{"action":"created","issue":{"url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/911","repository_url":"https://api.github.com/repos/opencobra/cobratoolbox","labels_url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/911/labels{/name}","comments_url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/911/comments","events_url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/911/events","html_url":"https://github.com/opencobra/cobratoolbox/pull/911","id":256962183,"number":911,"title":"Fixed mol2sdf to correctly report the number of metabolites without molfiles. Added iAF1260Molfiles to Tutorial","user":{"login":"laurentheirendt","id":20812112,"avatar_url":"https://avatars0.githubusercontent.com/u/20812112?v=4","gravatar_id":"","url":"https://api.github.com/users/laurentheirendt","html_url":"https://github.com/laurentheirendt","followers_url":"https://api.github.com/users/laurentheirendt/followers","following_url":"https://api.github.com/users/laurentheirendt/following{/other_user}","gists_url":"https://api.github.com/users/laurentheirendt/gists{/gist_id}","starred_url":"https://api.github.com/users/laurentheirendt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/laurentheirendt/subscriptions","organizations_url":"https://api.github.com/users/laurentheirendt/orgs","repos_url":"https://api.github.com/users/laurentheirendt/repos","events_url":"https://api.github.com/users/laurentheirendt/events{/privacy}","received_events_url":"https://api.github.com/users/laurentheirendt/received_events","type":"User","site_admin":false},"labels":[{"id":554296846,"url":"https://api.github.com/repos/opencobra/cobratoolbox/labels/do%20not%20merge","name":"do not merge","color":"f13d41","default":false},{"id":475074874,"url":"https://api.github.com/repos/opencobra/cobratoolbox/labels/needs%20response","name":"needs response","color":"de2080","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-09-12T08:38:07Z","updated_at":"2017-11-06T16:37:08Z","closed_at":null,"author_association":"COLLABORATOR","pull_request":{"url":"https://api.github.com/repos/opencobra/cobratoolbox/pulls/911","html_url":"https://github.com/opencobra/cobratoolbox/pull/911","diff_url":"https://github.com/opencobra/cobratoolbox/pull/911.diff","patch_url":"https://github.com/opencobra/cobratoolbox/pull/911.patch"},"body":"Continuation of PR #909.\r\n\r\nFurther review is needed.\r\n\r\ncc: @djinnome"},"comment":{"url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/comments/342206498","html_url":"https://github.com/opencobra/cobratoolbox/pull/911#issuecomment-342206498","issue_url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/911","id":342206498,"user":{"login":"djinnome","id":144210,"avatar_url":"https://avatars3.githubusercontent.com/u/144210?v=4","gravatar_id":"","url":"https://api.github.com/users/djinnome","html_url":"https://github.com/djinnome","followers_url":"https://api.github.com/users/djinnome/followers","following_url":"https://api.github.com/users/djinnome/following{/other_user}","gists_url":"https://api.github.com/users/djinnome/gists{/gist_id}","starred_url":"https://api.github.com/users/djinnome/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/djinnome/subscriptions","organizations_url":"https://api.github.com/users/djinnome/orgs","repos_url":"https://api.github.com/users/djinnome/repos","events_url":"https://api.github.com/users/djinnome/events{/privacy}","received_events_url":"https://api.github.com/users/djinnome/received_events","type":"User","site_admin":false},"created_at":"2017-11-06T16:37:08Z","updated_at":"2017-11-06T16:37:08Z","author_association":"NONE","body":"Hi @Gpreciat , I am not sure who changed the molecule charges. I used the molFiles from the original iAF1260 paper:  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1911197/bin/msb4100155-s7.zip\r\n\r\nAlso, it shouldn't actually matter what the charges are in the molFile, because the charges are recalculated for every pH environment  using `cxcalc` in MarvinBeans\r\n\r\n  (By the way, if you find an open source alternative to MarvinBeans for calculating the major microspecies, let me know!)\r\n\r\nSincerely,\r\n\r\nJeremy"}}
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