{"id":19107926,"url":"https://github.com/haschka/pdb2fasta","last_synced_at":"2026-06-17T12:32:10.100Z","repository":{"id":48240667,"uuid":"516801219","full_name":"haschka/pdb2fasta","owner":"haschka","description":"Extracts the fasta sequence from protein stored in a PDB file","archived":false,"fork":false,"pushed_at":"2023-01-31T22:56:30.000Z","size":27,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-22T10:41:39.554Z","etag":null,"topics":["bioinformatics","fasta-files","fasta-sequences","pdb-files","unix-tools"],"latest_commit_sha":null,"homepage":"","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/haschka.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":"2022-07-22T15:32:11.000Z","updated_at":"2024-08-12T15:10:35.000Z","dependencies_parsed_at":"2023-02-16T23:46:17.721Z","dependency_job_id":null,"html_url":"https://github.com/haschka/pdb2fasta","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/haschka/pdb2fasta","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fpdb2fasta","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fpdb2fasta/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fpdb2fasta/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fpdb2fasta/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/haschka","download_url":"https://codeload.github.com/haschka/pdb2fasta/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fpdb2fasta/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34449277,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-17T02:00:05.408Z","response_time":127,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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","fasta-files","fasta-sequences","pdb-files","unix-tools"],"created_at":"2024-11-09T04:14:26.411Z","updated_at":"2026-06-17T12:32:10.077Z","avatar_url":"https://github.com/haschka.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pdb2fasta in C\n\nExtracts the fasta sequence from protein stored in a PDB file.\n\nThis is a tool inspired by Pierre Poulain's pdb2fasta in bash\narticle c.f.: [https://cupnet.net/pdb2fasta/](https://cupnet.net/pdb2fasta/)\nThe tool outlined in this article however has several quriks and fails on \nPDB files such as [7VWC](https://www.rcsb.org/structure/7VWC) . \nActually it is also pdb2fasta in bash,awk,sed,etc. than pdb2fasta simply in bash. \n\nI thought it is time to join the pdb2fasta game and write my own. \n\nAs such, here, a hopefully better, more standard conformant tool in C.\n( and nothing but C ) \n\n### Compilation:\ncompile with the c compilier of your choice, here gcc\n```\ngcc pdb2fasta.c -o pdb2fasta\n```\nyou may add compilier flags, for a ultra high performant\nconverter tool. \n\n### Usage:\n```\n./pdb2fasta yourpdbfile.pdb\n```\nshould print a fasta formatted file to stdout\nwith one sequence specification per chain. \n\n### Special Features:\nThe tool omits strcmp() or other string comparisons functions\nby usage of 4 bytes integers that can store just enough data \nto hold a 3 character long C-string.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaschka%2Fpdb2fasta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhaschka%2Fpdb2fasta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaschka%2Fpdb2fasta/lists"}