{"id":18527222,"url":"https://github.com/jbarnoud/simoji","last_synced_at":"2025-05-14T21:32:46.690Z","repository":{"id":145284590,"uuid":"99505766","full_name":"jbarnoud/simoji","owner":"jbarnoud","description":"Run a GROMACS simulation with emojis!","archived":false,"fork":false,"pushed_at":"2017-08-06T21:59:07.000Z","size":24,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-05-13T17:17:29.284Z","etag":null,"topics":["emoji","gromacs","molecular-dynamics"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jbarnoud.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-08-06T18:32:46.000Z","updated_at":"2025-02-21T13:18:22.000Z","dependencies_parsed_at":null,"dependency_job_id":"2aca4919-490a-44ef-93c4-9ac33f7913cc","html_url":"https://github.com/jbarnoud/simoji","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/jbarnoud%2Fsimoji","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbarnoud%2Fsimoji/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbarnoud%2Fsimoji/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbarnoud%2Fsimoji/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jbarnoud","download_url":"https://codeload.github.com/jbarnoud/simoji/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254230746,"owners_count":22036230,"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":["emoji","gromacs","molecular-dynamics"],"created_at":"2024-11-06T17:54:33.792Z","updated_at":"2025-05-14T21:32:46.668Z","avatar_url":"https://github.com/jbarnoud.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Simoji -- Because an emoji is better than your atom name\n========================================================\n\nLikely by accident, Gromacs has no problem using emojis where it expects\nstrings. This means you can use emojis as atom types, atom names, residue names\nor molecule types for much more insightful simulations. Simoji replaces all\nnames in a topology and in a structure by emojis to run such emoji molecular\ndynamics simulations.\n\nUsage: `python3 simoji.py [options]`\n\nOptions:\n\n* `-f`: input structure (.gro)\n* `-p`: input topology (.top)\n* `-t`: input correspondence table\n* `-o`: output structure (.gro)\n* `-op`: output topology (.top)\n* `-ot`: output correspondence table\n\nThe emojis are chosen at random but coincide between the output structure and\nthe output topology so the files can be used together in a simulation. If the\n`-ot` option is provided, simoji writes a correspondence table between the\noriginal names and the chosen emojis. This correspondence table can be provided\nas an input with the `-t` option; this bypasses the random choice of the\nemojis.\n\nIf the topology file is provided with the `-p` option, and if it includes ITP\nfiles, the translated content of these ITP file is concatenated in the\nresulting topology.\n\nAs an example, here is a extract of the POPC topology in the Martini coarse\ngrained force field [1]:\n\n```\n[moleculetype]\n; molname nrexcl\n POPC 1\n\n[atoms]\n; id type resnr residu atom cgnr charge\n1 Q0 1 POPC NC3 1 1.0\n2 Qa 1 POPC PO4 2 -1.0\n3 Na 1 POPC GL1 3 0\n4 Na 1 POPC GL2 4 0\n5 C1 1 POPC C1A 5 0\n6 C1 1 POPC C2A 6 0\n7 C3 1 POPC D3A 7 0\n8 C1 1 POPC C4A 8 0\n9 C1 1 POPC C1B 9 0\n10 C1 1 POPC C2B 10 0\n11 C1 1 POPC C3B 11 0\n12 C1 1 POPC C4B 12 0\n```\n\nHere is the same fraction emojified:\n\n```\n[moleculetype]\n; molname nrexcl\n ⚛ 1\n\n[atoms]\n; id type resnr residu atom cgnr charge\n1 ⛽ 1 ⚛ 🍲 1 1.0\n2 📝 1 ⚛ 🌭 2 -1.0\n3 🐍 1 ⚛ 🍹 3 0\n4 🐍 1 ⚛ 🤐 4 0\n5 🕷 1 ⚛ 🕓 5 0\n6 🕷 1 ⚛ 🚊 6 0\n7 🚕 1 ⚛ 🚓 7 0\n8 🕷 1 ⚛ 🔇 8 0\n9 🕷 1 ⚛ 🕝 9 0\n10 🕷 1 ⚛ 🗨 10 0\n11 🕷 1 ⚛ 🎑 11 0\n12 🕷 1 ⚛ 👂 12 0\n```\n\nNote that simoji requires python 3. It will not work on python 2.\n\nYou should probably not use emojis in your serious simulations 😝.\n\n [1] The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations\n Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, and, and Alex H. de Vries\n The Journal of Physical Chemistry B 2007 111 (27), 7812-7824\n DOI: http://dx.doi.org/10.1021/jp071097f \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjbarnoud%2Fsimoji","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjbarnoud%2Fsimoji","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjbarnoud%2Fsimoji/lists"}