Archive Trac docs atomicstructure

Docs Atomicstructure

Legacy Trac archive page imported from docs_atomicstructure. Source: https://genapp.rocks/wiki/wiki/docs_atomicstructure. Review age, links, and examples before treating as current.

atomicstructure

• currently html5 only
• based upon jsmol
• field also allows attributes:

  "height" : "1234",
  "width"  : "555",
  "jsmoladd" : "jsmol script commands"
...

• the jsmoladd scripts commands will be executed before any sent by the application

• some fun ones

• set modelkitmode true

  • opens a left-click menu with commands to move bits about etc

• set spin on

• in your executable module:

  • write your output to a file

  • give the output json id this file name prepended by the input JSON's _base_directory value.

  • e.g. jsonOutput[ 'myoutputid' ] = jsonInput[ '_base_directory' ] + "/" + filename

    • if you created a subdirectory and put the file there, you will need that path added also
    • e.g. jsonOutput[ 'myoutputid' ] = jsonInput[ '_base_directory' ] + "/" + subdirectoryname + "/" + filename

  • alternative structure to send script commands (requires svn revision >= 584)

  • e.g. in your json results

    "myoutputid" : { 
         "file" : "pdbfilename.pdb",
         "script" : "script text"
    }

• there is an example in genapptest source for genapptest/modules/data_interpolation.json for field outputpdb

• formats supported

  • any jmol supported format http://chemapps.stolaf.edu/jmol/docs/#load
  • note: the link above mentions a JSON format, which might be what we use for direct output

• scripting details https://chemapps.stolaf.edu/jmol/docs/#functions

---

• future:
  • allow direct encapsulation (i.e. put structure in json output directly)
  • allow more directives thru json output