Create Interactive 3D Visualizations of Molecular Data

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Documentation for package ‘r3dmol’ version 0.1.2

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