{"id":28566558,"url":"https://github.com/orhanbalci/patoz","last_synced_at":"2025-11-11T11:19:40.121Z","repository":{"id":57674498,"uuid":"203540713","full_name":"orhanbalci/patoz","owner":"orhanbalci","description":"Protein Data Bank (pdb) file parser ","archived":false,"fork":false,"pushed_at":"2021-11-12T18:18:48.000Z","size":798,"stargazers_count":9,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-05-04T06:36:30.670Z","etag":null,"topics":["bioinformatics","nom","parser","pdb","protein-data-bank","protein-structure","rust"],"latest_commit_sha":null,"homepage":"","language":"Rust","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/orhanbalci.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}},"created_at":"2019-08-21T08:28:27.000Z","updated_at":"2023-09-15T05:38:38.000Z","dependencies_parsed_at":"2022-08-29T15:41:49.684Z","dependency_job_id":null,"html_url":"https://github.com/orhanbalci/patoz","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/orhanbalci%2Fpatoz","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/orhanbalci%2Fpatoz/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/orhanbalci%2Fpatoz/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/orhanbalci%2Fpatoz/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/orhanbalci","download_url":"https://codeload.github.com/orhanbalci/patoz/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/orhanbalci%2Fpatoz/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":258164596,"owners_count":22659140,"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":["bioinformatics","nom","parser","pdb","protein-data-bank","protein-structure","rust"],"created_at":"2025-06-10T15:11:16.593Z","updated_at":"2025-11-11T11:19:40.073Z","avatar_url":"https://github.com/orhanbalci.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Patoz\nProtein Data Bank (pdb) file parser\n\n![Build Status](https://github.com/orhanbalci/patoz/workflows/CI/badge.svg)\n![License](https://img.shields.io/github/license/orhanbalci/patoz.svg)\n\n⚠️ WIP This is a work in progress. Expect breaking changes frequently. Right now use at your own risk\n\n# 📦 Cargo.toml\n```\npatoz = \"0.1.0\"\n```\n# 🔧 Examples\n```rust\n\nuse std::{\n    fs::File,\n    io::{BufReader, Read},\n    path::PathBuf,\n};\n\nuse patoz::parse;\n\nfn main() {\n    let mut current_file_path = PathBuf::from(file!());\n    current_file_path.pop();\n    current_file_path.pop();\n    current_file_path.push(\"1BYI.pdb\");\n    let content = read_file(\u0026current_file_path);\n    if let Ok((_, mut res)) = parse(\u0026content) {\n        println!(\n            \"Classification : {:?}\",\n            res.header().header().unwrap().classification\n        );\n        println!(\"Id Code : {:?}\", res.header().header().unwrap().id_code);\n        println!(\"Keywords : {:?}\", res.header().keywds().unwrap().keywords);\n    }\n}\n\nfn read_file(path: \u0026PathBuf) -\u003e String {\n    let file = File::open(path).unwrap();\n    let mut buf_reader = BufReader::new(file);\n    let mut contents = String::new();\n    if let Ok(_read_res) = buf_reader.read_to_string(\u0026mut contents) {\n        contents\n    } else {\n        \"\".to_owned()\n    }\n}\n```\n# 📊  Status\n## Record Parser Status\n### Title Section\n- [x] [Header](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#HEADER)\n- [x] [Obslte](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#OBSLTE)\n- [x] [Title](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#TITLE)\n- [x] [Splt](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#SPLIT)\n- [x] [Caveat](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#CAVEAT)\n- [x] [Compnd](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#COMPND)\n- [x] [Source](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#SOURCE)\n- [x] [Keywds](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#KEYWDS)\n- [x] [Expdta](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#EXPDTA)\n- [x] [Nummdl](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#NUMMDL)\n- [x] [Mdltyp](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#MDLTYP)\n- [x] [Author](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#AUTHOR)\n- [x] [Sprsde](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#SPRSDE)\n- [x] [Revdat](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#REVDAT)\n- [x] [Jrnl](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#JRNL)\n    - [x] Auth\n    - [x] Titl\n    - [x] Edit\n    - [x] Ref\n    - [x] Publ\n    - [x] Refn\n    - [x] Pmid\n    - [x] Doi\n- [ ] [Remarks](http://www.wwpdb.org/documentation/file-format-content/format33/remarks.html)\n### Primary Structure Section\n- [x] [Dbref](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#DBREF)\n- [x] [Dbref1](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#DBREF1)\n- [x] [Seqadv](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#SEQADV)\n- [x] [Seqres](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#SEQRES)\n- [x] [Modres](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#MODRES)\n### Heterogen Section\n- [ ] [Het](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HET)\n- [ ] [Formul](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#FORMUL)\n- [ ] [Hetnam](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HETNAM)\n- [ ] [Hetsyn](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HETSYN)\n### Secondary Structure Section\n- [ ] [Helix](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX)\n- [ ] [Sheet](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#SHEET)\n### Connectivity Annotation Section\n- [ ] [Ssbond](http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#SSBOND)\n- [ ] [Link](http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#LINK)\n- [ ] [Cispep](http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#CISPEP)\n### Miscellaneous Features Section\n- [ ] [Site](http://www.wwpdb.org/documentation/file-format-content/format33/sect7.html#SITE)\n### Crystallographic and Coordinate Transformation Section\n- [ ] [Cryst1](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1)\n- [ ] [MtrixN](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#MTRIXn)\n- [ ] [OrigxN](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#ORIGXn)\n- [ ] [ScaleN](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#SCALEn)\n### Coordinate Section\n- [ ] [Model](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL)\n- [ ] [Atom](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM)\n- [ ] [Anisou](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ANISOU)\n- [ ] [Ter](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER)\n- [ ] [Hetatm](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM)\n- [ ] [Endmdl](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ENDMDL)\n### Connectivity Section\n- [ ] [Conect](http://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT)\n### Bookkeeping Section\n- [ ] [Master](http://www.wwpdb.org/documentation/file-format-content/format33/sect11.html#MASTER)\n- [ ] [End](http://www.wwpdb.org/documentation/file-format-content/format33/sect11.html#END)\n\n## 📝 License\n\nLicensed under MIT License ([LICENSE](LICENSE)).\n\n### 🚧 Contributions\n\nUnless you explicitly state otherwise, any contribution intentionally submitted for inclusion in this project by you, as defined in the MIT license, shall be licensed as above, without any additional terms or conditions.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Forhanbalci%2Fpatoz","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Forhanbalci%2Fpatoz","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Forhanbalci%2Fpatoz/lists"}