{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/perses/issues/61","labels_url":"https://api.github.com/repos/choderalab/perses/issues/61/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/perses/issues/61/comments","events_url":"https://api.github.com/repos/choderalab/perses/issues/61/events","html_url":"https://github.com/choderalab/perses/issues/61","id":122588205,"number":61,"title":"Topology proposals and system construction","user":{"login":"pgrinaway","id":4674712,"avatar_url":"https://avatars.githubusercontent.com/u/4674712?v=3","gravatar_id":"","url":"https://api.github.com/users/pgrinaway","html_url":"https://github.com/pgrinaway","followers_url":"https://api.github.com/users/pgrinaway/followers","following_url":"https://api.github.com/users/pgrinaway/following{/other_user}","gists_url":"https://api.github.com/users/pgrinaway/gists{/gist_id}","starred_url":"https://api.github.com/users/pgrinaway/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pgrinaway/subscriptions","organizations_url":"https://api.github.com/users/pgrinaway/orgs","repos_url":"https://api.github.com/users/pgrinaway/repos","events_url":"https://api.github.com/users/pgrinaway/events{/privacy}","received_events_url":"https://api.github.com/users/pgrinaway/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/choderalab/perses/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":40,"created_at":"2015-12-16T19:53:45Z","updated_at":"2016-01-14T23:54:03Z","closed_at":null,"body":"General question--how should topology proposals be organized, and how should they be matched with `System` construction?\r\n\r\nCurrently, under the small molecule scheme, there is:\r\n\r\n* `Transformation`\r\n   * `SmallMoleculeTransformation`\r\n       * `SingleSmallMolecule`\r\n       * `SmallMoleculeProteinComplex`\r\n\r\nSo, it's grouped by the task of constructing systems. However, @jchodera points out that it's wise to group by the type of proposal (again, using small molecules as an example):\r\n\r\n* `Transformation`\r\n   * `SmallMoleculeTransformation`\r\n      * `LibrarySmallMoleculeTransformation`\r\n      * `SyntheticAccessbilityTransformation`\r\n       ...etc.\r\n\r\nThoughts on this?"},"comment":{"url":"https://api.github.com/repos/choderalab/perses/issues/comments/171820745","html_url":"https://github.com/choderalab/perses/issues/61#issuecomment-171820745","issue_url":"https://api.github.com/repos/choderalab/perses/issues/61","id":171820745,"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":"2016-01-14T23:54:03Z","updated_at":"2016-01-14T23:54:03Z","body":"@pgrinaway if this class structure looks good, can you and @juliebehr take a stab at implementing a skeleton on Friday?  We should really get something basic up and running just to make sure we haven't forgotten something important with the design.  Then we can come back to concentrating on the sampler contents."}}