{"action":"created","issue":{"url":"https://api.github.com/repos/pandegroup/openmm/issues/1443","repository_url":"https://api.github.com/repos/pandegroup/openmm","labels_url":"https://api.github.com/repos/pandegroup/openmm/issues/1443/labels{/name}","comments_url":"https://api.github.com/repos/pandegroup/openmm/issues/1443/comments","events_url":"https://api.github.com/repos/pandegroup/openmm/issues/1443/events","html_url":"https://github.com/pandegroup/openmm/issues/1443","id":144305071,"number":1443,"title":"Add optional bond order to Topology object?","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":4,"created_at":"2016-03-29T15:44:01Z","updated_at":"2016-03-30T22:13:05Z","closed_at":null,"body":"In working toward making OpenMM more friendly toward small molecules and nonstandard residues, we've run into some nontrivial difficulties with the representation in `Topology` that relies only on connectivity and elemental atomic identities. Given this information alone, it makes it difficult to assign bond orders for parameterizing small molecules or nonstandard residues on the fly. In fact, if some protons are missing, it makes it impossible to do so without knowing the total charge of the residue.\r\n\r\nI wonder what people think about adding an (optional) bond order to the `Topology` object bonds. If this information is provided (e.g. when loading through `mol2` or other formats that explicitly provide bond order), this can be used to infer missing protons more reliably even for nonstandard residues, or avoid the use of the Antechamber `bondtype` program to guess bond orders for generating small molecule parameters. Again, this would be fully optional, but could be used by a few file readers (such as `mol2`, `SDF`, `PDBML`, etc.) or by looking up in the [chemical component dictionary](http://ligand-expo.rcsb.org/ld-download.html) to fill in bond orders."},"comment":{"url":"https://api.github.com/repos/pandegroup/openmm/issues/comments/203662875","html_url":"https://github.com/pandegroup/openmm/issues/1443#issuecomment-203662875","issue_url":"https://api.github.com/repos/pandegroup/openmm/issues/1443","id":203662875,"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},"created_at":"2016-03-30T22:13:05Z","updated_at":"2016-03-30T22:13:05Z","body":"I don't claim to understand the PDBML/mmCIF formats either. They seem to be documented in a not-particularly-clear way. I'll see if I can bug the Rutgers RCSB folks at some point for clarification about what bond order information is actually specified.\r\n\r\nThere may be more clarity on what is needed here as we make more rapid progress on making OpenMM more small molecule friendly in the coming weeks. There may still be a way to get by without this feature, but let's see if there is any further input from others too."}}