{"action":"created","issue":{"url":"https://api.github.com/repos/tbereau/auto_martini/issues/4","repository_url":"https://api.github.com/repos/tbereau/auto_martini","labels_url":"https://api.github.com/repos/tbereau/auto_martini/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/tbereau/auto_martini/issues/4/comments","events_url":"https://api.github.com/repos/tbereau/auto_martini/issues/4/events","html_url":"https://github.com/tbereau/auto_martini/issues/4","id":133914970,"number":4,"title":"Problems with nitriles","user":{"login":"SGenheden","id":5080718,"avatar_url":"https://avatars.githubusercontent.com/u/5080718?v=3","gravatar_id":"","url":"https://api.github.com/users/SGenheden","html_url":"https://github.com/SGenheden","followers_url":"https://api.github.com/users/SGenheden/followers","following_url":"https://api.github.com/users/SGenheden/following{/other_user}","gists_url":"https://api.github.com/users/SGenheden/gists{/gist_id}","starred_url":"https://api.github.com/users/SGenheden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SGenheden/subscriptions","organizations_url":"https://api.github.com/users/SGenheden/orgs","repos_url":"https://api.github.com/users/SGenheden/repos","events_url":"https://api.github.com/users/SGenheden/events{/privacy}","received_events_url":"https://api.github.com/users/SGenheden/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-16T08:31:00Z","updated_at":"2016-02-16T09:04:19Z","closed_at":null,"body":"Having trouble parameterising some molecules with a nitrile group. With a simple benzonitrile:\r\n\r\n`auto_martini --smi \"c1ccc(cc1)C#N\" --mol bni`\r\n\r\nI get the following error message\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"/Users/samuel/Documents/Programs/auto_martini/auto_martini\", line 1203, in <module>\r\n    ringAtomsFlat, True)\r\nValueError: need more than 0 values to unpack\r\n```"},"comment":{"url":"https://api.github.com/repos/tbereau/auto_martini/issues/comments/184586147","html_url":"https://github.com/tbereau/auto_martini/issues/4#issuecomment-184586147","issue_url":"https://api.github.com/repos/tbereau/auto_martini/issues/4","id":184586147,"user":{"login":"tbereau","id":806194,"avatar_url":"https://avatars.githubusercontent.com/u/806194?v=3","gravatar_id":"","url":"https://api.github.com/users/tbereau","html_url":"https://github.com/tbereau","followers_url":"https://api.github.com/users/tbereau/followers","following_url":"https://api.github.com/users/tbereau/following{/other_user}","gists_url":"https://api.github.com/users/tbereau/gists{/gist_id}","starred_url":"https://api.github.com/users/tbereau/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tbereau/subscriptions","organizations_url":"https://api.github.com/users/tbereau/orgs","repos_url":"https://api.github.com/users/tbereau/repos","events_url":"https://api.github.com/users/tbereau/events{/privacy}","received_events_url":"https://api.github.com/users/tbereau/received_events","type":"User","site_admin":false},"created_at":"2016-02-16T09:04:19Z","updated_at":"2016-02-16T09:04:19Z","body":"Try running from the refactor branch\r\n\r\n`git checkout refactor`\r\n\r\nthe executable is slightly different:\r\n\r\n`python auto_martini.py --smi \"c1ccc(cc1)C#N\" --mol bni`\r\n\r\nYou'll notice that if fails:\r\n\r\n> WARNING:__main__:ALOGPS can't predict fragment: N#Cc1[c][c][c][c][c]1\r\n\r\nlooks like the prediction algorithm wasn't trained against cyanide. You can always fall back on the atom-based Wildman-Crippen prediction algorithm (`--fpred`):\r\n\r\n`python auto_martini.py --smi \"c1ccc(cc1)C#N\" --mol bni --fpred --aa bni_aa.gro --cg bni_cg.gro`\r\n\r\nwhich works on my end. However, you might want to check that the bead type assigned to the cyanide group is correct (the Wildman-Crippen isn't as good a prediction algorithm as alogps).\r\n\r\nCheers,\r\nTristan"}}