{"action":"opened","issue":{"url":"https://api.github.com/repos/madscatt/zazzie/issues/37","repository_url":"https://api.github.com/repos/madscatt/zazzie","labels_url":"https://api.github.com/repos/madscatt/zazzie/issues/37/labels{/name}","comments_url":"https://api.github.com/repos/madscatt/zazzie/issues/37/comments","events_url":"https://api.github.com/repos/madscatt/zazzie/issues/37/events","html_url":"https://github.com/madscatt/zazzie/issues/37","id":177784910,"number":37,"title":"Clean up TAMC input","user":{"login":"stvn66","id":9484229,"avatar_url":"https://avatars.githubusercontent.com/u/9484229?v=3","gravatar_id":"","url":"https://api.github.com/users/stvn66","html_url":"https://github.com/stvn66","followers_url":"https://api.github.com/users/stvn66/followers","following_url":"https://api.github.com/users/stvn66/following{/other_user}","gists_url":"https://api.github.com/users/stvn66/gists{/gist_id}","starred_url":"https://api.github.com/users/stvn66/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stvn66/subscriptions","organizations_url":"https://api.github.com/users/stvn66/orgs","repos_url":"https://api.github.com/users/stvn66/repos","events_url":"https://api.github.com/users/stvn66/events{/privacy}","received_events_url":"https://api.github.com/users/stvn66/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-09-19T13:30:24Z","updated_at":"2016-09-19T13:30:24Z","closed_at":null,"body":"- [ ] Add missing inputs:\r\n  - [ ] ionic conditions of buffer, mentioned in [issue 29](https://github.com/madscatt/zazzie/issues/29)\r\n  - [ ] B-DNA persistence length (advanced)\r\n  - [ ] B-DNA twist energy prefactor (advanced)\r\n- [ ] Rename `double-stranded nucleic acid worm-like chain torsion` to `B-DNA bead--rod torsion`\r\n- [ ] Resolve `move direction` for B-DNA by either\r\n  - [ ] removing it from the input\r\n  - [ ] adding a parenthetical statement saying \"NOT for B-DNA\"\r\n- [ ] Remove unused inputs:\r\n  - [ ] number of base pairs per bead\r\n  - [ ] soft rotation averaged over N beads\r\n  - [ ] DCD save frequency\r\n  - [ ] random seed\r\n  - [ ] print debugging information\r\n  - [ ] save file labeling information\r\n  - [ ] keep coarse-grain B-DNA and protein pdb and dcd files\r\n  - [ ] keep duplicate structure when move fails\r\n  - [ ] remove binary pkl cg file\r\n- [ ] Refactor other advanced inputs\r\n  - [ ] low/high Rg cutoff\r\n  - [ ] Z coordinate filter\r\n  - [ ] Z cutoff\r\n  - [ ] plot Rg during run\r\n  - [ ] directed Monte Carlo\r\n  - [ ] check box to use atomic constraints\r\n  - [ ] check box to use non-bonding energies"}}
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