{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/openpathsampling/issues/435","repository_url":"https://api.github.com/repos/choderalab/openpathsampling","labels_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/435/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/435/comments","events_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/435/events","html_url":"https://github.com/choderalab/openpathsampling/pull/435","id":136806581,"number":435,"title":"Single trajectory analysis","user":{"login":"dwhswenson","id":8178546,"avatar_url":"https://avatars.githubusercontent.com/u/8178546?v=3","gravatar_id":"","url":"https://api.github.com/users/dwhswenson","html_url":"https://github.com/dwhswenson","followers_url":"https://api.github.com/users/dwhswenson/followers","following_url":"https://api.github.com/users/dwhswenson/following{/other_user}","gists_url":"https://api.github.com/users/dwhswenson/gists{/gist_id}","starred_url":"https://api.github.com/users/dwhswenson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwhswenson/subscriptions","organizations_url":"https://api.github.com/users/dwhswenson/orgs","repos_url":"https://api.github.com/users/dwhswenson/repos","events_url":"https://api.github.com/users/dwhswenson/events{/privacy}","received_events_url":"https://api.github.com/users/dwhswenson/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"jhprinz","id":5091934,"avatar_url":"https://avatars.githubusercontent.com/u/5091934?v=3","gravatar_id":"","url":"https://api.github.com/users/jhprinz","html_url":"https://github.com/jhprinz","followers_url":"https://api.github.com/users/jhprinz/followers","following_url":"https://api.github.com/users/jhprinz/following{/other_user}","gists_url":"https://api.github.com/users/jhprinz/gists{/gist_id}","starred_url":"https://api.github.com/users/jhprinz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhprinz/subscriptions","organizations_url":"https://api.github.com/users/jhprinz/orgs","repos_url":"https://api.github.com/users/jhprinz/repos","events_url":"https://api.github.com/users/jhprinz/events{/privacy}","received_events_url":"https://api.github.com/users/jhprinz/received_events","type":"User","site_admin":false},"milestone":null,"comments":11,"created_at":"2016-02-26T20:29:04Z","updated_at":"2016-03-07T19:41:35Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/openpathsampling/pulls/435","html_url":"https://github.com/choderalab/openpathsampling/pull/435","diff_url":"https://github.com/choderalab/openpathsampling/pull/435.diff","patch_url":"https://github.com/choderalab/openpathsampling/pull/435.patch"},"body":"Usually we try to define states based on some information that we get from some longer MD trajectories in the state. This PR adds an analysis class to figure out a few useful facts from initial trajectories. This also serves as a quick example of how traditional analysis can be framed in terms of path ensembles. We use `Ensemble.split` to obtain:\r\n\r\n- [x] Continuous time spent in each state of a transition\r\n- [x] Lifetime in a state (time from first frame in state to, but not including, first frame in another state)\r\n- [x] Transition duration (time from leaving initial state before entering final state)\r\n- [x] Flux through the state boundary\r\n\r\nThis allows us to do all sorts of stuff, like plot the transition segments in a different color atop the whole trajectory, or get any properties of the distribution of the associated times (mean, std dev, etc). Also includes a new function to get the frame indices for subtrajectories of a given trajectory (useful when plotting).\r\n\r\nThis was started while I was working on Octomore, but it will be broadly useful."},"comment":{"url":"https://api.github.com/repos/choderalab/openpathsampling/issues/comments/193417408","html_url":"https://github.com/choderalab/openpathsampling/pull/435#issuecomment-193417408","issue_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/435","id":193417408,"user":{"login":"jhprinz","id":5091934,"avatar_url":"https://avatars.githubusercontent.com/u/5091934?v=3","gravatar_id":"","url":"https://api.github.com/users/jhprinz","html_url":"https://github.com/jhprinz","followers_url":"https://api.github.com/users/jhprinz/followers","following_url":"https://api.github.com/users/jhprinz/following{/other_user}","gists_url":"https://api.github.com/users/jhprinz/gists{/gist_id}","starred_url":"https://api.github.com/users/jhprinz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhprinz/subscriptions","organizations_url":"https://api.github.com/users/jhprinz/orgs","repos_url":"https://api.github.com/users/jhprinz/repos","events_url":"https://api.github.com/users/jhprinz/events{/privacy}","received_events_url":"https://api.github.com/users/jhprinz/received_events","type":"User","site_admin":false},"created_at":"2016-03-07T19:41:35Z","updated_at":"2016-03-07T19:41:35Z","body":"Merging..."}}