[{"_1":2,"_161":-5,"_162":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_140":141},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_88":-5,"_89":90,"_129":-5,"_130":11,"_131":21,"_132":11,"_133":-5,"_134":11,"_135":-5,"_136":137,"_138":91,"_139":-7},"canonicalUrl","https://hub.docker.com/r/jongseopark/dali/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","jongseopark","reponame","dali","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":74,"_79":11,"_80":81,"_85":33,"_86":87},"categories",[],"content_types",[44],"image","date_registered","2021-08-27T18:58:47.390113Z","description","Local version of DALI with openmpi","is_private","last_updated","2021-09-01T12:21:01.21691Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",131,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# ***DALI_prepare***\n\n*[DALI search](http://ekhidna2.biocenter.helsinki.fi/dali/)*\n\n
\n
\n\n*[Link to GitHub related with this docker image](https://github.com/jongseo-park/DALI_prepare)*\n\n\n
\n\nThe running of the local version of DALI search needs several DB files.\n\nThe DB is created from PDB files with the file name of 4 letter code. \n\nThis repository has a script for the preparing of those things.\n\n
\n\n단백질 구조 비교를 위한 DALI search 를 local 에서 작동시키기 위해서는 먼저 데이터베이스를 준비해야 합니다.\n\n데이터베이스는 PDB 파일로부터 만들어지고, 모든 PDB 파일은 4 letter code 로 준비되어 있어야만 합니다.\n\n이 저장소에서는 해당 데이터베이스를 준비하는 것을 도와주는 스크립트를 공유합니다.\n\n사용법은 아래와 같습니다.\n\n(한글 사용법을 아래에 따로 작성해 두었습니다.)\n\n
\n\n- - -\n\n## ***How to use***\n\n### **1. Pull the docker image**\n\n docker pull jongseopark/dali\n\n
\n\n### **2. Directory setup**\n\nBefore run the docker container and this script, \n\nIt is recommended setting of the directory as follows.\n\n Working_dir/\n\n dali_prepare.py\n\n pdb/\n several_pdb_files.pdb\n ...\n ...\n \n dat/\n empty_directory\n\n\nIf you have many PDB files in multiple folders, please prepare as follows.\n\n Working_dir/\n\n dali_prepare.py\n\n pdbs/\n folder1/\n pdb_files.pdb\n ...\n\n folder2/\n pdb_files.pdb\n ...\n \n ...\n\n dat/\n empty_directory\n\n
\n\n### **3. Run the docker container from the image with mounting of the working directory**\n\n docker run \n -it \n -v \"/path/to/working/directory/:/home/dali/run/\" \n -u dali \n jongseopark/dali:v01\n\n
\n\n### **4. Run the script**\n\nRun the script with several arguments as follows.\n\n\n\n python3 dali_prepare.py\n\n --dalipath /opt/DaliLite.v5/\n --pdbpath ./pdb/\n --datpath ./dat/\n\n --renamer y\n (or --importer y)\n (or --listmaker y)\n\nYou have to select only one function at a time (renamer / importer / listmaker).\n\nIf you have many PDB files in multiple folders, then use the ***'pdbspath'*** and ***'renamer2'*** arguments as follows.\n\n python3 dali_prepare.py\n\n --dalipath /opt/DaliLite.v5/\n --pdbspath ./pdbs/\n --datpath ./dat/\n\n --renamer2 y\n\n\n1. When you run the ***'renamer'*** or ***'renamer2'***, the name of your PDB files will be changed to 4 letter codes without overlap, and the log file for replacement (.txt) will be written in the path to PDB.\n\n2. When you run the ***'importer'***, DALI will make the data files (.dat) from your PDB files. For this function, you have to replace the name of your PDB files as 4 letter codes such as **'abcd'**.\n\n3. When you run the ***'listmaker'***, the script collect the name of data files (.dat) from your **'datpath'** (./dat/), and write a **'dat.list'** file comprising all of the name of .dat files in the working directory.\n \n\n
\n\n### **4. Run the DALI**\n\nThe docker image already has a local version of DALI (DaliLite.v5) that supports multicore processing (using openmpi).\n\nYou can use it as follows (np = the number of processors).\n\n dali.pl --query ./query.list --db ./dat.list --dat1 /working/dir/query_DAT --dat2 /working/dir/DAT/ --np 10 --TITLE title_you_want --clean\n\nNote that the query.list file has the identical format as the dat.list file.\n\nPlease refer to the manual in the hompage of DALI server.\n\n
