{"id":37022151,"url":"https://github.com/biojava/biojava-spark","last_synced_at":"2026-01-14T02:38:18.779Z","repository":{"id":8248732,"uuid":"57403837","full_name":"biojava/biojava-spark","owner":"biojava","description":":collision: Algorithms that are built around BioJava and run on Apache Spark","archived":false,"fork":false,"pushed_at":"2022-01-10T21:08:11.000Z","size":67826,"stargazers_count":8,"open_issues_count":0,"forks_count":3,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-09-09T16:34:49.590Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-2.1","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biojava.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":"2016-04-29T18:06:39.000Z","updated_at":"2023-08-28T11:30:09.000Z","dependencies_parsed_at":"2022-08-06T23:15:42.294Z","dependency_job_id":null,"html_url":"https://github.com/biojava/biojava-spark","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/biojava/biojava-spark","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biojava%2Fbiojava-spark","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biojava%2Fbiojava-spark/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biojava%2Fbiojava-spark/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biojava%2Fbiojava-spark/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biojava","download_url":"https://codeload.github.com/biojava/biojava-spark/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biojava%2Fbiojava-spark/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28408711,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T01:52:23.358Z","status":"online","status_checked_at":"2026-01-14T02:00:06.678Z","response_time":107,"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":[],"created_at":"2026-01-14T02:38:18.135Z","updated_at":"2026-01-14T02:38:18.764Z","avatar_url":"https://github.com/biojava.png","language":"Java","readme":"# BioJava-Spark\n\nAlgorithms that are built around BioJava and are running on Apache Spark\n\n[![Build Status](https://travis-ci.org/biojava/biojava-spark.svg?branch=master)](https://travis-ci.org/biojava/biojava-spark)\n[![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE)\n[![Status](http://img.shields.io/badge/status-experimental-red.svg?style=flat)](https://github.com/biojava/biojava-spark)\n[![Version](http://img.shields.io/badge/version-0.2.1-blue.svg?style=flat)](https://github.com/biojava/biojava-spark/)\n\n## Starting up\n\n### Some initial instructions can be found on the mmtf-spark project\nhttps://github.com/sbl-sdsc/mmtf-spark\n\n## First download and untar a Hadoop sequence file of the PDB (~7 GB download) \n\n```bash\nwget http://mmtf.rcsb.org/v1.0/hadoopfiles/full.tar\ntar -xvf full.tar\n```\nOr you can get a C-alpha, phosphate, ligand only version (~800 Mb download)\n\n```bash\nwget http://mmtf.rcsb.org/v1.0/hadoopfiles/reduced.tar\ntar -xvf reduced.tar\n```\n### Second add the biojava-spark dependecy to your pom\n\n```xml\n\u003cdependency\u003e\n\t\u003cgroupId\u003eorg.biojava\u003c/groupId\u003e\n\t\u003cartifactId\u003ebiojava-spark\u003c/artifactId\u003e\n\t\u003cversion\u003e0.2.1\u003c/version\u003e\n\u003c/dependency\u003e\n```\n\n## Extra Biojava examples\n\n### Do some simple quality filtering\n\n```java\nfloat maxResolution = 3.0f;\nfloat maxRfree = 0.3f;\nStructureDataRDD structureData = new StructureDataRDD(\"/path/to/file\")\n\t\t\t.filterResolution(maxResolution)\n\t\t\t.filterRfree(maxRfree);\n```\n\n### Summarsing the elements in the PDB\n\n```java\nMap\u003cString, Long\u003e elementCountMap = BiojavaSparkUtils.findAtoms(structureData).countByElement();\n```\n\n### Finding inter-atomic contacts from the PDB\n\n```java\nDouble mean = BiojavaSparkUtils.findContacts(structureData,\n\t\tnew AtomSelectObject()\n\t\t\t\t.groupNameList(new String[] {\"PRO\",\"LYS\"})\n\t\t\t\t.elementNameList(new String[] {\"C\"})\n\t\t\t\t.atomNameList(new String[] {\"CA\"}),\n\t\t\t\tcutoff)\n\t\t.getDistanceDistOfAtomInts(\"CA\", \"CA\")\n\t\t.mean();\nSystem.out.println(\"\\nMean PRO-LYS CA-CA distance: \" + mean);\n```\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiojava%2Fbiojava-spark","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiojava%2Fbiojava-spark","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiojava%2Fbiojava-spark/lists"}