{"id":13736069,"url":"https://github.com/swsoyee/r3dmol","last_synced_at":"2025-10-22T06:08:29.259Z","repository":{"id":38423826,"uuid":"292432744","full_name":"swsoyee/r3dmol","owner":"swsoyee","description":"🧬 An R package for visualizing molecular data in 3D","archived":false,"fork":false,"pushed_at":"2023-10-25T09:29:39.000Z","size":32952,"stargazers_count":88,"open_issues_count":7,"forks_count":4,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-09-16T14:08:41.419Z","etag":null,"topics":["3d","computational-biology","computational-chemistry","hacktoberfest","htmlwidgets","molecular-graphics","molecular-modeling","protein","protein-structure","r","visualization"],"latest_commit_sha":null,"homepage":"https://swsoyee.github.io/r3dmol/","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/swsoyee.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":".github/FUNDING.yml","license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null},"funding":{"github":["swsoyee"],"patreon":null,"open_collective":null,"ko_fi":null,"tidelift":null,"community_bridge":null,"liberapay":null,"issuehunt":null,"otechie":null,"custom":null}},"created_at":"2020-09-03T01:18:42.000Z","updated_at":"2024-08-18T09:45:18.000Z","dependencies_parsed_at":"2022-08-09T04:31:07.999Z","dependency_job_id":"84c3572d-1514-49b1-a0fa-9adfbc634138","html_url":"https://github.com/swsoyee/r3dmol","commit_stats":{"total_commits":333,"total_committers":5,"mean_commits":66.6,"dds":"0.18018018018018023","last_synced_commit":"0eefc1c2c430fff0122ae71ae8c9cc4e8912190c"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/swsoyee%2Fr3dmol","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/swsoyee%2Fr3dmol/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/swsoyee%2Fr3dmol/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/swsoyee%2Fr3dmol/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/swsoyee","download_url":"https://codeload.github.com/swsoyee/r3dmol/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224732131,"owners_count":17360416,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["3d","computational-biology","computational-chemistry","hacktoberfest","htmlwidgets","molecular-graphics","molecular-modeling","protein","protein-structure","r","visualization"],"created_at":"2024-08-03T03:01:15.308Z","updated_at":"2025-10-22T06:08:24.214Z","avatar_url":"https://github.com/swsoyee.png","language":"JavaScript","readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# r3dmol\n\n\u003cimg src=\"man/figures/logo.png\" align=\"right\" style = \"height:150px;\"/\u003e\n\n\u003c!-- badges: start --\u003e\n[![CRAN status](https://www.r-pkg.org/badges/version/r3dmol)](https://CRAN.R-project.org/package=r3dmol)\n[![Codecov test coverage](https://codecov.io/gh/swsoyee/r3dmol/branch/master/graph/badge.svg)](https://codecov.io/gh/swsoyee/r3dmol?branch=master)\n[![R-CMD-check](https://github.com/swsoyee/r3dmol/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/swsoyee/r3dmol/actions/workflows/R-CMD-check.yaml)\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)\n[![Metacran downloads](https://cranlogs.r-pkg.org/badges/grand-total/r3dmol)](https://cran.r-project.org/package=r3dmol)\n\u003c!-- badges: end --\u003e\n\nThis is an R package that provides support for [`3Dmol.js`](https://3dmol.csb.pitt.edu/index.html) as a [`htmlwidgets`](https://www.htmlwidgets.org/).\n\n## Installation\n\n\u003e **Important**: This package is still very early in its development stages. Please give the repository a star on Github if you find the package is useful. In addition, we need your feedback to improve the package, feel free to create an issue if you have any question or feature requirement. You are more than welcome to submit a PR to make any feasible improvements.\n\nYou could install the released version of r3dmol from [CRAN](https://CRAN.R-project.org) with:\n\n``` r\ninstall.packages(\"r3dmol\")\n```\n\nAnd the development version from [GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"swsoyee/r3dmol\")\n```\n\n## Example\n\n```{r, demo, eval=FALSE}\nlibrary(r3dmol)\n\nr3dmol(                         # Set up the initial viewer\n  viewer_spec = m_viewer_spec(\n    cartoonQuality = 10,\n    lowerZoomLimit = 50,\n    upperZoomLimit = 350\n  )\n) %\u003e%\n  m_add_model(                  # Add model to scene\n    data = pdb_6zsl,\n    format = \"pdb\"\n  ) %\u003e%\n  m_zoom_to() %\u003e%               # Zoom to encompass the whole scene\n  m_set_style(                  # Set style of structures\n    style = m_style_cartoon(\n      color = \"#00cc96\"\n    )\n  ) %\u003e%\n  m_set_style(                  # Set style of specific selection\n    sel = m_sel(ss = \"s\"),      # (selecting by secondary)\n    style = m_style_cartoon(\n      color = \"#636efa\",\n      arrows = TRUE\n    )\n  ) %\u003e%\n  m_set_style(                  # Style the alpha helix\n    sel = m_sel(ss = \"h\"),      # (selecting by alpha helix)\n    style = m_style_cartoon(\n      color = \"#ff7f0e\"\n    )\n  ) %\u003e%\n  m_rotate(                     # Rotate the scene by given angle on given axis\n    angle = 90,\n    axis = \"y\"\n  ) %\u003e%\n  m_spin()                      # Animate the scene by spinning it\n```\n![spin demo](man/figures/spin_demo.gif)  \nYou can find more demo at [here](https://swsoyee.github.io/r3dmol/articles/r3dmol.html).\n\n## About `3Dmol.js`\n\n\u003e Nicholas Rego, David Koes, [3Dmol.js: molecular visualization with WebGL](https://academic.oup.com/bioinformatics/article/31/8/1322/213186), Bioinformatics, Volume 31, Issue 8, 15 April 2015, Pages 1322–1324,\n\n## Code of Conduct\n\nPlease note that the r3dmol project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n","funding_links":["https://github.com/sponsors/swsoyee"],"categories":["JavaScript","Visualization"],"sub_categories":["Chemical Data"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fswsoyee%2Fr3dmol","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fswsoyee%2Fr3dmol","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fswsoyee%2Fr3dmol/lists"}