{"id":28498295,"url":"https://github.com/yanganto/nestingblock","last_synced_at":"2025-07-07T00:05:34.407Z","repository":{"id":26711912,"uuid":"30169177","full_name":"yanganto/NestingBlock","owner":"yanganto","description":null,"archived":false,"fork":false,"pushed_at":"2015-02-03T09:03:18.000Z","size":168,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-06-08T13:43:39.000Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/yanganto.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":"2015-02-02T03:17:02.000Z","updated_at":"2015-02-03T09:03:18.000Z","dependencies_parsed_at":"2022-08-18T02:05:50.632Z","dependency_job_id":null,"html_url":"https://github.com/yanganto/NestingBlock","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/yanganto/NestingBlock","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yanganto%2FNestingBlock","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yanganto%2FNestingBlock/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yanganto%2FNestingBlock/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yanganto%2FNestingBlock/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/yanganto","download_url":"https://codeload.github.com/yanganto/NestingBlock/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yanganto%2FNestingBlock/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263407133,"owners_count":23461803,"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":"2025-06-08T13:37:10.751Z","updated_at":"2025-07-07T00:05:34.395Z","avatar_url":"https://github.com/yanganto.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NestingBlock\n\nThis is program of modeling side-chain interaction of peptides in helix/coil states.\n\nIt can be easy to calculate the fraction helix of peptides based on Lifson-Roig theory by using following command:\n\n\t$ python3 NestingBlock.py test-LifsonRoig\n\nIt also can list the equation of equilibrium constant with special force in the block within helix state by using following command:\n\n\t$ python3 NestingBlock.py test-NestingBlock\n\n  =========\n | SNOPSIS |\n  =========\n\n $ python3 NestingBlock.py [-p protocol modified] [-c change wnc value] [-v] protocol_file\n\n  ==================\n | FUNCTION LETTERS |\n  ==================\n\n-p protocol modified, --protocol=protocol modified\n\n\tThe \u003cprotocol modified\u003e is an python command written in the protocol file. \n\tUse this option can over write the the setting already in the protocol file.\n\n-c change wnc value, --chwnc=change wnc value\n\n\t\u003cchange wnc value\u003e is format like this A.w=1.44, which means change the w value of Ala to 1.44\n\n-v \n\tverbose.\n\n  =========\n | Example |\n  =========\n\nCalculating the fraction helix of peptie, and override the w value of Ala to 1.2\n \n\t$ python3 NestingBlock.py -c A.w=1.2 test-LifsonRoig\n \nList the equation of equilibrium constant with special force in the block within helix state,\nand change the mode to basic lifson roig (without concering dipole and cap issue)\n\n\t$ python3 NestingBlock.py -p mod=\\\"\\\" test-NestingBlock\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fyanganto%2Fnestingblock","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fyanganto%2Fnestingblock","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fyanganto%2Fnestingblock/lists"}