{"id":30523988,"url":"https://github.com/lightonai/newma-md","last_synced_at":"2025-08-26T20:52:21.141Z","repository":{"id":40967158,"uuid":"249708165","full_name":"lightonai/newma-md","owner":"lightonai","description":"Conformational exploration SARS-CoV-2 (coronavirus responsible for COVID-19)","archived":false,"fork":false,"pushed_at":"2022-06-22T01:31:23.000Z","size":604,"stargazers_count":15,"open_issues_count":1,"forks_count":5,"subscribers_count":4,"default_branch":"master","last_synced_at":"2023-03-05T14:12:30.167Z","etag":null,"topics":["change-point-detection","covid-19","molecular-dynamics","newma","photonic-computing"],"latest_commit_sha":null,"homepage":"https://medium.com/@LightOnIO","language":"Jupyter Notebook","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/lightonai.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":"2020-03-24T12:55:41.000Z","updated_at":"2022-09-14T04:53:12.000Z","dependencies_parsed_at":"2022-08-31T22:10:52.267Z","dependency_job_id":null,"html_url":"https://github.com/lightonai/newma-md","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"purl":"pkg:github/lightonai/newma-md","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lightonai%2Fnewma-md","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lightonai%2Fnewma-md/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lightonai%2Fnewma-md/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lightonai%2Fnewma-md/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lightonai","download_url":"https://codeload.github.com/lightonai/newma-md/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lightonai%2Fnewma-md/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272254537,"owners_count":24901063,"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":"2025-08-26T02:00:07.904Z","response_time":60,"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":["change-point-detection","covid-19","molecular-dynamics","newma","photonic-computing"],"created_at":"2025-08-26T20:52:20.379Z","updated_at":"2025-08-26T20:52:21.127Z","avatar_url":"https://github.com/lightonai.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# \u003cimg src=\"_static/lighton_small.png\" width=60/\u003e Conformational exploration SARS-CoV-2 (coronavirus responsible for COVID-19)\n\n[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)  [![Twitter](https://img.shields.io/twitter/follow/LightOnIO?style=social)](https://twitter.com/LightOnIO)\n\nThis repository contains the script to reproduce the results of the blog post [**Coronavirus “SARS-CoV-2” conformational change-points detected with optical random features**](https://medium.com/@LightOnIO/accelerating-sars-cov2-molecular-dynamics-studies-with-optical-random-features-b8cffdb99b01) as well as the results of [**Optical Random Features versus SARS-CoV-2 Glycoprotein Trajectory: Round#2**](https://medium.com/@LightOnIO/optical-random-features-versus-sars-cov-2-glycoprotein-trajectory-round-2-adcf04d6036d).\n\n## \n\n## Requirements\n\nWe advise creating a `virtualenv` before running these commands. You can create one with `python3 -m venv \u003cvenv_name\u003e`. Activate it with source `\u003cpath_to_venv\u003e/bin/activate`  before proceeding. We used `python 3.7`for all the simulations.\n\n- Clone the repository and then do `pip install -r requirements.txt`.\n- Download the dataset from [this page](https://figshare.com/articles/6_molecular_dynamics_simulations_of_coronavirus_2019-nCoV_protease_model_in_complex_with_different_conformations_of_lopinavir_/11764158). You should put the dataset in the  same folder as the repository. Otherwise, make sure to update the variable `path traj`.\n\n## \n\n## Replicate our results\n\nFor replicating the results of [**Coronavirus “SARS-CoV-2” conformational change-points detected with optical random features**](https://medium.com/@LightOnIO/accelerating-sars-cov2-molecular-dynamics-studies-with-optical-random-features-b8cffdb99b01): start by running\n\n```\npython newma_coronavirus.py\n```\n\nThis outputs a numpy zipped archive. To analyse the results and create your own plot, use the notebook `notebooks/corona_exploration.ipynb`.\n\nFor replicating the results of [**Optical Random Features versus SARS-CoV-2 Glycoprotein Trajectory: Round#2**](https://medium.com/@LightOnIO/optical-random-features-versus-sars-cov-2-glycoprotein-trajectory-round-2-adcf04d6036d): start by running\n\n```\npython newma_coronavirus_DESRES.py\n```\n\nThis outputs a numpy zipped archive. To analyse the results and create your own plot, use the notebook `notebooks/corona_exploration_DESRES.ipynb`.\n\n## \u003cimg src=\"_static/lighton_cloud_small.png\" width=120/\u003e Access to Optical Processing Units\n\nTo request access to LightOn Cloud and try our photonic co-processor, please visit: \u003chttps://cloud.lighton.ai/\u003e\n\nFor researchers, we also have a LightOn Cloud for Research program, please visit \u003chttps://cloud.lighton.ai/lighton-research/\u003e for more information.\n\n## \n\n## Hardware Specifications\n\nAll our results were obtains on a Intel(R) Xeon(R) Gold 6128 CPU @3.40GHz with 12 cores.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flightonai%2Fnewma-md","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flightonai%2Fnewma-md","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flightonai%2Fnewma-md/lists"}