{"action":"created","issue":{"url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/100","repository_url":"https://api.github.com/repos/open-forcefield-group/smarty","labels_url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/100/labels{/name}","comments_url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/100/comments","events_url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/100/events","html_url":"https://github.com/open-forcefield-group/smarty/issues/100","id":169754761,"number":100,"title":"Constraint specification for SMARTY XML ForceField","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":[{"id":394634040,"url":"https://api.github.com/repos/open-forcefield-group/smarty/labels/design%20choice","name":"design choice","color":"fbca04","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":19,"created_at":"2016-08-06T16:38:54Z","updated_at":"2016-11-23T22:44:14Z","closed_at":null,"body":"At some point, we'll need to expand `ForceField` to allow us to specify which bonds or angles should be constrained.\n\nOne way to do this is to extend the `ffxml` format to allow this to be specified via SMIRKS. For example:\n\n``` XML\n<Constraints>\n  <!-- bonds involving hydrogen -->\n  <Constraint smirks=\"[#1:1]-[*:2]\"/> <!-- add constraint between atoms 1 and 2 using equilibrium bond distance -->\n  <!-- angles involving hydrogen -->\n  <Constraint smirks=\"[#1:1]-[*:2]-[#1:3]\"/> <!-- add constraint between atoms 1 and 3 using auto-calculated distance from equilibrium bond and angles -->\n</Constraints>\n```\n"},"comment":{"url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/comments/262648156","html_url":"https://github.com/open-forcefield-group/smarty/issues/100#issuecomment-262648156","issue_url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/100","id":262648156,"user":{"login":"bannanc","id":11968541,"avatar_url":"https://avatars.githubusercontent.com/u/11968541?v=3","gravatar_id":"","url":"https://api.github.com/users/bannanc","html_url":"https://github.com/bannanc","followers_url":"https://api.github.com/users/bannanc/followers","following_url":"https://api.github.com/users/bannanc/following{/other_user}","gists_url":"https://api.github.com/users/bannanc/gists{/gist_id}","starred_url":"https://api.github.com/users/bannanc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bannanc/subscriptions","organizations_url":"https://api.github.com/users/bannanc/orgs","repos_url":"https://api.github.com/users/bannanc/repos","events_url":"https://api.github.com/users/bannanc/events{/privacy}","received_events_url":"https://api.github.com/users/bannanc/received_events","type":"User","site_admin":false},"created_at":"2016-11-23T22:44:14Z","updated_at":"2016-11-23T22:44:14Z","body":"I just got finished reading through this, I'm a little confused about the implication of the TIP water with the explicit H-H bond: \r\n\r\n> Also, just FYI, TIP water has an explicit (though artificial) bond from H1 to H2, and thus in SMARTS would be a divalent hydrogen: `[#1X2]`\r\n\r\nIf we had Tip3p water then the H-H bond would exist and `[#1X2]` would match. Assuming you just start from a water molecule then that H-H bond isn't explicitly there and the `[#1X2]` would not match, correct? My understanding is the angle pattern (`[#1:1]-[#8X2H2:2]-[#1:3]`) would then be used to indicate all three distances (not really bond lengths) would be kept constant. \r\n\r\nOtherwise this format makes sense to me. \r\n"}}
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