{"action":"created","issue":{"url":"https://api.github.com/repos/cdk/depict/issues/8","repository_url":"https://api.github.com/repos/cdk/depict","labels_url":"https://api.github.com/repos/cdk/depict/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/cdk/depict/issues/8/comments","events_url":"https://api.github.com/repos/cdk/depict/issues/8/events","html_url":"https://github.com/cdk/depict/issues/8","id":300684059,"number":8,"title":"Downloaded cdkdepict 0.3 works differently than on the server","user":{"login":"sauliusg","id":10668420,"avatar_url":"https://avatars3.githubusercontent.com/u/10668420?v=4","gravatar_id":"","url":"https://api.github.com/users/sauliusg","html_url":"https://github.com/sauliusg","followers_url":"https://api.github.com/users/sauliusg/followers","following_url":"https://api.github.com/users/sauliusg/following{/other_user}","gists_url":"https://api.github.com/users/sauliusg/gists{/gist_id}","starred_url":"https://api.github.com/users/sauliusg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sauliusg/subscriptions","organizations_url":"https://api.github.com/users/sauliusg/orgs","repos_url":"https://api.github.com/users/sauliusg/repos","events_url":"https://api.github.com/users/sauliusg/events{/privacy}","received_events_url":"https://api.github.com/users/sauliusg/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2018-02-27T15:47:24Z","updated_at":"2018-02-28T09:01:33Z","closed_at":"2018-02-27T18:00:41Z","author_association":"NONE","body":"Hi,\r\nI'm trying to reproduce the http://www.simolecule.com/cdkdepict/depict.html server action locally on my host, but the local version, both from pre-compiled jars and compiled from sources, fails to parse non-kekulisable SMILES, such as 'n1cccc1' or '[Cu]12(Oc3c(C(=[N]2N=C(O1)c1ccc(O)cc1)C)cc(Br)cc3)[n]1ccccc1' ;). My locally installed version fails \"... with root cause\r\norg.openscience.cdk.exception.InvalidSmilesException: could not parse 'n1cccc1', a valid kekulé structure could not be assigned\". Compiling CDK and/or Depict from sources works exactly the same (i.e. raises exception), as does a command-line wrapper around CDK 2.1 or 2.2.\r\nWhile this behaviour apparently stems from the underlying CDK SmilesParser, and seems to be a feature, not a bug, the on-line 'cdkdepict' version mentioned above does parse these SMILES and depicts them nicely ;) (see the attached screen-shot):\r\n![screenshot from 2018-02-27 17-23-24](https://user-images.githubusercontent.com/10668420/36738342-f70fe226-1be5-11e8-8ae5-597e0458b70f.png) Does this mean that the server uses different/newer CDK libraries? If so, would it be possible to have them pushed into the GitHub repo (maybe as an experimental branch)?\r\nException messages would also be helpful to debug the case, if presented next to the broken image icon.\r\nThe platform for running the 'cdkdepict' 0.3 was:\r\n    saulius@koala depict-0.3/ $ java -version\r\n    openjdk version \"1.8.0_151\"\r\n    OpenJDK Runtime Environment (build 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12)\r\n    OpenJDK 64-Bit Server VM (build 25.151-b12, mixed mode)\r\n    saulius@koala depict-0.3/ $ uname -a\r\n    Linux koala 4.13.0-32-generic #35~16.04.1-Ubuntu SMP Thu Jan 25 10:13:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux\r\n    saulius@koala depict-0.3/ $ osname\r\n    Ubuntu-16.04\r\n\r\nSincerely,\r\nSaulius (join(\"@\", ( \"grazulis\", join(\".\", (\"ibt\",\"lt\")))) to mail me directly ;)"},"comment":{"url":"https://api.github.com/repos/cdk/depict/issues/comments/369166871","html_url":"https://github.com/cdk/depict/issues/8#issuecomment-369166871","issue_url":"https://api.github.com/repos/cdk/depict/issues/8","id":369166871,"user":{"login":"sauliusg","id":10668420,"avatar_url":"https://avatars3.githubusercontent.com/u/10668420?v=4","gravatar_id":"","url":"https://api.github.com/users/sauliusg","html_url":"https://github.com/sauliusg","followers_url":"https://api.github.com/users/sauliusg/followers","following_url":"https://api.github.com/users/sauliusg/following{/other_user}","gists_url":"https://api.github.com/users/sauliusg/gists{/gist_id}","starred_url":"https://api.github.com/users/sauliusg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sauliusg/subscriptions","organizations_url":"https://api.github.com/users/sauliusg/orgs","repos_url":"https://api.github.com/users/sauliusg/repos","events_url":"https://api.github.com/users/sauliusg/events{/privacy}","received_events_url":"https://api.github.com/users/sauliusg/received_events","type":"User","site_admin":false},"created_at":"2018-02-28T09:01:33Z","updated_at":"2018-02-28T09:01:33Z","author_association":"NONE","body":"> As to your other question, as far as I am aware the CDK Depict uses the latest and greatest version. At least I use it to test the latest functionality…\r\n\r\nI tried the leading edge :) CDK (2.1 bundle compiled from https://github.com/cdk/cdk.git master affc8d4 commit), but it also throws exception when parsing invalid SMILES, whereas your Web version does not :). Could you maybe e-mail me the CDK jar bundle from the privately, for a test? It is very difficult to search for my bugs when I can not reproduce different behaviour..."}}
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