{"action":"created","issue":{"url":"https://api.github.com/repos/MonZop/BioBlender/issues/32","labels_url":"https://api.github.com/repos/MonZop/BioBlender/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/MonZop/BioBlender/issues/32/comments","events_url":"https://api.github.com/repos/MonZop/BioBlender/issues/32/events","html_url":"https://github.com/MonZop/BioBlender/issues/32","id":70391701,"number":32,"title":"The Rewrite: BB2 Redux","user":{"login":"zeffii","id":619340,"avatar_url":"https://avatars.githubusercontent.com/u/619340?v=3","gravatar_id":"","url":"https://api.github.com/users/zeffii","html_url":"https://github.com/zeffii","followers_url":"https://api.github.com/users/zeffii/followers","following_url":"https://api.github.com/users/zeffii/following{/other_user}","gists_url":"https://api.github.com/users/zeffii/gists{/gist_id}","starred_url":"https://api.github.com/users/zeffii/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zeffii/subscriptions","organizations_url":"https://api.github.com/users/zeffii/orgs","repos_url":"https://api.github.com/users/zeffii/repos","events_url":"https://api.github.com/users/zeffii/events{/privacy}","received_events_url":"https://api.github.com/users/zeffii/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":138,"created_at":"2015-04-23T11:45:56Z","updated_at":"2015-06-29T10:52:01Z","closed_at":null,"body":"Over the next couple of days (unless something unforeseen happens) I have time to make a start with  building the add-on from scratch. Getting it to match the working features of BB2 will take a while. It's difficult to put a time frame on it until the process gets rolling. \r\n\r\nThe decision to start from scratch is not done in haste. I think some of the responders on this repository have expressed similar feelings about how to proceed. There's lots that can be taken from the current code-base, but a lot that I really want to sanitize and arrange into separate files. The core of this was written when Blender 2.5 was still young and the API not very well defined, and prone to convoluted solutions.\r\n\r\nIf I can reach feature parity and structure the code better then I will consider it a success, speeding up the import (and avoiding recursive updates) is not my first priority, making it easier for others to contribute is far more important.\r\n\r\nTicks indicates functionality seems to be restored for that panel, certainly report any issues with those sectons. The unticked sections have had no major checks done other than suppressing import errors. The section labelled `next` is either being worked on or that's where the most recent code changes have taken place. \r\n\r\n- [x] gui_panel_ep.py\r\n- [x] gui_panel_mlp.py\r\n- [ ] gui_panel_nma_viz.py\r\n- [ ] gui_panel_output_animation.py\r\n- [x] gui_panel_pdb_import.py\r\n- [ ] gui_panel_pdb_output.py `<---next`\r\n- [ ] gui_panel_physics_sim.py\r\n- [x] gui_panel_view.py"},"comment":{"url":"https://api.github.com/repos/MonZop/BioBlender/issues/comments/116604340","html_url":"https://github.com/MonZop/BioBlender/issues/32#issuecomment-116604340","issue_url":"https://api.github.com/repos/MonZop/BioBlender/issues/32","id":116604340,"user":{"login":"MonZop","id":10231334,"avatar_url":"https://avatars.githubusercontent.com/u/10231334?v=3","gravatar_id":"","url":"https://api.github.com/users/MonZop","html_url":"https://github.com/MonZop","followers_url":"https://api.github.com/users/MonZop/followers","following_url":"https://api.github.com/users/MonZop/following{/other_user}","gists_url":"https://api.github.com/users/MonZop/gists{/gist_id}","starred_url":"https://api.github.com/users/MonZop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MonZop/subscriptions","organizations_url":"https://api.github.com/users/MonZop/orgs","repos_url":"https://api.github.com/users/MonZop/repos","events_url":"https://api.github.com/users/MonZop/events{/privacy}","received_events_url":"https://api.github.com/users/MonZop/received_events","type":"User","site_admin":false},"created_at":"2015-06-29T10:52:01Z","updated_at":"2015-06-29T10:52:01Z","body":"Once again, I am going back to a panel that was already 'closed'. \r\nOne of the possible ways to look at a moleucle, is by using the Van der Waals spheres. This was encoded as a choice in the import panel, but it woudl better fit in the BB view panel.\r\nThe result should be that, when Vad der Waals is selcted, each atom sphere, instead of having its 'atomic' or 'covalent' radius, should be represented by a sphere with tis VdW radius (typically much larger that the covalent). Spheres will naturally compenetrate, like this \r\n![pbti_vdw](https://cloud.githubusercontent.com/assets/10231334/8406534/8ff07d4a-1e5d-11e5-8266-9564932c8da9.png)\r\n\r\n\r\n\r\nThe VdW sphere is the one used for calculating the surface by the rolling probe algorithm.\r\n"}}