{"id":26933141,"url":"https://github.com/xiaohan2012/epitope-similarity","last_synced_at":"2025-06-18T02:32:43.503Z","repository":{"id":14599325,"uuid":"17316325","full_name":"xiaohan2012/epitope-similarity","owner":"xiaohan2012","description":"Epitope similarity between two structures","archived":false,"fork":false,"pushed_at":"2015-01-07T11:43:00.000Z","size":320,"stargazers_count":0,"open_issues_count":3,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-04-02T09:17:36.013Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/xiaohan2012.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":"2014-03-01T14:19:24.000Z","updated_at":"2015-01-07T11:43:01.000Z","dependencies_parsed_at":"2022-08-28T10:41:35.644Z","dependency_job_id":null,"html_url":"https://github.com/xiaohan2012/epitope-similarity","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/xiaohan2012/epitope-similarity","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiaohan2012%2Fepitope-similarity","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiaohan2012%2Fepitope-similarity/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiaohan2012%2Fepitope-similarity/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiaohan2012%2Fepitope-similarity/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xiaohan2012","download_url":"https://codeload.github.com/xiaohan2012/epitope-similarity/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiaohan2012%2Fepitope-similarity/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260474115,"owners_count":23014656,"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":"2025-04-02T09:17:38.273Z","updated_at":"2025-06-18T02:32:38.488Z","avatar_url":"https://github.com/xiaohan2012.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"epitope-similarity\n==================\n\nEpitope similarity calculation between two structures\n\n#Before you run\n\n```\n\u003e cd epitope-similarity\n\u003e virtualenv venv\n\u003e source venv/bin/activate\n\u003e pip install -r requirements.txt\n```\n\n#Check if everything is ok\n\n`\u003e python test/similarity_test.py`\n\n\t\n#How to use\n\n1. Without any specification: `python get_sim_score.py --query-pdb test/data/sample1.pdb  --against-pdb test/data/sample2.pdb`\n2. With epitope specification: `python get_sim_score.py --query-pdb test/data/sample1.pdb  --query-epitope 211,213,214,224,225,226,227,228,229 --against-pdb test/data/sample2.pdb --against-epitope 216,217,218,219,220,221`\n3. With spinimage parametrization: `python get_sim_score.py --query-pdb test/data/sample1.pdb --against-pdb test/data/sample2.pdb  --spin-image-radius-step=2 --spin-image-height-step=5 --sphere-radius-step=2`\n4. With cutoff parametrization: `python get_sim_score.py --query-pdb test/data/sample1.pdb --against-pdb test/data/sample2.pdb  --cutoff=10`\n\nYou can specify the fingerprint path and skip the fp calcualtion step by using the option --query-fp and --against_fp, for example: \n\n`python get_sim_score.py --query-pdb test/data/sample1.pdb --against-pdb test/data/sample2.pdb --query-fp=fp/h2-v2/sample1.pdb.fp --against-fp=fp/h2-v2/sample2.pdb.fp`\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxiaohan2012%2Fepitope-similarity","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fxiaohan2012%2Fepitope-similarity","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxiaohan2012%2Fepitope-similarity/lists"}