72/pdb. https://www.rcsb.org/structure/1J72

Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution in PDB format

Description

Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution in PDB format

Usage

pdb_6zsl

Format

PDB Format.

Source

DOI: 10.2210/pdb6ZSL/pdb. https://www.rcsb.org/structure/6zsl

Shiny bindings for r3dmol

Description

Output and render functions for using r3dmol within Shiny applications and interactive Rmd documents.

Usage

r3dmolOutput(outputId, width = "100%", height = "400px")

renderR3dmol(expr, env = parent.frame(), quoted = FALSE)

Arguments

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

magrittr

%>%

Multiple sdf file example

Description

Multiple sdf file example

Usage

sdf_multiple

Format

sdf format

Source

https://github.com/3dmol/3Dmol.js/blob/master/tests/test_structs/multiple.sdf

Multiple xyz file example

Description

Multiple xyz file example

Usage

xyz_multiple

Format

xyz format

Source

https://github.com/3dmol/3Dmol.js/blob/master/tests/test_structs/multiple2.xyz