{"action":"created","issue":{"url":"https://api.github.com/repos/cooperative-computing-lab/awe/issues/5","repository_url":"https://api.github.com/repos/cooperative-computing-lab/awe","labels_url":"https://api.github.com/repos/cooperative-computing-lab/awe/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/cooperative-computing-lab/awe/issues/5/comments","events_url":"https://api.github.com/repos/cooperative-computing-lab/awe/issues/5/events","html_url":"https://github.com/cooperative-computing-lab/awe/issues/5","id":160027203,"number":5,"title":"Replace MSMBuilder for Clustering","user":{"login":"jeffkinnison","id":3553147,"avatar_url":"https://avatars.githubusercontent.com/u/3553147?v=3","gravatar_id":"","url":"https://api.github.com/users/jeffkinnison","html_url":"https://github.com/jeffkinnison","followers_url":"https://api.github.com/users/jeffkinnison/followers","following_url":"https://api.github.com/users/jeffkinnison/following{/other_user}","gists_url":"https://api.github.com/users/jeffkinnison/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffkinnison/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffkinnison/subscriptions","organizations_url":"https://api.github.com/users/jeffkinnison/orgs","repos_url":"https://api.github.com/users/jeffkinnison/repos","events_url":"https://api.github.com/users/jeffkinnison/events{/privacy}","received_events_url":"https://api.github.com/users/jeffkinnison/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cooperative-computing-lab/awe/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"closed","locked":false,"assignee":{"login":"jeffkinnison","id":3553147,"avatar_url":"https://avatars.githubusercontent.com/u/3553147?v=3","gravatar_id":"","url":"https://api.github.com/users/jeffkinnison","html_url":"https://github.com/jeffkinnison","followers_url":"https://api.github.com/users/jeffkinnison/followers","following_url":"https://api.github.com/users/jeffkinnison/following{/other_user}","gists_url":"https://api.github.com/users/jeffkinnison/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffkinnison/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffkinnison/subscriptions","organizations_url":"https://api.github.com/users/jeffkinnison/orgs","repos_url":"https://api.github.com/users/jeffkinnison/repos","events_url":"https://api.github.com/users/jeffkinnison/events{/privacy}","received_events_url":"https://api.github.com/users/jeffkinnison/received_events","type":"User","site_admin":false},"assignees":[{"login":"jeffkinnison","id":3553147,"avatar_url":"https://avatars.githubusercontent.com/u/3553147?v=3","gravatar_id":"","url":"https://api.github.com/users/jeffkinnison","html_url":"https://github.com/jeffkinnison","followers_url":"https://api.github.com/users/jeffkinnison/followers","following_url":"https://api.github.com/users/jeffkinnison/following{/other_user}","gists_url":"https://api.github.com/users/jeffkinnison/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffkinnison/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffkinnison/subscriptions","organizations_url":"https://api.github.com/users/jeffkinnison/orgs","repos_url":"https://api.github.com/users/jeffkinnison/repos","events_url":"https://api.github.com/users/jeffkinnison/events{/privacy}","received_events_url":"https://api.github.com/users/jeffkinnison/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2016-06-13T19:33:32Z","updated_at":"2016-07-20T14:37:01Z","closed_at":"2016-07-20T14:37:01Z","body":"AWE currently requires a legacy build of [MSMBuilder] (https://github.com/msmbuilder/msmbuilder-legacy \"MSMBuilder Legacy GitHub repository\") to perform clustering per the tutorial. This version of MSMBuilder is not Python 3-compatible and several features used to extract models for the Walkers have been removed in newer versions. Additionally, MSMBuilder does some file format conversions that can lead to bad trajectories when extracted due to interpolating hydrogen positions. \r\n\r\nThe clustering process needs to be updated to use a more recent version of MSMBuilder.\r\n\r\nMSMBuilder uses [scikit-learn] (http://scikit-learn.org/stable/ \"scikit-learn Homepage\") to do clustering. If converting to a newer version of MSMBuilder is not viable, AWE should include its own clustering utility built on scikit-learn to simplify the installation process and system preparation.\r\n"},"comment":{"url":"https://api.github.com/repos/cooperative-computing-lab/awe/issues/comments/233968752","html_url":"https://github.com/cooperative-computing-lab/awe/issues/5#issuecomment-233968752","issue_url":"https://api.github.com/repos/cooperative-computing-lab/awe/issues/5","id":233968752,"user":{"login":"jeffkinnison","id":3553147,"avatar_url":"https://avatars.githubusercontent.com/u/3553147?v=3","gravatar_id":"","url":"https://api.github.com/users/jeffkinnison","html_url":"https://github.com/jeffkinnison","followers_url":"https://api.github.com/users/jeffkinnison/followers","following_url":"https://api.github.com/users/jeffkinnison/following{/other_user}","gists_url":"https://api.github.com/users/jeffkinnison/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffkinnison/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffkinnison/subscriptions","organizations_url":"https://api.github.com/users/jeffkinnison/orgs","repos_url":"https://api.github.com/users/jeffkinnison/repos","events_url":"https://api.github.com/users/jeffkinnison/events{/privacy}","received_events_url":"https://api.github.com/users/jeffkinnison/received_events","type":"User","site_admin":false},"created_at":"2016-07-20T14:37:01Z","updated_at":"2016-07-20T14:37:01Z","body":"Feature added by #11 \r\n"}}
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