Package: r3dmol 0.2.0

r3dmol: Create Interactive 3D Visualizations of Molecular Data

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.

Authors:Wei Su [aut, cre], Brady Johnston [aut]

r3dmol_0.2.0.tar.gz
r3dmol_0.2.0.zip(r-4.5)r3dmol_0.2.0.zip(r-4.4)r3dmol_0.2.0.zip(r-4.3)
r3dmol_0.2.0.tgz(r-4.4-any)r3dmol_0.2.0.tgz(r-4.3-any)
r3dmol_0.2.0.tar.gz(r-4.5-noble)r3dmol_0.2.0.tar.gz(r-4.4-noble)
r3dmol_0.2.0.tgz(r-4.4-emscripten)r3dmol_0.2.0.tgz(r-4.3-emscripten)
r3dmol.pdf |r3dmol.html✨
r3dmol/json (API)
NEWS

# Install 'r3dmol' in R:
install.packages('r3dmol', repos = c('https://swsoyee.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/swsoyee/r3dmol/issues

Datasets:
  • cif_254385 - Cif file example
  • cube_benzene_homo - Gaussian cube file example
  • 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
  • xyz_multiple - Multiple xyz file example

On CRAN:

3dcomputational-biologycomputational-chemistryhacktoberfesthtmlwidgetsmolecular-graphicsmolecular-modelingproteinprotein-structurevisualization

6.23 score 88 stars 1 packages 130 scripts 388 downloads 85 exports 31 dependencies

Last updated 1 years agofrom:0eefc1c2c4. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:%>%m_add_arrowm_add_as_one_moleculem_add_boxm_add_curvem_add_customm_add_cylinderm_add_isosurfacem_add_labelm_add_linem_add_modelm_add_modelsm_add_models_as_framesm_add_outlinem_add_property_labelsm_add_res_labelsm_add_shapem_add_spherem_add_stylem_add_surfacem_add_unit_cellm_animatem_bio3dm_button_add_res_labelsm_button_add_stylem_button_add_surfacem_button_animatem_button_manualm_button_set_stylem_button_spinm_button_zoom_tom_centerm_clearm_create_model_fromm_enable_fogm_fetch_pdbm_get_modelm_glimpsem_gridm_is_animatedm_multi_resi_selm_pngm_remove_all_labelsm_remove_all_modelsm_remove_all_shapesm_remove_all_surfacesm_remove_labelm_remove_unit_cellm_renderm_replicate_unit_cellm_rotatem_selm_set_background_colorm_set_color_by_elementm_set_default_cartoon_qualitym_set_heightm_set_hover_durationm_set_preceived_distancem_set_projectionm_set_slabm_set_stylem_set_viewm_set_widthm_set_zoom_limitsm_shape_specm_shiny_demom_spinm_stop_animatem_style_ballnstickm_style_cartoonm_style_labelm_style_linem_style_spherem_style_stickm_style_surfacem_translatem_translate_scenem_vector3m_vibratem_viewer_specm_zoomm_zoom_tor3dmolr3dmolOutputrenderR3dmol

Dependencies:base64encbio3dbslibcachemclidigestevaluatefastmapfontawesomefsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimeR6rappdirsRcpprjsonrlangrmarkdownsasstinytexxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Cif file examplecif_254385
Gaussian cube file examplecube_benzene_homo
Initialise a WebGL-based viewerinit r3dmol
Add arrow shapem_add_arrow
Create and add model to viewerm_add_as_one_molecule
Create and add shapem_add_anyShape m_add_box m_add_curve
Add custom shape component from user supplied functionm_add_custom
Add Cylinder Between Pointsm_add_cylinder
Construct isosurface from volumetric data in gaussian cube formatm_add_isosurface
Add label to viewerm_add_label
Add Lines Between Pointsm_add_line
Create and add model to vieweradd_model m_add_model m_add_models
Create and add model to viewerm_add_models_as_frames
Add colored outline to all objects in scene.m_add_outline
Add property labelsm_add_property_labels
Add Residue Labelsm_add_res_labels
Add shape object to viewerm_add_shape
Add Sphere Shapem_add_sphere
Add Style to Selectionm_add_style
Add surface representation to atomsm_add_surface
Unit cell visualizationm_add_unit_cell m_remove_unit_cell m_replicate_unit_cell m_unit_cell
Animate all models in viewer from their respective framesm_animate
Load structure from package bio3dm_bio3d
Add a button for adding residue labelsm_button_add_res_labels
Add button for Adding a Stylem_button_add_style
Add a button for adding a surfacem_button_add_surface
Add a button for starting and stopping animationsm_button_animate
Add button into viewerm_button_manual
Add a button for overwriting a stylem_button_set_style
Add a button for spinning the scenem_button_spin
Add a button for zooming to a selectionm_button_zoom_to
Re-center the viewer around the provided selectionm_center
Clear scene of all objectsm_clear
Enable/disable fog for content far from the cameram_enable_fog
Fetch Structure from PDBm_fetch_pdb
Quickly View Given Structurem_glimpse
Create a grid of viewers that share a WebGL canvasm_grid
Selection Across Multiple Residuesm_multi_resi_sel
Convert widgets to PNG imagem_png
Remove all labels from viewerm_remove_all_labels
Delete all existing modelsm_remove_all_models
Remove all shape objects from viewerm_remove_all_shapes
Remove all labels from viewerm_remove_all_surfaces
Remove label from viewerm_remove_label
Render current state of viewerm_render
Rotate scene by angle degrees around axism_rotate
Selection Function for r3dmolm_sel
Set color by elementm_set_color_by_element
Set the default cartoon quality for newly created modelsm_set_default_cartoon_quality
Set the duration of the hover delaym_set_hover_duration
Set the distance between the model and the cameram_set_preceived_distance
Set view projection schemem_set_projection
Set slab of viewm_set_slab
Overwrite Previous Stylem_set_style
Sets the view to the specified translation, zoom, rotation and stylem_set_view
Set viewer propertiesm_set_background_color m_set_height m_set_viewer m_set_width
Set lower and upper limit stops for zoomm_set_zoom_limits
Specify Styling for Generic Shapesm_shape_spec
Run examples of using 'r3dmol' in a Shiny appm_shiny_demo
Continuously rotate a scene around the specified axism_spin
Stop animation of all models in viewerm_stop_animate
Specifying Style for Ball and Stickm_style_ballnstick
Specify Styling for Cartoonm_style_cartoon
Specify Styling for Labelsm_style_label
Specify Styling for Linesm_style_line
Specify Styling for Spherem_style_sphere
Specify Styling for Stickm_style_stick
Specify Styling for Surfacem_style_surface
Translate current view or models by x,y screen coordinatesm_translate m_translate_scene
Create a 3 dimensional vectorm_vector3
Add model's vibrationm_vibrate
Specifying setup options for viewerm_viewer_spec
Zoom current view by a constant factorm_zoom
Zoom to center of atom selectionm_zoom_to
Crystal Structure of Mutant Macrophage Capping Protein (Cap G) with Actin-severing Activity in the Ca2+-Free Form in PDB formatpdb_1j72
Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution in PDB formatpdb_6zsl
Shiny bindings for r3dmolr3dmol-shiny r3dmolOutput renderR3dmol
Multiple sdf file examplesdf_multiple
Multiple xyz file examplexyz_multiple