{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/yank/issues/259","labels_url":"https://api.github.com/repos/choderalab/yank/issues/259/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/yank/issues/259/comments","events_url":"https://api.github.com/repos/choderalab/yank/issues/259/events","html_url":"https://github.com/choderalab/yank/pull/259","id":88906185,"number":259,"title":"[WIP] Use MDTraj DSL to specify ligand atoms.","user":{"login":"andrrizzi","id":1682142,"avatar_url":"https://avatars.githubusercontent.com/u/1682142?v=3","gravatar_id":"","url":"https://api.github.com/users/andrrizzi","html_url":"https://github.com/andrrizzi","followers_url":"https://api.github.com/users/andrrizzi/followers","following_url":"https://api.github.com/users/andrrizzi/following{/other_user}","gists_url":"https://api.github.com/users/andrrizzi/gists{/gist_id}","starred_url":"https://api.github.com/users/andrrizzi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrrizzi/subscriptions","organizations_url":"https://api.github.com/users/andrrizzi/orgs","repos_url":"https://api.github.com/users/andrrizzi/repos","events_url":"https://api.github.com/users/andrrizzi/events{/privacy}","received_events_url":"https://api.github.com/users/andrrizzi/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-06-17T04:11:59Z","updated_at":"2015-09-29T20:40:18Z","closed_at":"2015-06-19T04:04:12Z","pull_request":{"url":"https://api.github.com/repos/choderalab/yank/pulls/259","html_url":"https://github.com/choderalab/yank/pull/259","diff_url":"https://github.com/choderalab/yank/pull/259.diff","patch_url":"https://github.com/choderalab/yank/pull/259.patch"},"body":"This address #161 .\r\n\r\nI changed the parameter --ligname=RESNAME [default: MOL] to --ligdsl=LIGANDDSL [default: “resname MOL”] that takes a DSL string.\r\n\r\nI wanted to call the parameter simply ligand but it’s in conflict with systembuilder --ligand and I got the error \"docopt.DocoptLanguageError: --ligand is not a unique prefix: --ligand, --ligand?\".\r\n\r\nShould I change its name to something else? \"--ligatoms=DSLSTRING\" ? Or maybe change the name of the parameter for systembuilder?\r\n\r\nOnce the name is settled, I'll change also the syntax in the documentation, the examples and nosetests."},"comment":{"url":"https://api.github.com/repos/choderalab/yank/issues/comments/144185152","html_url":"https://github.com/choderalab/yank/pull/259#issuecomment-144185152","issue_url":"https://api.github.com/repos/choderalab/yank/issues/259","id":144185152,"user":{"login":"andrrizzi","id":1682142,"avatar_url":"https://avatars.githubusercontent.com/u/1682142?v=3","gravatar_id":"","url":"https://api.github.com/users/andrrizzi","html_url":"https://github.com/andrrizzi","followers_url":"https://api.github.com/users/andrrizzi/followers","following_url":"https://api.github.com/users/andrrizzi/following{/other_user}","gists_url":"https://api.github.com/users/andrrizzi/gists{/gist_id}","starred_url":"https://api.github.com/users/andrrizzi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrrizzi/subscriptions","organizations_url":"https://api.github.com/users/andrrizzi/orgs","repos_url":"https://api.github.com/users/andrrizzi/repos","events_url":"https://api.github.com/users/andrrizzi/events{/privacy}","received_events_url":"https://api.github.com/users/andrrizzi/received_events","type":"User","site_admin":false},"created_at":"2015-09-29T20:40:18Z","updated_at":"2015-09-29T20:40:18Z","body":"Can we close this? Is there anything else that must be implemented to address this?"}}