This is help for version 1.0.14.11.28 or newer. The help text for other versions can be viewed using the --help command when running the application.

Technical details

Where to find MotiveQuery

MotiveQuery is freely available online since May 2014 at http://ncbr.muni.cz/MotiveQuery. There is no login requirement for accessing MotiveQuery.

What you need in order to run MotiveQuery

Up to date internet browser with WebGL support.
JavaScript enabled.

Check if your browser is WebGL and Javascript compliant.

Note that you can run MotiveQuery and download the results even if your browser doesn't support WebGL. WebGL is only necessary for the 3D visualization functionality.

In some older browsers, the interactive user guide which provides help for the GUI interface does not work optimally.

Running the Offline Service

The service can be executed using the command (latest .NET Framework required):

WebChemistry.MotiveQuery.Service.exe workingFolder configuration.json

In Linux (where available) and MacOS, the latest version the Mono Framework must be used to run the application:

mono WebChemistry.MotiveQuery.Service.exe workingFolder configuration.json

Alternatively, on Linux and MacOS, an official version of .NET Framework should become available during 2015.

Configuration

The configuration is specified using the JSON format.

Configuration Example

This is the general shape of the JSON input configuration.

{
  "InputFolders": [
    "c:\\TestData\\PDB\\SampleSet1"
  ],
  "Queries": [
    {
      "Id": "my_id",
      "QueryString": "Residues(\"NAG\")"
    }
  ],
  "StatisticsOnly": false,
  "CSAPath": "c:\\data\\csa.dat",
  "MaxParallelism": 8
}

There has to be exactly one configuration file for each validation run. Every value, as well as settings' names, is surrounded in quotation marks (" " or ' '). Backslashes (\) have to be escaped (\\). File system paths can be absolute as well as relative (/ works as well in paths).

Attributes

InputFolders [ String[] ]

Queries [ QueryInfo[] ]

StatisticsOnly [ Boolean ]

CSAPath [ String ]

MaxParallelism [ Int32 ]

General Output Structure

WorkingDirectory - Working directory of the application.

result - Directory containing the result of the computation.

log.txt - Contains the console output of the application.
status.json - Contains general information of the computation (running time, version, etc.).