{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/yank-examples/issues/14","repository_url":"https://api.github.com/repos/choderalab/yank-examples","labels_url":"https://api.github.com/repos/choderalab/yank-examples/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/yank-examples/issues/14/comments","events_url":"https://api.github.com/repos/choderalab/yank-examples/issues/14/events","html_url":"https://github.com/choderalab/yank-examples/pull/14","id":185507285,"number":14,"title":"Add the initial p-xylene explicit example with documentation.","user":{"login":"Lnaden","id":3809383,"avatar_url":"https://avatars.githubusercontent.com/u/3809383?v=3","gravatar_id":"","url":"https://api.github.com/users/Lnaden","html_url":"https://github.com/Lnaden","followers_url":"https://api.github.com/users/Lnaden/followers","following_url":"https://api.github.com/users/Lnaden/following{/other_user}","gists_url":"https://api.github.com/users/Lnaden/gists{/gist_id}","starred_url":"https://api.github.com/users/Lnaden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Lnaden/subscriptions","organizations_url":"https://api.github.com/users/Lnaden/orgs","repos_url":"https://api.github.com/users/Lnaden/repos","events_url":"https://api.github.com/users/Lnaden/events{/privacy}","received_events_url":"https://api.github.com/users/Lnaden/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2016-10-26T20:53:40Z","updated_at":"2016-10-27T15:18:27Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/yank-examples/pulls/14","html_url":"https://github.com/choderalab/yank-examples/pull/14","diff_url":"https://github.com/choderalab/yank-examples/pull/14.diff","patch_url":"https://github.com/choderalab/yank-examples/pull/14.patch"},"body":"Fixes #3 \r\n\r\nShould we fill in more of the README.md file with this so people have more of a walk-through? Or should we put the walkthroughs on getyank.org and point to them from here?"},"comment":{"url":"https://api.github.com/repos/choderalab/yank-examples/issues/comments/256672358","html_url":"https://github.com/choderalab/yank-examples/pull/14#issuecomment-256672358","issue_url":"https://api.github.com/repos/choderalab/yank-examples/issues/14","id":256672358,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"created_at":"2016-10-27T15:18:27Z","updated_at":"2016-10-27T15:18:27Z","body":"> I am leaving the input mol2 files, but I am also leaving any file people may need to reconstruct the input files (just incase they want to from scratch). I'll modify the pdbfixer argument as well.\r\n\r\nWe're currently generating a bunch of files that aren't going to be used, so we want to make sure not to be doing that.\r\n\r\nThe only files we need to retain are:\r\n* `README.md` - documentation\r\n* Let's split `setup.py` into `setup-protein.sh` (doesn't require OpenEye) and `setup-ligand.sh` (requires OpenEye) if you want to retain both parts\r\n* `run.sh` - shell run example\r\n* `run-torque.sh` - Torque run example\r\n* `yank.yaml`\r\n* `receptor.pdbfixer.pdb` - output of `setup-protein.sh`\r\n* `p-xylene.mol2` - Tripos mol2 file\r\n* `generate-mol2-from-name.py` - OpenEye script to create small molecule\r\n\r\nEverything else is superfluous and shouldn't be included.\r\n\r\nWe'll have to make sure the dependencies for this package include `pdbfixer`.\r\n\r\n> Before this gets merged though, there are some debugging things I am working on to make sure that the example runs. Right now it doesn't"}}
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