{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3","repository_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling","labels_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3/comments","events_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3/events","html_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3","id":169583519,"number":3,"title":"Set up host-guest ligand unbinding TIS","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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-08-05T11:02:36Z","updated_at":"2016-08-05T11:05:54Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/pulls/3","html_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3","diff_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3.diff","patch_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3.patch"},"body":"Here's a clean new PR so that you can comment line by line, @jhprinz @dwhswenson \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/comments/237823943","html_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3#issuecomment-237823943","issue_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3","id":237823943,"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":"2016-08-05T11:05:54Z","updated_at":"2016-08-05T11:05:54Z","body":"OK, this clearly is weird. What kind of syntax do you need here?\r\n```\r\n...\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/collectivevariable.py\", line 325, in to_dict\r\n    dct[callable_argument] = ObjectJSON.callable_to_dict(self.cv_callable)\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/dictify.py\", line 346, in callable_to_dict\r\n    word_wrap(err, 60))\r\nRuntimeError: Cannot store function! \r\n\r\nThe function you try to save requires the following modules\r\nto be installed: ['simtk.unit'] which are not marked as\r\nsafe! You can change the list of safe modules using\r\n\r\n        FunctionCV._safe_modules.extend([\r\n            simtk.unit\r\n        ])\r\n\r\ninclude the import statement in your function like\r\n\r\n        import simtk.unit\r\n```\r\nConsidering the function contains `import simtk.unit`, this is weird:\r\n```python\r\ndef compute_cv(snapshot, center, compute_contacts):\r\n    import simtk.unit\r\n    [distances, residue_pairs] = compute_contacts(snapshot)\r\n    return distances[0] / simtk.unit.angstroms\r\n```"}}
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