{"id":15118943,"url":"https://github.com/pfizer-opensource/torsional-strain","last_synced_at":"2025-12-24T16:33:49.651Z","repository":{"id":121675711,"uuid":"164144809","full_name":"pfizer-opensource/torsional-strain","owner":"pfizer-opensource","description":null,"archived":false,"fork":false,"pushed_at":"2023-03-14T13:19:09.000Z","size":170,"stargazers_count":20,"open_issues_count":0,"forks_count":7,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-01-18T06:33:10.624Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pfizer-opensource.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":"2019-01-04T19:05:37.000Z","updated_at":"2024-04-01T19:14:00.000Z","dependencies_parsed_at":null,"dependency_job_id":"37e97c35-71ef-49dc-82fe-95539bbbadbb","html_url":"https://github.com/pfizer-opensource/torsional-strain","commit_stats":null,"previous_names":["pfizer-opensource/torsional-strain"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/pfizer-opensource/torsional-strain","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfizer-opensource%2Ftorsional-strain","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfizer-opensource%2Ftorsional-strain/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfizer-opensource%2Ftorsional-strain/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfizer-opensource%2Ftorsional-strain/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pfizer-opensource","download_url":"https://codeload.github.com/pfizer-opensource/torsional-strain/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfizer-opensource%2Ftorsional-strain/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":277315117,"owners_count":25797567,"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","status":"online","status_checked_at":"2025-09-27T02:00:08.978Z","response_time":73,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-09-26T01:53:40.751Z","updated_at":"2025-09-28T01:31:25.620Z","avatar_url":"https://github.com/pfizer-opensource.png","language":"Python","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"readme":"# Calculation of Torsional Strain Energy\n\n## Setting up the Environment\nThis step will get you setup with an evironment within which you can run the \ncode in this repository using Orion.\n1. Get access to OpenEye Orion and Magpie. If you are a licensed Orion user and \n   don't have access, please contact [OpenEye Support](support@eyesopen.com).\n2. Activate a conda distribution (typically something like `source $CONDA/activate`)\n3. Create an environment\n        `conda env create -v -f environment.yaml -n torsion`\n4. Activate the environment\n        `conda activate torsion`\n5. Install OpenEye packages  \n    a. Insert your magpie token into the first line of `requirements_dev.txt`:  \n            `--extra-index-url https://token:YOUR_TOKEN@magpie.eyesopen.com/simple/`  \n    b. Install packages with `pip install -r requirements_dev.txt`\n6. Configure the orion CLI  \n            `ocli --profile=default config profile`\n\nYou should now have an environment capable of running the orion code.\n\n## Uploading the Floe to Orion\n1. Activate the environment\n2. Run `invoke clean package upload`\n\nThis will add a package called `torsional-strain 1.0.0` with a floe called `Torsional Strain Energy` to Orion. \n![Floe Screenshot](floe_screenshot.jpg?raw=true \"Floe Screenshot\")\n\n## Running the Floe\nThe floe requires only one input: a dataset of molecules for which we want to calculate torsional strain.  \nThe floe generates two datasets as primary outputs:\n1. `output`: one output molecule per input molecule, with total molecular strain, strains at every torsion, and the torsional energy profiles of all the torsions attached as SD properties\n2. `qm_confs`: QM-optimized conformers for each torsional fragment for each molecule  \n  \nThe floe also generates datasets for torsional fragments, pre-QM torsional conformers, and conformers that fail various QM stages.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpfizer-opensource%2Ftorsional-strain","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpfizer-opensource%2Ftorsional-strain","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpfizer-opensource%2Ftorsional-strain/lists"}