# Create Interactive 3D Visualizations of Molecular Data

## Documentation for package ‘r3dmol’ version 0.1.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

add_model | Create and add model to viewer
cif_254385 | Cif file example
cube_benzene_homo | Gaussian cube file example
init | Initialise a WebGL-based viewer
m_add_anyShape | Create and add shape
m_add_arrow | Add arrow shape
m_add_as_one_molecule | Create and add model to viewer
m_add_box | Create and add shape
m_add_curve | Create and add shape
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_model | Create and add model to viewer
m_add_models | Create and add model to viewer
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 | Overwrite Previous Style
m_add_surface | Add surface representation to atoms
m_add_unit_cell | Unit cell visualization
m_animate | Animate all models in viewer from their respective frames
m_bio3d | Load structure from package bio3d
m_button | Add button into viewer
m_center | Re-center the viewer around the provided selection
m_clear | Clear scene of all objects
m_create_model_from | Create a new model from atoms specified by sel
m_enable_fog | Enable/disable fog for content far from the camera
m_fetch_pdb | Fetch Structure from PDB
m_get_model | Return specified model
m_glimpse | Quickly View Given Structure
m_grid | Create a grid of viewers that share a WebGL canvas
m_is_animated | Get viewer animate status
m_multi_resi_sel | Selection Across Multiple Residues
m_png | Convert widgets to PNG image
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
m_remove_unit_cell | Unit cell visualization
m_render | Render current state of viewer
m_replicate_unit_cell | Unit cell visualization
m_rotate | Rotate scene by angle degrees around axis
m_sel | Selection Function for r3dmol
m_set_background_color | Set viewer properties
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_height | Set viewer properties
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 | Add Style to Selection
m_set_view | Sets the view to the specified translation, zoom, rotation and style
m_set_viewer | Set viewer properties
m_set_width | Set viewer properties
m_set_zoom_limits | Set lower and upper limit stops for zoom
m_shape_spec | Specify Styling for Generic Shapes
m_shiny_demo | Run examples of using 'r3dmol' in a Shiny app
m_spin | Continuously rotate a scene around the specified axis
m_stop_animate | Stop animation of all models in viewer
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_translate | Translate current view or models by x,y screen coordinates
m_translate_scene | Translate current view or models by x,y screen coordinates
m_unit_cell | Unit cell visualization
m_vector3 | Create a 3 dimensional vector
m_vibrate | Add model's vibration
m_viewer_spec | Specifying setup options for viewer
m_zoom | Zoom current view by a constant factor
m_zoom_to | Zoom to center of atom selection
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
r3dmol | Initialise a WebGL-based viewer
r3dmol-shiny | Shiny bindings for r3dmol
r3dmolOutput | Shiny bindings for r3dmol
renderR3dmol | Shiny bindings for r3dmol
sdf_multiple | Multiple sdf file example
xyz_multiple | Multiple xyz file example