{"id":15750398,"url":"https://github.com/beebus/osra-iterate","last_synced_at":"2026-04-17T00:33:33.997Z","repository":{"id":79609706,"uuid":"105310858","full_name":"beebus/osra-iterate","owner":"beebus","description":"Bash Script to iterate through .TIF Images in a folder and run the OSRA program to attempt to convert the TIF images into ChemDraw files (.CDXML).","archived":false,"fork":false,"pushed_at":"2021-03-20T19:01:06.000Z","size":4,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-06T11:55:48.912Z","etag":null,"topics":["bash","bash-script","bash-scripting","chemical-structures","cheminformatics","chemistry","image-processing","image-recognition","jpg","linux","molecular-structures","molecule","molecules","ocr","optical-recognition","organic-chemistry","osra","pdf","reactions","tif-images"],"latest_commit_sha":null,"homepage":"","language":"Shell","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/beebus.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-09-29T19:45:45.000Z","updated_at":"2021-03-20T19:01:08.000Z","dependencies_parsed_at":"2023-05-13T08:00:30.490Z","dependency_job_id":null,"html_url":"https://github.com/beebus/osra-iterate","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/beebus%2Fosra-iterate","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/beebus%2Fosra-iterate/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/beebus%2Fosra-iterate/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/beebus%2Fosra-iterate/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/beebus","download_url":"https://codeload.github.com/beebus/osra-iterate/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246429493,"owners_count":20775808,"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":["bash","bash-script","bash-scripting","chemical-structures","cheminformatics","chemistry","image-processing","image-recognition","jpg","linux","molecular-structures","molecule","molecules","ocr","optical-recognition","organic-chemistry","osra","pdf","reactions","tif-images"],"created_at":"2024-10-04T06:40:35.951Z","updated_at":"2026-04-17T00:33:28.972Z","avatar_url":"https://github.com/beebus.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# osra-iterate\nBash Script to Iterate through TIF Images in Folder and Run OSRA\n\nThis shows the command line usage of the OSRA open source software.\n\nExecute the osra_iterate.sh bash script by using the following command (or similar) within a Linux terminal and with the folder that contains osra_iterate.sh as the current working directory:\n\n./osra_iterate.sh ~/Share/input/ ~/Share/output/\n\nWhat is OSRA?\n\nOSRA (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or MOL files – a computer recognizable molecular structure format. OSRA can read a document in any of the over 90 graphical formats parseable by GraphicsMagick (https://sourceforge.net/p/osra/wiki/Dependencies#GraphicsMagick) – including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate the SMILES or MOL representation of the molecular structure images encountered within that document, or RSMI/RXN for reactions.\n\nNote that any software designed for optical recognition is unlikely to be perfect, and the output produced might, and probably will, contain errors, so curation by a human knowledgeable in chemical structures is highly recommended.\n\nOSRA can process the following types of images:\n* Computer-generated 2D structures, such as found on the PubChem website (http://pubchem.ncbi.nlm.nih.gov/), black-and-white and color.\n* Black-and-white PDF and PostScript files, including multi-page ones.\n* Scanned images – black-and-white, a resolution of 300 dpi is recommended, though 150 dpi can also produce fair results. Please make sure the scanned image is of reasonable quality – an input that's too noisy will only generate garbage output.\n* Reactions and Polymers\n\nYou can download a free version (https://sourceforge.net/p/osra/wiki/Download/) of the source code or support OSRA development by purchasing binary installation executables for Windows (https://store.payproglobal.com/checkout?products[1][id]=38760), and Linux (https://store.payproglobal.com/checkout?products[1][id]=38761).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbeebus%2Fosra-iterate","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbeebus%2Fosra-iterate","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbeebus%2Fosra-iterate/lists"}