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NGL molecular viewer

• NGL provides a WebGL based molecular viewer
• examples
  • 
  • module json (note height & width must be specified, else the viewer will have no size):

     ...
     ,{
            "role"            : "output"
            ,"id"              : "nglplot"
            ,"label"           : "Example NGL"
            ,"type"            : "ngl"
            ,"height"          : "500px"
            ,"width"           : "600px"
      }
      ...

• executable JSON output

{
    "loadname"    : "myfile.pdb"
    ,"loadparams" : {
                       "ext" : "pdb"
                       ,"name" : "a name"
                       ,"asTrajectory" : true
                    }
    ,"representation" : "cartoon"

}

• executable JSON output with single-representation parameters

{
    "loadname"    : "myfile.pdb"
    ,"loadparams" : {
                       "ext" : "pdb"
                       ,"asTrajectory" : true
                    }
    ,"representation" : "cartoon"
    ,"representationParams" : {
                                  "colorScheme" : "bfactor"
                               }
}

• executable JSON output with multiple selection-specific representations

{
    "loadname"    : "myfile.pdb"
    ,"loadparams" : {
                       "ext" : "pdb"
                       ,"asTrajectory" : true
                    }
    ,"representations" : [
                             {
                                 "type" : "cartoon"
                                 ,"params" : {
                                                 "sele" : "all"
                                                 ,"color" : "blue"
                                              }
                             }
                             ,{
                                 "type" : "cartoon"
                                 ,"params" : {
                                                 "sele" : "bfactor > 0.5"
                                                 ,"color" : "red"
                                              }
                              }
                         ]
}

• notes:
  • Required:
  • "loadname" is passed to stage.loadFile()
  • Optional:
  • "loadparams" is passed as the 2nd argument to stage.loadFile()
    • "loadparams" : "ext" is an optional file extension to determine file type (if not specified in "loadname").
    • "loadparams" : "name" is an optional name for the data
    • "loadparams" : "asTrajectory" is optional, but required for multimodel PDB's to be used as trajectories
  • "representation" is an optional startup representation
    • default "cartoon"
    • possibilities:

    backbone
    ball+stick
    cartoon
    contact
    helixorient
    hyperball
    label
    licorice
    line
    point
    ribbon
    rocket
    rope
    spacefill
    surface
    trace
    tube

- "representationParams" is optional and is passed as the 2nd argument to `component.addRepresentation( type, params )`
  - use this when a single representation needs parameters such as `colorScheme`
- "representations" is an optional array of objects with:
  - "type" passed as the 1st argument to `component.addRepresentation()`
  - "params" passed as the 2nd argument to `component.addRepresentation()`
  - when present, `representations` is used instead of the single `representation` / `representationParams` form
- dynamic updates reload the current structure in the existing NGL widget
  - this supports refreshed snapshots during a run
  - it is not a true coordinate streaming transport

• TO DO:
  • add trajectory controls