{"action":"closed","issue":{"url":"https://api.github.com/repos/biojava/biojava/issues/377","labels_url":"https://api.github.com/repos/biojava/biojava/issues/377/labels{/name}","comments_url":"https://api.github.com/repos/biojava/biojava/issues/377/comments","events_url":"https://api.github.com/repos/biojava/biojava/issues/377/events","html_url":"https://github.com/biojava/biojava/issues/377","id":127762061,"number":377,"title":"Biojava structutre object not creating ligand bonds","user":{"login":"abradle","id":6000929,"avatar_url":"https://avatars.githubusercontent.com/u/6000929?v=3","gravatar_id":"","url":"https://api.github.com/users/abradle","html_url":"https://github.com/abradle","followers_url":"https://api.github.com/users/abradle/followers","following_url":"https://api.github.com/users/abradle/following{/other_user}","gists_url":"https://api.github.com/users/abradle/gists{/gist_id}","starred_url":"https://api.github.com/users/abradle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/abradle/subscriptions","organizations_url":"https://api.github.com/users/abradle/orgs","repos_url":"https://api.github.com/users/abradle/repos","events_url":"https://api.github.com/users/abradle/events{/privacy}","received_events_url":"https://api.github.com/users/abradle/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"abradle","id":6000929,"avatar_url":"https://avatars.githubusercontent.com/u/6000929?v=3","gravatar_id":"","url":"https://api.github.com/users/abradle","html_url":"https://github.com/abradle","followers_url":"https://api.github.com/users/abradle/followers","following_url":"https://api.github.com/users/abradle/following{/other_user}","gists_url":"https://api.github.com/users/abradle/gists{/gist_id}","starred_url":"https://api.github.com/users/abradle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/abradle/subscriptions","organizations_url":"https://api.github.com/users/abradle/orgs","repos_url":"https://api.github.com/users/abradle/repos","events_url":"https://api.github.com/users/abradle/events{/privacy}","received_events_url":"https://api.github.com/users/abradle/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/biojava/biojava/milestones/6","html_url":"https://github.com/biojava/biojava/milestones/BioJava%204.2.0","labels_url":"https://api.github.com/repos/biojava/biojava/milestones/6/labels","id":1172839,"number":6,"title":"BioJava 4.2.0","description":"","creator":{"login":"andreasprlic","id":187599,"avatar_url":"https://avatars.githubusercontent.com/u/187599?v=3","gravatar_id":"","url":"https://api.github.com/users/andreasprlic","html_url":"https://github.com/andreasprlic","followers_url":"https://api.github.com/users/andreasprlic/followers","following_url":"https://api.github.com/users/andreasprlic/following{/other_user}","gists_url":"https://api.github.com/users/andreasprlic/gists{/gist_id}","starred_url":"https://api.github.com/users/andreasprlic/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andreasprlic/subscriptions","organizations_url":"https://api.github.com/users/andreasprlic/orgs","repos_url":"https://api.github.com/users/andreasprlic/repos","events_url":"https://api.github.com/users/andreasprlic/events{/privacy}","received_events_url":"https://api.github.com/users/andreasprlic/received_events","type":"User","site_admin":false},"open_issues":17,"closed_issues":11,"state":"open","created_at":"2015-06-19T18:16:59Z","updated_at":"2016-01-21T17:30:09Z","due_on":"2016-02-15T08:00:00Z","closed_at":null},"comments":1,"created_at":"2016-01-20T19:15:01Z","updated_at":"2016-01-21T17:30:09Z","closed_at":"2016-01-21T17:30:09Z","body":"Hi all,\r\n\r\nThe below code prints out empty lists. It doesn't appear to be making bonds for the Ligand ZYB. I don't believe this problem is specific to 4CUP. Am I doing something wrong? Any help would be appreciated.\r\n\r\n\r\n```java\r\npackage org.trial.debug;\r\n\r\nimport java.io.IOException;\r\n\r\nimport org.biojava.nbio.structure.Atom;\r\nimport org.biojava.nbio.structure.Chain;\r\nimport org.biojava.nbio.structure.Group;\r\nimport org.biojava.nbio.structure.Structure;\r\nimport org.biojava.nbio.structure.StructureException;\r\nimport org.biojava.nbio.structure.StructureIO;\r\nimport org.biojava.nbio.structure.align.util.AtomCache;\r\nimport org.biojava.nbio.structure.io.FileParsingParameters;\r\n\r\npublic class DebugBioJava {\r\n\tpublic static void main(String[] args) throws IOException, StructureException{\r\n\t\tString pdbId = \"4CUP\";\r\n\t\tAtomCache cache = new AtomCache();\r\n\t\tcache.setUseMmCif(false);\r\n\t\tFileParsingParameters params = cache.getFileParsingParams();\r\n\t\tparams.setLoadChemCompInfo(true);\r\n\t\tparams.setCreateAtomBonds(true);\r\n\t\tcache.setFileParsingParams(params);\r\n\t\tStructureIO.setAtomCache(cache);\r\n\t\tStructure s = StructureIO.getStructure(pdbId);\r\n\t\t//Load structure without any SS assignment\r\n\t\t//\r\n\t\tfor(Chain c: s.getChains()){\r\n\t\t\tfor(Group g: c.getAtomGroups()){\r\n\t\t\t\tif(g.getPDBName().equals(\"ZYB\")){\r\n\t\t\t\t\tfor(Atom a: g.getAtoms()){\r\n\t\t\t\t\t\tSystem.out.println(a.getBonds());\r\n\t\t\t\t\t}\r\n\t\t\t\t}\r\n\t\t\t}\r\n\t\t}\r\n\t}\r\n}\r\n```\r\n\r\nOUTPUT:\r\n````\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n[]\r\n````"}}