{"id":13736081,"url":"https://github.com/zachcp/chemdoodle","last_synced_at":"2025-05-08T12:32:04.262Z","repository":{"id":32750848,"uuid":"36341776","full_name":"zachcp/chemdoodle","owner":"zachcp","description":"htmlwidgets for chemdoodle web components","archived":true,"fork":false,"pushed_at":"2021-04-11T22:43:33.000Z","size":680,"stargazers_count":18,"open_issues_count":5,"forks_count":9,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-05-06T07:04:36.219Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://zachcp.github.io/chemdoodle/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/zachcp.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-05-27T04:02:45.000Z","updated_at":"2023-09-04T14:15:10.000Z","dependencies_parsed_at":"2022-06-27T00:34:52.722Z","dependency_job_id":null,"html_url":"https://github.com/zachcp/chemdoodle","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zachcp%2Fchemdoodle","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zachcp%2Fchemdoodle/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zachcp%2Fchemdoodle/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zachcp%2Fchemdoodle/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zachcp","download_url":"https://codeload.github.com/zachcp/chemdoodle/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253068703,"owners_count":21848863,"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":[],"created_at":"2024-08-03T03:01:15.443Z","updated_at":"2025-05-08T12:32:03.334Z","avatar_url":"https://github.com/zachcp.png","language":"R","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  eval=FALSE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# chemdoodle\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\n\n\nThis repo is for the creation of an HTMLWidget for visualizing\nmoleules based on the [ChemDoodle WebComponent](http://web.chemdoodle.chttps://github.com/rajarshi/cdkr/tree/master/rcdkom/) library,\nthe [HTMLWidgets](http://www.htmlwidgets.org/) package, and the\n[Chemistry Development Kit](https://github.com/cdk) via [rCDK](https://github.com/rajarshi/cdkr/tree/master/rcdk). **Warning: development in flux and liable to break until version 1.0!**\n\n### Install\n\nAnd the development version from [GitHub](https://github.com/) with:\n\n\n```{r}\n# install.packages(\"devtools\")\n# devtools::install_github(\"zachcp/chemdoodle\")\n```\n\n\n### Basic Viewer\n\n```{r}\nlibrary(chemdoodle)\nchemdoodle_viewer(\"C1CCCCC1\", width = 100, height = 100)\n```\n\n### Transform Canvas\n\n```{r}\nchemdoodle_transform(\"C1CCCCC1\", width = 100, height = 100)\n```\n\n\n### Slideshow Canvas\n\n```{r}\nchemdoodle_slideshow(c(\"C1CCCCC1\", \"CNCNCNC1CCCCC1\", \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\",\n                       \"CC1=C(C=C(C2=C1C(=C)OC2=O)OC)OC\"), 200,200, bondscale=15)\n\n```\n\n### Sketcher\n\nThe ChemDoodle Sketcher needs extra work for functionality. You can use `drawMolecule()` to create a seketcher and the molecule is captured as ChemDoodle JSON which can be converted to\na CDK Atom and be passed around, converter or whatever. Currently round-tripping (putting the molecule back) doesn't work because there are some issues around properly scaling the compound.\n\n\n```{r, eval=FALSE}\n#experimetal/new features\n\n# gets a molecule from the chemdoodle sketcher\nmoljson \u003c- drawMolecule()\n\n# processed the Molecule JSON to a CDK AtomContainer - this can be saved,\n# written to Smiles etc.\nmol \u003c- processChemDoodleJson(moljson)\n\n# convert to SMILES\nsmi \u003c- toSmiles(mol)\n\n# convert to InChi\ninchi \u003c- toInChi(mol)\n\n# try sending a molecule to the sketcher (needs work)\ndrawMolecule(mol=mol)\n\n```\n\n### Access the Sketcher as a ShinyApp \n\n```{r, eval=FALSE}\n# you can also try a minimal shiny example\nshiny::runApp(appDir = \"examples/minimalshinyapp/\")\n```\n\n","funding_links":[],"categories":["Visualization"],"sub_categories":["Chemical Data"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzachcp%2Fchemdoodle","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzachcp%2Fchemdoodle","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzachcp%2Fchemdoodle/lists"}