{"action":"created","issue":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/401","labels_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/401/labels{/name}","comments_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/401/comments","events_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/401/events","html_url":"https://github.com/ReactionMechanismGenerator/RMG-Py/issues/401","id":89858019,"number":401,"title":"SMILES string [C] interpreted as quintuplet C with 4 radicals","user":{"login":"rwest","id":93807,"avatar_url":"https://avatars.githubusercontent.com/u/93807?v=3","gravatar_id":"","url":"https://api.github.com/users/rwest","html_url":"https://github.com/rwest","followers_url":"https://api.github.com/users/rwest/followers","following_url":"https://api.github.com/users/rwest/following{/other_user}","gists_url":"https://api.github.com/users/rwest/gists{/gist_id}","starred_url":"https://api.github.com/users/rwest/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rwest/subscriptions","organizations_url":"https://api.github.com/users/rwest/orgs","repos_url":"https://api.github.com/users/rwest/repos","events_url":"https://api.github.com/users/rwest/events{/privacy}","received_events_url":"https://api.github.com/users/rwest/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-06-21T03:25:38Z","updated_at":"2016-01-22T21:17:04Z","closed_at":null,"body":"A thermo search for \r\n```\r\nmultiplicity 1\r\n1 C u0 p2 c0\r\n```\r\nfinds a match in the primary thermo library (and a bad estimate via group additivity).\r\n\r\nA thermo search for \r\n```\r\nmultiplicity 3\r\n1 C u2 p1 c0\r\n```\r\nfinds a few matches (including another bad group additive estimate)\r\n\r\nHowever, the SMILES string `[C]` is interpreted as \r\n```\r\nmultiplicity 5\r\n1 C u4 p0 c0\r\n```\r\nwhich causes RMG to crash, because there's no such thing as four radicals according to the HBI radical tree, and there's no other way to guess the thermo.\r\n\r\nTwo thoughts, maybe both should be implemented:\r\n 1. [ ] 1. Allow quad-radicals in the HBI database, so at least it doesn't crash.\r\n 2. [ ] 2. Change it so that the SMILES `[C]` is interpreted as the most stable electronic state of a single carbon atom (the triplet?)\r\n"},"comment":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/comments/174051606","html_url":"https://github.com/ReactionMechanismGenerator/RMG-Py/issues/401#issuecomment-174051606","issue_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/401","id":174051606,"user":{"login":"bslakman","id":2792693,"avatar_url":"https://avatars.githubusercontent.com/u/2792693?v=3","gravatar_id":"","url":"https://api.github.com/users/bslakman","html_url":"https://github.com/bslakman","followers_url":"https://api.github.com/users/bslakman/followers","following_url":"https://api.github.com/users/bslakman/following{/other_user}","gists_url":"https://api.github.com/users/bslakman/gists{/gist_id}","starred_url":"https://api.github.com/users/bslakman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bslakman/subscriptions","organizations_url":"https://api.github.com/users/bslakman/orgs","repos_url":"https://api.github.com/users/bslakman/repos","events_url":"https://api.github.com/users/bslakman/events{/privacy}","received_events_url":"https://api.github.com/users/bslakman/received_events","type":"User","site_admin":false},"created_at":"2016-01-22T21:17:04Z","updated_at":"2016-01-22T21:17:04Z","body":"Bumping this up, still an issue when searching [C] on the website (or [Si]). Perhaps I should hack the interpretation of [Si] as it seems you have done on your branch for [C], @rwest? And/or globally forbid `Si u4` ?"}}