{"action":"created","issue":{"url":"https://api.github.com/repos/alchemistry/fileformat/issues/13","repository_url":"https://api.github.com/repos/alchemistry/fileformat","labels_url":"https://api.github.com/repos/alchemistry/fileformat/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/alchemistry/fileformat/issues/13/comments","events_url":"https://api.github.com/repos/alchemistry/fileformat/issues/13/events","html_url":"https://github.com/alchemistry/fileformat/issues/13","id":179051850,"number":13,"title":"Evaluate alternative formats","user":{"login":"avirshup","id":9388007,"avatar_url":"https://avatars.githubusercontent.com/u/9388007?v=3","gravatar_id":"","url":"https://api.github.com/users/avirshup","html_url":"https://github.com/avirshup","followers_url":"https://api.github.com/users/avirshup/followers","following_url":"https://api.github.com/users/avirshup/following{/other_user}","gists_url":"https://api.github.com/users/avirshup/gists{/gist_id}","starred_url":"https://api.github.com/users/avirshup/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/avirshup/subscriptions","organizations_url":"https://api.github.com/users/avirshup/orgs","repos_url":"https://api.github.com/users/avirshup/repos","events_url":"https://api.github.com/users/avirshup/events{/privacy}","received_events_url":"https://api.github.com/users/avirshup/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-09-24T21:05:57Z","updated_at":"2016-11-02T18:55:15Z","closed_at":null,"body":"Speaking personally, the best outcome of this would be to find that someone has already solved the problems we're thinking about, or at least at least has a solution that can be extended to cover this project's specific application focuses (#1 and #10)\n\nBelow is a continuously-updated list of other projects. Everything here should be with a grain of salt, as it's an attempt to glean information from many different specifications :)\n\n**MOSAIC**\nFormats: XML, HDF5 (with straightforward extensions based on the data model)\nLicense: Creative Commons 3.0\nUnits: List of supported units in spec\nDesign criteria: https://mosaic-data-model.github.io/design_criteria.html\nData stored: topology, CG info, selections (i.e., subsets of the file's data), references to other \"universes\"; \"properties\" (unclear if these are whole-system properties or atomic properties?)\nSpecification: https://mosaic-data-model.github.io/\n\n**Rich molecule format**\n_todo_\n\n**H5MD**\nType: Binary (HDF5)\nSelf-describing: yes\nDomain: molecular dynamics\nFlexible units: [yes](http://nongnu.org/h5md/modules/units.html)\nHuman readable: not without HDF5 viewer\nLicense: GPL (need to understand copyleft implications here)\n[Data stored](http://nongnu.org/h5md/h5md.html): MD state data; atoms and their connectivity. Arbitrary atom lists/groups can be defined (nothing specific for chains/residues/etc)\nSpecification: http://nongnu.org/h5md/\n\n**Amber NetCDF**\nType: Binary (HDF5)\nSelf-describing: Yes\nHuman readable: not directly (GUI viewers available)\nFlexible units: yes\nDomain: biomolecular dynamics\nData stored: Trajectory (no topology)\nSpecification: http://ambermd.org/netcdf/nctraj.xhtml\n\n**MDTraj HDF5**\nType: HDF5\nSelf-describing: Yes\nHuman readable: no\nData stored: Trajectory (+ topology as a JSON string)\nFlexible units: yes\nDomain: biomolecular dynamics\nSpecification: https://github.com/mdtraj/mdtraj/wiki/HDF5-Trajectory-Format\nNotes: This is an extension of Amber NetCDF format. FF-focused topology storage (as JSON)\n\n**Chemical Markup Language (CML)**\nType: XML\nHuman readable: yes\nSelf-describing: sort of - must adhere to a schema\nSpecification: http://www.xml-cml.org/\nFlexible units: yes\nDomain: small molecule modeling\nData stored: coordinates, molecular properties, topology w/ stereochemistry, calculation parameters, electronic wavefunctions, computational metadata (i.e. hostname, programVersion, etc.). No support for biomolecules or trajectories.\nNotes: I like this project's aims, but there's a LOT of conceptual overhead for understanding XML schema. I don't think I've ever used software that supports CML.\n\n**PDBx / MMCif**\nType: CIF (text-based, see http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax)\nSelf-describing: yes\nFlexible units: no\nDomain: Crystallography / NMR\nSpecification: http://mmcif.wwpdb.org/docs/tutorials/content/atomic-description.html\nhttp://mmcif.wwpdb.org/docs/tutorials/content/molecular-entities.html\nNotes: Vast improvement over original PDB. Medium-to-high conceptual overhead. Parsers are still hard to come by.\nData stored: everything you'd expect in a PDB file: topology + coordinates + crystallographic metadata. \n\n**Chemical JSON**\nType: JSON (text-based)\nSelf-describing: yes\nNotes: I think this is more of a proof-of-principle (implemented in Avogadro) than a mature spec, but interesting nonetheless. JSON is by far the easiest language here to read and write, both with machines and by hand.\nSpecification: http://wiki.openchemistry.org/Chemical_JSON\n"},"comment":{"url":"https://api.github.com/repos/alchemistry/fileformat/issues/comments/257964506","html_url":"https://github.com/alchemistry/fileformat/issues/13#issuecomment-257964506","issue_url":"https://api.github.com/repos/alchemistry/fileformat/issues/13","id":257964506,"user":{"login":"arose","id":272250,"avatar_url":"https://avatars.githubusercontent.com/u/272250?v=3","gravatar_id":"","url":"https://api.github.com/users/arose","html_url":"https://github.com/arose","followers_url":"https://api.github.com/users/arose/followers","following_url":"https://api.github.com/users/arose/following{/other_user}","gists_url":"https://api.github.com/users/arose/gists{/gist_id}","starred_url":"https://api.github.com/users/arose/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arose/subscriptions","organizations_url":"https://api.github.com/users/arose/orgs","repos_url":"https://api.github.com/users/arose/repos","events_url":"https://api.github.com/users/arose/events{/privacy}","received_events_url":"https://api.github.com/users/arose/received_events","type":"User","site_admin":false},"created_at":"2016-11-02T18:55:15Z","updated_at":"2016-11-02T18:55:15Z","body":"I would like to add a format we recently put into production on http://www.rcsb.org, see http://mmtf.rcsb.org/\r\n\r\n__MMTF (macromolecular transmission format)__\r\nType: messagepack/json\r\nSelf-describing: \r\nHuman readable: no\r\nData stored: coordinates, topology, some metadata\r\nFlexible units: no\r\nDomain: efficient transmission and parsing of macormolecules\r\nSpecification: https://github.com/rcsb/mmtf/blob/master/spec.md"}}
{"actor":{"display_login":"arose"}}