\n
\n\n\n*Thanks.*\n\n- - -\n- - -\n
\n\n*For Korean*\n\n
\n\n## ***사용법***\n\n### **1. 도커 이미지 준비하기**\n\n docker pull jongseopark/dali\n\n
\n\n### **2. 디렉토리 설정**\n\n도커 컨테이너와 스크립트를 사용하기 전에 디렉토리를 세팅하는 것을 추천합니다.\n\n디렉토리는 아래와 같이 구성하면 되겠습니다.\n\n Working_dir/\n\n dali_prepare.py\n\n pdb/\n several_pdb_files.pdb\n ...\n ...\n \n dat/\n empty_directory\n\n\n만일 많은 PDB 파일을 담고 있는 여러 폴더가 있다면 아래와 같이 준비하세요.\n\n\n Working_dir/\n\n dali_prepare.py\n\n pdbs/\n folder1/\n pdb_files.pdb\n ...\n\n folder2/\n pdb_files.pdb\n ...\n \n ...\n\n dat/\n empty_directory\n\n
\n\n### **3. 도커 이미지를 이용하여 컨테이너 만들고 작업 디렉토리 연결하기**\n\n docker run \n -it \n -v \"/path/to/working/directory/:/home/dali/run/\" \n -u dali \n jongseopark/dali:v01\n\n
\n\n### **4. 스크립트 실행**\n\n아래의 옵션들을 활용하여 스크립트를 실행합니다.\n\n\n\n python3 dali_prepare.py\n\n --dalipath /opt/DaliLite.v5/\n --pdbpath ./pdb/\n --datpath ./dat/\n\n --renamer y\n (or --importer y)\n (or --listmaker y)\n\n한 번에 한 가지의 기능만을 사용해야 합니다 (renamer / importer / listmaker).\n\n만일 많은 PDB 파일을 담고 있는 여러 폴더가 있을 때 파일 이름을 변경하고 싶다면 아래와 같이 ***'pdbspath'*** 와 ***'renamer2'*** 옵션을 이용하세요.\n\n python3 dali_prepare.py\n\n --dalipath /opt/DaliLite.v5/\n --pdbspath ./pdbs/\n --datpath ./dat/\n\n --renamer2 y\n\n\n1. ***'renamer'*** 또는 ***'renamer2'*** 를 실행시키면, 모든 PDB 파일의 이름이 서로 중복되지 않는 4 letter code 로 변경됩니다. 그리고 이름 변경에 대한 로그파일 (.txt) 이 pdbpath 에 생성됩니다.\n\n2. ***'importer'*** 를 실행시키면, DALI 는 PDB 파일을 이용하여 데이터 파일 (.dat) 을 생성합니다. 이 때, PDB 파일의 이름은 모두 **'abcd'** 와 같은 4 letter code 로 되어있어야만 합니다.\n\n3. ***'listmaker'*** 를 실행시키면, 스크립트는 모든 데이터 파일 (.dat) 의 이름을 읽어들인 후 **'dat.list'** 파일에 옮겨붙입니다. dat.list 파일은 작업 디렉토리 내에 생성됩니다.\n \n\n
\n\n### **4. DALI 실행**\n\n도커 이미지에는 다중 코어 프로세싱 작업이 가능하도록 셋업된 (using openmpi) DALI 의 local version 이 설치되어 있습니다.\n\n아래와 같이 사용할 수 있습니다.\n\n(np = the number of processors).\n\n dali.pl --query ./query.list --db ./dat.list --dat1 /working/dir/query_DAT --dat2 /working/dir/DAT/ --np 10 --TITLE title_you_want --clean\n\n\n참고로, query.list 파일은 dat.list 파일과 동일한 형식으로 작성하면 됩니다.\n\nDALI 의 자세한 사용법은 홈페이지를 참조하세요.\n\n
\n
\n\n\n*감사합니다.*","has_starred","hub_user","immutable_tags_settings",{"_75":11,"_76":77},"enabled","rules",[78],".*","is_automated","permissions",{"_82":21,"_83":11,"_84":11},"read","write","admin","user","storage_size",317538996,"orgData","recentTags",[91],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":100,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":66,"_128":21},"content_type","creator",10703569,"full_size",317527271,"id",165334075,"images",[101],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":66,"_117":-5},"architecture","amd64","digest","sha256:3e2636b0f98b1ce4b91fc336017d8cfe6ee969c90b9f75bf715d7ed54f15c30a","features","","last_pulled","2026-09-27T02:53:17.846757407Z","last_pushed","2021-09-01T12:21:01Z","os","linux","os_features","os_version","size","variant","2021-09-01T12:21:00.856973Z","last_updater","last_updater_username","media_type","latest","repository",15238990,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":142,"_149":150,"_136":159,"_160":11},{"_40":143,"_42":144,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":145,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":146,"_79":11,"_80":148,"_85":33,"_86":87},[],[44],[56],{"_75":11,"_76":147},[78],{"_82":21,"_83":11,"_84":11},"tags",{"_151":64,"_152":-5,"_153":-5,"_154":155},"count","next","previous","results",[156],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":157,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":66,"_128":21},[158],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":66,"_117":-5},[],"canDeleteTags","actionData","errors"]

jongseopark/dali

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