{"id":17255220,"url":"https://github.com/unixjunkie/durandal","last_synced_at":"2025-04-14T05:41:34.223Z","repository":{"id":144782326,"uuid":"1633382","full_name":"UnixJunkie/Durandal","owner":"UnixJunkie","description":"Entropy-accelerated exact clustering of protein decoys (PDB files).","archived":false,"fork":false,"pushed_at":"2012-10-24T01:37:24.000Z","size":416,"stargazers_count":5,"open_issues_count":1,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-27T19:39:37.993Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://www.riken.jp/zhangiru/software.html","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/UnixJunkie.png","metadata":{"files":{"readme":"README.txt","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2011-04-19T00:43:49.000Z","updated_at":"2022-07-15T18:05:58.000Z","dependencies_parsed_at":"2023-03-22T11:53:50.065Z","dependency_job_id":null,"html_url":"https://github.com/UnixJunkie/Durandal","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FDurandal","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FDurandal/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FDurandal/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FDurandal/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/Durandal/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248830418,"owners_count":21168272,"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":"2024-10-15T07:10:59.252Z","updated_at":"2025-04-14T05:41:34.204Z","avatar_url":"https://github.com/UnixJunkie.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Copyright (C) 2010, 2011 Zhang Initiative Research Unit,\n# Advance Science Institute, RIKEN\n# 2-1 Hirosawa, Wako, Saitama 351-0198, Japan\n# This program is free software: you can redistribute it and/or modify\n# it under the terms of the GNU Lesser General Public License as published by\n# the Free Software Foundation, either version 3 of the License, or\n# (at your option) any later version.\n# This program is distributed in the hope that it will be useful,\n# but WITHOUT ANY WARRANTY; without even the implied warranty of\n# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n# GNU Lesser General Public License for more details.\n# You should have received a copy of the GNU Lesser General Public License\n# along with this program. If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n\nIF YOU USE THIS SOFTWARE, PLEASE CITE THE CORRESPONDING PUBLICATION:\n====================================================================\n\n@article{Berenger2011,\nauthor = {Berenger, Francois and Zhou, Yong and Shrestha, Rojan and\n          Zhang, Kam Y. J.},\ntitle = {Entropy-accelerated exact clustering of protein decoys},\nvolume = {27},\nnumber = {7},\npages = {939-945},\nyear = {2011},\ndoi = {10.1093/bioinformatics/btr072},\nURL = {http://bioinformatics.oxfordjournals.org/content/27/7/939.abstract},\njournal = {Bioinformatics},\n}\n\nPreconditions:\n==============\n\nThe alignment expected by the Durandal software is 1 to 1.\nFor example, if 2 structures A and B are to be optimally superposed before\ncomputing the CARMSD, both PDB files (A.pdb and B.pdb) must have same numbers\nof alpha carbons.\nThe first alpha carbon in A.pdb will be matched to the first alpha carbon in\nB.pdb.\nThe second alpha carbon in A.pdb will be matched to the second alpha carbon in\nB.pdb.\nAnd so on until the end of both files.\nIf it is not the case, please edit all your PDB files in advance.\n\nOutput format (cluster listings):\n=================================\n\nUse the -v option to get easily readable cluster listings.\nThen, the output will look like this:\n\npole position centers(5):\n./pdbs/02.pdb\n./pdbs/03.pdb\n./pdbs/05.pdb\n./pdbs/07.pdb\n./pdbs/09.pdb\nmembers(3):\n./pdbs/01.pdb\n./pdbs/03.pdb\n./pdbs/07.pdb\nmembers(3):\n./pdbs/02.pdb\n./pdbs/05.pdb\n./pdbs/09.pdb\nmembers(2):\n./pdbs/00.pdb\n./pdbs/06.pdb\nmembers(2):\n./pdbs/04.pdb\n./pdbs/08.pdb\n\nA cluster is listed after a 'members(N):' line.\nThe first PDB of the cluster is the cluster center,\nother PDBs are cluster members.\n\nClusters are listed in a biggest-first (most members) order.\n\nThe 'pole position centers(N):' and following lines\nindicate that there were other possible biggest clusters;\nonly their centers are listed.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fdurandal","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Fdurandal","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fdurandal/lists"}