{"action":"created","comment":{"url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/comments/49533397","id":49533397,"diff_hunk":"@@ -0,0 +1,461 @@\n+\n+\n+#\n+# JD: adopted from 'pytopol' from https://github.com/resal81/PyTopol\n+#\n+\n+class System(object):\n+    def __init__(self):\n+        self.molecules = tuple([])\n+\n+        self.atomtypes        = []\n+        self.bondtypes        = []\n+        self.nonbond_params   = []\n+        self.angletypes       = []\n+        self.dihedraltypes    = []\n+        self.impropertypes    = []\n+        self.cmaptypes        = []\n+        self.interactiontypes = []\n+        self.pairtypes        = []\n+        self.constrainttypes  = []\n+        self.forcefield=  None\n+\n+        self.information = {} # like 'atomtypes': self.atomtypes\n+\n+\n+\n+class Molecule(object):\n+\n+    def __init__(self):\n+        self.chains    = []\n+        self.atoms     = []\n+        self.residues  = []\n+\n+        self.bonds     = []\n+        self.angles    = []\n+        self.dihedrals = []\n+        self.impropers = []\n+\n+        self.cmaps     = []\n+        self.pairs     = []\n+        self.exclusion_numb = None  # 0, 1, 2, ..\n+        self.virtual_sites3 = []\n+        self.exclusions = []\n+        self.settles    = []\n+        self.constraints= []\n+","path":"gromacs/fileformats/blocks.py","position":133,"original_position":46,"commit_id":"e97eb383ac470cbad977fc725e7943f8a80258a1","original_commit_id":"07d3a24dcf118041d2d9af652aa47ba9efb87f9d","user":{"login":"orbeckst","id":237980,"avatar_url":"https://avatars.githubusercontent.com/u/237980?v=3","gravatar_id":"","url":"https://api.github.com/users/orbeckst","html_url":"https://github.com/orbeckst","followers_url":"https://api.github.com/users/orbeckst/followers","following_url":"https://api.github.com/users/orbeckst/following{/other_user}","gists_url":"https://api.github.com/users/orbeckst/gists{/gist_id}","starred_url":"https://api.github.com/users/orbeckst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/orbeckst/subscriptions","organizations_url":"https://api.github.com/users/orbeckst/orgs","repos_url":"https://api.github.com/users/orbeckst/repos","events_url":"https://api.github.com/users/orbeckst/events{/privacy}","received_events_url":"https://api.github.com/users/orbeckst/received_events","type":"User","site_admin":false},"body":"@MichalKononenko , don't worry!!! Code review is frank and it is always very helpful to have multiple pairs of eyes. Thanks for contributing to the project!","created_at":"2016-01-12T23:52:31Z","updated_at":"2016-01-12T23:52:31Z","html_url":"https://github.com/Becksteinlab/GromacsWrapper/pull/25#discussion_r49533397","pull_request_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/25","_links":{"self":{"href":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/comments/49533397"},"html":{"href":"https://github.com/Becksteinlab/GromacsWrapper/pull/25#discussion_r49533397"},"pull_request":{"href":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/25"}}},"pull_request":{"url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/25","id":53629957,"html_url":"https://github.com/Becksteinlab/GromacsWrapper/pull/25","diff_url":"https://github.com/Becksteinlab/GromacsWrapper/pull/25.diff","patch_url":"https://github.com/Becksteinlab/GromacsWrapper/pull/25.patch","issue_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/issues/25","number":25,"state":"closed","locked":false,"title":"Itp reader","user":{"login":"jandom","id":395931,"avatar_url":"https://avatars.githubusercontent.com/u/395931?v=3","gravatar_id":"","url":"https://api.github.com/users/jandom","html_url":"https://github.com/jandom","followers_url":"https://api.github.com/users/jandom/followers","following_url":"https://api.github.com/users/jandom/following{/other_user}","gists_url":"https://api.github.com/users/jandom/gists{/gist_id}","starred_url":"https://api.github.com/users/jandom/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jandom/subscriptions","organizations_url":"https://api.github.com/users/jandom/orgs","repos_url":"https://api.github.com/users/jandom/repos","events_url":"https://api.github.com/users/jandom/events{/privacy}","received_events_url":"https://api.github.com/users/jandom/received_events","type":"User","site_admin":false},"body":"hi Oli, \r\n\r\nI've had this feature in gromacs wrapper for a long time now... it's time to push out and give back to the community. it