{"action":"created","issue":{"url":"https://api.github.com/repos/openforcefield/openforcefield/issues/121","repository_url":"https://api.github.com/repos/openforcefield/openforcefield","labels_url":"https://api.github.com/repos/openforcefield/openforcefield/issues/121/labels{/name}","comments_url":"https://api.github.com/repos/openforcefield/openforcefield/issues/121/comments","events_url":"https://api.github.com/repos/openforcefield/openforcefield/issues/121/events","html_url":"https://github.com/openforcefield/openforcefield/issues/121","id":373584261,"node_id":"MDU6SXNzdWUzNzM1ODQyNjE=","number":121,"title":"Implement support for PDB+(MOL/SMI) in Molecule.from_file","user":{"login":"j-wags","id":16329175,"node_id":"MDQ6VXNlcjE2MzI5MTc1","avatar_url":"https://avatars2.githubusercontent.com/u/16329175?v=4","gravatar_id":"","url":"https://api.github.com/users/j-wags","html_url":"https://github.com/j-wags","followers_url":"https://api.github.com/users/j-wags/followers","following_url":"https://api.github.com/users/j-wags/following{/other_user}","gists_url":"https://api.github.com/users/j-wags/gists{/gist_id}","starred_url":"https://api.github.com/users/j-wags/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/j-wags/subscriptions","organizations_url":"https://api.github.com/users/j-wags/orgs","repos_url":"https://api.github.com/users/j-wags/repos","events_url":"https://api.github.com/users/j-wags/events{/privacy}","received_events_url":"https://api.github.com/users/j-wags/received_events","type":"User","site_admin":false},"labels":[{"id":574114608,"node_id":"MDU6TGFiZWw1NzQxMTQ2MDg=","url":"https://api.github.com/repos/openforcefield/openforcefield/labels/enhancement","name":"enhancement","color":"84b6eb","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-10-24T17:05:18Z","updated_at":"2018-10-25T22:11:10Z","closed_at":null,"author_association":"NONE","body":"Currently I've made Molecule.from_file() raise an exception if the user passes in a PDB file and asks for it to be read by a RDKitToolkitWrapper. This is because RDKit can not perceive bond orders/aromaticity from PDB CONECT records or geometry (which is dangerous to begin with). \r\n\r\nHowever, it seems to be possible for RDKit to load coordinates from a PDB, and then get bond information from a MOL or SMI file of the same molecule. This could be a useful input method. \r\n\r\nMore information: https://github.com/rdkit/rdkit/issues/1031#issuecomment-240308113"},"comment":{"url":"https://api.github.com/repos/openforcefield/openforcefield/issues/comments/433222914","html_url":"https://github.com/openforcefield/openforcefield/issues/121#issuecomment-433222914","issue_url":"https://api.github.com/repos/openforcefield/openforcefield/issues/121","id":433222914,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMzIyMjkxNA==","user":{"login":"j-wags","id":16329175,"node_id":"MDQ6VXNlcjE2MzI5MTc1","avatar_url":"https://avatars2.githubusercontent.com/u/16329175?v=4","gravatar_id":"","url":"https://api.github.com/users/j-wags","html_url":"https://github.com/j-wags","followers_url":"https://api.github.com/users/j-wags/followers","following_url":"https://api.github.com/users/j-wags/following{/other_user}","gists_url":"https://api.github.com/users/j-wags/gists{/gist_id}","starred_url":"https://api.github.com/users/j-wags/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/j-wags/subscriptions","organizations_url":"https://api.github.com/users/j-wags/orgs","repos_url":"https://api.github.com/users/j-wags/repos","events_url":"https://api.github.com/users/j-wags/events{/privacy}","received_events_url":"https://api.github.com/users/j-wags/received_events","type":"User","site_admin":false},"created_at":"2018-10-25T22:11:10Z","updated_at":"2018-10-25T22:11:10Z","author_association":"NONE","body":"Thanks for the lead, @davidlmobley  -- posting this here for my own reference: https://github.com/openforcefield/openforcefield/blob/master/openforcefield/typing/engines/smirnoff/forcefield.py#L329\r\n\r\nI'll poke around a bit to see if OE has an equivalent to the RDKit thing, and email OE if not.\r\n\r\nYes -- I think letting folks make molecules from a PDB file alone is risky, and worth discussion (broad usability vs. potential mistakes). Let's chat about this tomorrow in Irvine."}}
{"actor":{"display_login":"j-wags"}}