{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/openmoltools/issues/201","repository_url":"https://api.github.com/repos/choderalab/openmoltools","labels_url":"https://api.github.com/repos/choderalab/openmoltools/issues/201/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/openmoltools/issues/201/comments","events_url":"https://api.github.com/repos/choderalab/openmoltools/issues/201/events","html_url":"https://github.com/choderalab/openmoltools/issues/201","id":138789051,"number":201,"title":"Lots of OpenEye warnings","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":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":15,"created_at":"2016-03-06T13:01:27Z","updated_at":"2016-03-15T17:17:08Z","closed_at":null,"body":"I'm now seeing a ton of OpenEye warnings in travis:\r\n```\r\ntest_openeye.test_charge_fail1 ... Warning: [4-(2,4-dichloro-5-methoxy-phenyl)iminio-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinolin-1-ium-3-ylidene]methyleneazanide failed due to unspecified stereochemistry with strict stereo enabled\r\nok (0.0292s)\r\ntest_openeye.test_charge_fail2 ... Warning: [4-(2,4-dichloro-5-methoxy-phenyl)iminio-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinolin-1-ium-3-ylidene]methyleneazanide failed due to unspecified stereochemistry with strict stereo enabled\r\nok (0.0284s)\r\ntest_openeye.test_charge_success1 ... Warning: BCIChargeCorrector: BCI charge corrections will not be done for\r\nWarning: [4-(2,4-dichloro-5-methoxy-phenyl)iminio-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinolin-1-ium-3-ylidene]methyleneazanide because the bcc parameter for the C33-N34 bond (BCIType 150225) is missing\r\nWarning:  Getting BCCs for [4-(2,4-dichloro-5-methoxy-phenyl)iminio-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinolin-1-ium-3-ylidene]methyleneazanide was unsuccessful; stopping the charging process for this molecule\r\nWarning:  Getting BCCs for [4-(2,4-dichloro-5-methoxy-phenyl)iminio-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinolin-1-ium-3-ylidene]methyleneazanide was unsuccessful; stopping the charging process for this molecule\r\nok (2.4720s)\r\ntest_openeye.test_charge_success2 ... Warning: BCIChargeCorrector: BCI charge corrections will not be done for\r\nWarning: [4-(2,4-dichloro-5-methoxy-phenyl)iminio-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinolin-1-ium-3-ylidene]methyleneazanide because the bcc parameter for the C33-N34 bond (BCIType 150225) is missing\r\nWarning:  Getting BCCs for [4-(2,4-dichloro-5-methoxy-phenyl)iminio-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinolin-1-ium-3-ylidene]methyleneazanide was unsuccessful; stopping the charging process for this molecule\r\nWarning:  Getting BCCs for [4-(2,4-dichloro-5-methoxy-phenyl)iminio-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinolin-1-ium-3-ylidene]methyleneazanide was unsuccessful; stopping the charging process for this molecule\r\nok (2.0829s)\r\ntest_openeye.test_binary_mixture_rename ... Warning: SelectElfDiverseConfs: elfPop.NumConfs 1 <= elfLimit 1\r\nWarning: SelectElfDiverseConfs: elfPop.NumConfs 1 <= elfLimit 1\r\n```\r\n@davidlmobley: Have you noticed these before?"},"comment":{"url":"https://api.github.com/repos/choderalab/openmoltools/issues/comments/196931255","html_url":"https://github.com/choderalab/openmoltools/issues/201#issuecomment-196931255","issue_url":"https://api.github.com/repos/choderalab/openmoltools/issues/201","id":196931255,"user":{"login":"andrrizzi","id":1682142,"avatar_url":"https://avatars.githubusercontent.com/u/1682142?v=3","gravatar_id":"","url":"https://api.github.com/users/andrrizzi","html_url":"https://github.com/andrrizzi","followers_url":"https://api.github.com/users/andrrizzi/followers","following_url":"https://api.github.com/users/andrrizzi/following{/other_user}","gists_url":"https://api.github.com/users/andrrizzi/gists{/gist_id}","starred_url":"https://api.github.com/users/andrrizzi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrrizzi/subscriptions","organizations_url":"https://api.github.com/users/andrrizzi/orgs","repos_url":"https://api.github.com/users/andrrizzi/repos","events_url":"https://api.github.com/users/andrrizzi/events{/privacy}","received_events_url":"https://api.github.com/users/andrrizzi/received_events","type":"User","site_admin":false},"created_at":"2016-03-15T17:17:08Z","updated_at":"2016-03-15T17:17:08Z","body":"Yes, thank you, this is still unclear.\r\n\r\nI don't think I'm expert enough about this topic to judge, but the `N` in the group `=C=[N-]` was being assigned a positive partial charge. I understand that the group is not an acceptable tautomeric form. I'd like to know if it safe to go ahead and run the simulation with the partial charges of the reasonable guess, or if it better for the user perspective to stop (i.e. to raise an exception) and ask the user to clarify better the molecule's form."}}