{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/perses/issues/328","repository_url":"https://api.github.com/repos/choderalab/perses","labels_url":"https://api.github.com/repos/choderalab/perses/issues/328/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/perses/issues/328/comments","events_url":"https://api.github.com/repos/choderalab/perses/issues/328/events","html_url":"https://github.com/choderalab/perses/issues/328","id":225348949,"number":328,"title":"Create simple command-line interface","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars2.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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-04-30T19:36:09Z","updated_at":"2017-05-04T17:09:29Z","closed_at":null,"body":"The simplest way to get something usable right now is to write an application driver for relative free energy calculations that can be called from the command-line. \r\n\r\nPossible syntax might be something like\r\n```bash\r\nperses relative-binding --method=nonequilibrium --complex complex.pdb --current=current.mol2 --perturbed=perturbed.mol2 [--matchindex=3] --work work.out --currenttraj=current.h5 --perturbedtraj=perturbed.h5\r\n```\r\nwhere `complex.pdb` has the small molecule `current.mol2` and the perturbed molecule is `perturbed.mol2`, `method` lets us select between `nonequilibrium` and `sams`, the `matchindex` is a way of selecting amongst a deterministic set of prioritized mappings, `work.out` contains the work data to analyze, and the trajectories for the current and perturbed complexes are written in HDF5 format by MDTraj (which also contains the topology).\r\n\r\nThe [`docopt` dispatch method in yank](https://github.com/choderalab/yank/blob/master/Yank/cli.py) may be useful if you intend to write a few command-line drivers.\r\n\r\nReusable components of the application driver can then be refactored into library functions and tasklets that are called by a distributed application driver."},"comment":{"url":"https://api.github.com/repos/choderalab/perses/issues/comments/299249079","html_url":"https://github.com/choderalab/perses/issues/328#issuecomment-299249079","issue_url":"https://api.github.com/repos/choderalab/perses/issues/328","id":299249079,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars2.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":"2017-05-04T17:09:29Z","updated_at":"2017-05-04T17:09:29Z","body":"Two more observations:\r\n* SAMS simulations would probably instead have a single output trajectory for ligand-in-complex and a single trajectory for ligand-in-solution\r\n* Nonequilibrium switching would presumably also include another argument to say whether the complex phase or solution phase is being simulated\r\n* Depending on how #344 is implemented, we may need an argument for checkpoint file\r\n"}}
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