comes with a number of tests (bash scripts and python scripts) that check both the gromacs energies (mdrun-rerun) and consistency of the itp/top files produced\r\n\r\nCheers, \r\n\r\n- Jan","created_at":"2015-12-14T22:13:51Z","updated_at":"2016-01-12T23:52:31Z","closed_at":"2015-12-18T21:46:10Z","merged_at":"2015-12-18T21:46:10Z","merge_commit_sha":"0ec0efd1e366dc6fe40b08c1ec683bfd101583cd","assignee":{"login":"orbeckst","id":237980,"avatar_url":"https://avatars.githubusercontent.com/u/237980?v=3","gravatar_id":"","url":"https://api.github.com/users/orbeckst","html_url":"https://github.com/orbeckst","followers_url":"https://api.github.com/users/orbeckst/followers","following_url":"https://api.github.com/users/orbeckst/following{/other_user}","gists_url":"https://api.github.com/users/orbeckst/gists{/gist_id}","starred_url":"https://api.github.com/users/orbeckst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/orbeckst/subscriptions","organizations_url":"https://api.github.com/users/orbeckst/orgs","repos_url":"https://api.github.com/users/orbeckst/repos","events_url":"https://api.github.com/users/orbeckst/events{/privacy}","received_events_url":"https://api.github.com/users/orbeckst/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/25/commits","review_comments_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/25/comments","review_comment_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/comments{/number}","comments_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/issues/25/comments","statuses_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/statuses/e97eb383ac470cbad977fc725e7943f8a80258a1","head":{"label":"jandom:itp-reader","ref":"itp-reader","sha":"e97eb383ac470cbad977fc725e7943f8a80258a1","user":{"login":"jandom","id":395931,"avatar_url":"https://avatars.githubusercontent.com/u/395931?v=3","gravatar_id":"","url":"https://api.github.com/users/jandom","html_url":"https://github.com/jandom","followers_url":"https://api.github.com/users/jandom/followers","following_url":"https://api.github.com/users/jandom/following{/other_user}","gists_url":"https://api.github.com/users/jandom/gists{/gist_id}","starred_url":"https://api.github.com/users/jandom/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jandom/subscriptions","organizations_url":"https://api.github.com/users/jandom/orgs","repos_url":"https://api.github.com/users/jandom/repos","events_url":"https://api.github.com/users/jandom/events{/privacy}","received_events_url":"https://api.github.com/users/jandom/received_events","type":"User","site_admin":false},"repo":{"id":47986241,"name":"GromacsWrapper","full_name":"jandom/GromacsWrapper","owner":{"login":"jandom","id":395931,"avatar_url":"https://avatars.githubusercontent.com/u/395931?v=3","gravatar_id":"","url":"https://api.github.com/users/jandom","html_url":"https://github.com/jandom","followers_url":"https://api.github.com/users/jandom/followers","following_url":"https://api.github.com/users/jandom/following{/other_user}","gists_url":"https://api.github.com/users/jandom/gists{/gist_id}","starred_url":"https://api.github.com/users/jandom/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jandom/subscriptions","organizations_url":"https://api.github.com/users/jandom/orgs","repos_url":"https://api.github.com/users/jandom/repos","events_url":"https://api.github.com/users/jandom/events{/privacy}","received_events_url":"https://api.github.com/users/jandom/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/jandom/GromacsWrapper","description":"GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into python scripts. This is generally superior to shell scripts because of python’s better error handling and superior data structures. It also allows for modularization and code re-use. In addition, commands, warnings and errors are logged to a file so that there exists a complete history of what has been