Function reference • r3dmol

Common Basic functions.
`r3dmol()`	Initialise a WebGL-based viewer
`m_render()`	Render current state of viewer
`m_png()`	Convert widgets to PNG image
`m_grid()`	Create a grid of viewers that share a WebGL canvas
`m_glimpse()`	Quickly View Given Structure
`m_clear()`	Clear scene of all objects
`m_enable_fog()`	Enable/disable fog for content far from the camera
`m_shiny_demo()`	Run examples of using `r3dmol` in a Shiny app
`r3dmolOutput()` `renderR3dmol()`	Shiny bindings for r3dmol
Add / Set / Remove Functions for adding, setting and removing elements to the view.
`m_add_model()` `m_add_models()`	Create and add model to viewer
`m_add_box()` `m_add_curve()`	Create and add shape
`m_add_arrow()`	Add arrow shape
`m_add_as_one_molecule()`	Create and add model to viewer
`m_add_custom()`	Add custom shape component from user supplied function
`m_add_cylinder()`	Add Cylinder Between Points
`m_add_isosurface()`	Construct isosurface from volumetric data in gaussian cube format
`m_add_label()`	Add label to viewer
`m_add_line()`	Add Lines Between Points
`m_add_models_as_frames()`	Create and add model to viewer
`m_add_outline()`	Add colored outline to all objects in scene.
`m_add_property_labels()`	Add property labels
`m_add_res_labels()`	Add Residue Labels
`m_add_shape()`	Add shape object to viewer
`m_add_sphere()`	Add Sphere Shape
`m_add_style()`	Add Style to Selection
`m_add_surface()`	Add surface representation to atoms
`m_add_unit_cell()` `m_replicate_unit_cell()` `m_remove_unit_cell()`	Unit cell visualization
`m_set_color_by_element()`	Set color by element
`m_set_default_cartoon_quality()`	Set the default cartoon quality for newly created models
`m_set_hover_duration()`	Set the duration of the hover delay
`m_set_preceived_distance()`	Set the distance between the model and the camera
`m_set_projection()`	Set view projection scheme
`m_set_slab()`	Set slab of view
`m_set_style()`	Overwrite Previous Style
`m_set_view()`	Sets the view to the specified translation, zoom, rotation and style
`m_set_width()` `m_set_height()` `m_set_background_color()`	Set viewer properties
`m_set_zoom_limits()`	Set lower and upper limit stops for zoom
`m_remove_all_labels()`	Remove all labels from viewer
`m_remove_all_models()`	Delete all existing models
`m_remove_all_shapes()`	Remove all shape objects from viewer
`m_remove_all_surfaces()`	Remove all labels from viewer
`m_remove_label()`	Remove label from viewer
Style / Selections / Specifications Functions for setting the style of models, and doing selections.
`m_style_ballnstick()`	Specifying Style for Ball and Stick
`m_style_cartoon()`	Specify Styling for Cartoon
`m_style_label()`	Specify Styling for Labels
`m_style_line()`	Specify Styling for Lines
`m_style_sphere()`	Specify Styling for Sphere
`m_style_stick()`	Specify Styling for Stick
`m_style_surface()`	Specify Styling for Surface
`m_sel()`	Selection Function for r3dmol
`m_multi_resi_sel()`	Selection Across Multiple Residues
`m_shape_spec()`	Specify Styling for Generic Shapes
`m_viewer_spec()`	Specifying setup options for viewer
Importing Models Importing models from {bio3d} and fetching from pdb.
`m_fetch_pdb()`	Fetch Structure from PDB
`m_bio3d()`	Load structure from package bio3d
Animate Functions for creating animation.
`m_animate()`	Animate all models in viewer from their respective frames
`m_vibrate()`	Add model's vibration
`m_center()`	Re-center the viewer around the provided selection
`m_rotate()`	Rotate scene by angle degrees around axis
`m_spin()`	Continuously rotate a scene around the specified axis
`m_stop_animate()`	Stop animation of all models in viewer
`m_translate()` `m_translate_scene()`	Translate current view or models by x,y screen coordinates
`m_zoom()`	Zoom current view by a constant factor
`m_zoom_to()`	Zoom to center of atom selection
Button Functions for adding buttons to interact with visualizations.
`m_button_add_res_labels()`	Add a button for adding residue labels
`m_button_add_style()`	Add button for Adding a Style
`m_button_add_surface()`	Add a button for adding a surface
`m_button_animate()`	Add a button for starting and stopping animations
`m_button_manual()`	Add button into viewer
`m_button_set_style()`	Add a button for overwriting a style
`m_button_spin()`	Add a button for spinning the scene
`m_button_zoom_to()`	Add a button for zooming to a selection
Class Constructor Convenience functions for constructing class for r3dmol.
`m_vector3()`	Create a 3 dimensional vector
Dataset Datasets provide by package for demo.
`pdb_1j72`	Crystal Structure of Mutant Macrophage Capping Protein (Cap G) with Actin-severing Activity in the Ca2+-Free Form in PDB format
`pdb_6zsl`	Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution in PDB format
`sdf_multiple`	Multiple sdf file example
`cif_254385`	Cif file example
`xyz_multiple`	Multiple xyz file example
`cube_benzene_homo`	Gaussian cube file example

Reference

Common

Add / Set / Remove

Style / Selections / Specifications

Importing Models

Animate

Button

Class Constructor

Dataset