done.","fork":true,"url":"https://api.github.com/repos/jandom/GromacsWrapper","forks_url":"https://api.github.com/repos/jandom/GromacsWrapper/forks","keys_url":"https://api.github.com/repos/jandom/GromacsWrapper/keys{/key_id}","collaborators_url":"https://api.github.com/repos/jandom/GromacsWrapper/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/jandom/GromacsWrapper/teams","hooks_url":"https://api.github.com/repos/jandom/GromacsWrapper/hooks","issue_events_url":"https://api.github.com/repos/jandom/GromacsWrapper/issues/events{/number}","events_url":"https://api.github.com/repos/jandom/GromacsWrapper/events","assignees_url":"https://api.github.com/repos/jandom/GromacsWrapper/assignees{/user}","branches_url":"https://api.github.com/repos/jandom/GromacsWrapper/branches{/branch}","tags_url":"https://api.github.com/repos/jandom/GromacsWrapper/tags","blobs_url":"https://api.github.com/repos/jandom/GromacsWrapper/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/jandom/GromacsWrapper/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/jandom/GromacsWrapper/git/refs{/sha}","trees_url":"https://api.github.com/repos/jandom/GromacsWrapper/git/trees{/sha}","statuses_url":"https://api.github.com/repos/jandom/GromacsWrapper/statuses/{sha}","languages_url":"https://api.github.com/repos/jandom/GromacsWrapper/languages","stargazers_url":"https://api.github.com/repos/jandom/GromacsWrapper/stargazers","contributors_url":"https://api.github.com/repos/jandom/GromacsWrapper/contributors","subscribers_url":"https://api.github.com/repos/jandom/GromacsWrapper/subscribers","subscription_url":"https://api.github.com/repos/jandom/GromacsWrapper/subscription","commits_url":"https://api.github.com/repos/jandom/GromacsWrapper/commits{/sha}","git_commits_url":"https://api.github.com/repos/jandom/GromacsWrapper/git/commits{/sha}","comments_url":"https://api.github.com/repos/jandom/GromacsWrapper/comments{/number}","issue_comment_url":"https://api.github.com/repos/jandom/GromacsWrapper/issues/comments{/number}","contents_url":"https://api.github.com/repos/jandom/GromacsWrapper/contents/{+path}","compare_url":"https://api.github.com/repos/jandom/GromacsWrapper/compare/{base}...{head}","merges_url":"https://api.github.com/repos/jandom/GromacsWrapper/merges","archive_url":"https://api.github.com/repos/jandom/GromacsWrapper/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/jandom/GromacsWrapper/downloads","issues_url":"https://api.github.com/repos/jandom/GromacsWrapper/issues{/number}","pulls_url":"https://api.github.com/repos/jandom/GromacsWrapper/pulls{/number}","milestones_url":"https://api.github.com/repos/jandom/GromacsWrapper/milestones{/number}","notifications_url":"https://api.github.com/repos/jandom/GromacsWrapper/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/jandom/GromacsWrapper/labels{/name}","releases_url":"https://api.github.com/repos/jandom/GromacsWrapper/releases{/id}","created_at":"2015-12-14T16:14:49Z","updated_at":"2015-12-14T16:14:50Z","pushed_at":"2015-12-21T20:44:55Z","git_url":"git://github.com/jandom/GromacsWrapper.git","ssh_url":"git@github.com:jandom/GromacsWrapper.git","clone_url":"https://github.com/jandom/GromacsWrapper.git","svn_url":"https://github.com/jandom/GromacsWrapper","homepage":"http://gromacswrapper.readthedocs.org","size":10972,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"develop"}},"base":{"label":"Becksteinlab:develop","ref":"develop","sha":"128aed729c3857950db6031d4c4c43eef8d8d7ef","user":{"login":"Becksteinlab","id":11325701,"avatar_url":"https://avatars.githubusercontent.com/u/11325701?v=3","gravatar_id":"","url":"https://api.github.com/users/Becksteinlab","html_url":"https://github.com/Becksteinlab","followers_url":"https://api.github.com/users/Becksteinlab/followers","following_url":"https://api.github.com/users/Becksteinlab/following{/other_user}","gists_url":"https://api.github.com/users/Becksteinlab/gists{/gist_id}","starred_url":"https://api.github.com/users/Becksteinlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Becksteinlab/subscriptions","organizations_url":"https://api.github.com/users/Becksteinlab/orgs","repos_url":"https://api.github.com/users/Becksteinlab/repos","events_url":"https://api.github.com/users/Becksteinlab/events{/privacy}","received_events_url":"https://api.github.com/users/Becksteinlab/received_events","type":"Organization","site_admin":false},"repo":{"id":597114,"name":"GromacsWrapper","full_name":"Becksteinlab/GromacsWrapper","owner":{"login":"Becksteinlab","id":11325701,"avatar_url":"https://avatars.githubusercontent.com/u/11325701?v=3","gravatar_id":"","url":"https://api.github.com/users/Becksteinlab","html_url":"https://github.com/Becksteinlab","followers_url":"https://api.github.com/users/Becksteinlab/followers","following_url":"https://api.github.com/users/Becksteinlab/following{/other_user}","gists_url":"https://api.github.com/users/Becksteinlab/gists{/gist_id}","starred_url":"https://api.github.com/users/Becksteinlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Becksteinlab/subscriptions","organizations_url":"https://api.github.com/users/Becksteinlab/orgs","repos_url":"https://api.github.com/users/Becksteinlab/repos","events_url":"https://api.github.com/users/Becksteinlab/events{/privacy}","received_events_url":"https://api.github.com/users/Becksteinlab/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/Becksteinlab/GromacsWrapper","description":"GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into python scripts. This is generally superior to shell scripts because of python’s better error handling and superior data structures. It also allows for modularization and code re-use. In addition, commands, warnings and errors are logged to a file so that there exists a complete history of what has been done.","fork":false,"url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper","forks_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/forks","keys_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/keys{/key_id}","collaborators_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/teams","hooks_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/hooks","issue_events_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/issues/events{/number}","events_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/events","assignees_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/assignees{/user}","branches_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/branches{/branch}","tags_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/tags","blobs_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/git/refs{/sha}","trees_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/git/trees{/sha}","statuses_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/statuses/{sha}","languages_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/languages","stargazers_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/stargazers","contributors_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/contributors","subscribers_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/subscribers","subscription_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/subscription","commits_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/commits{/sha}","git_commits_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/git/commits{/sha}","comments_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/comments{/number}","issue_comment_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/issues/comments{/number}","contents_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/contents/{+path}","compare_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/compare/{base}...{head}","merges_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/merges","archive_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/downloads","issues_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/issues{/number}","pulls_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls{/number}","milestones_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/milestones{/number}","notifications_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/labels{/name}","releases_url":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/releases{/id}","created_at":"2010-04-06T14:08:26Z","updated_at":"2015-12-20T03:43:15Z","pushed_at":"2015-12-18T21:46:10Z","git_url":"git://github.com/Becksteinlab/GromacsWrapper.git","ssh_url":"git@github.com:Becksteinlab/GromacsWrapper.git","clone_url":"https://github.com/Becksteinlab/GromacsWrapper.git","svn_url":"https://github.com/Becksteinlab/GromacsWrapper","homepage":"http://gromacswrapper.readthedocs.org","size":10997,"stargazers_count":35,"watchers_count":35,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":8,"mirror_url":null,"open_issues_count":11,"forks":8,"open_issues":11,"watchers":35,"default_branch":"develop"}},"_links":{"self":{"href":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/25"},"html":{"href":"https://github.com/Becksteinlab/GromacsWrapper/pull/25"},"issue":{"href":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/issues/25"},"comments":{"href":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/issues/25/comments"},"review_comments":{"href":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/25/comments"},"review_comment":{"href":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/pulls/25/commits"},"statuses":{"href":"https://api.github.com/repos/Becksteinlab/GromacsWrapper/statuses/e97eb383ac470cbad977fc725e7943f8a80258a1"}}}}