src/python/pipeline_test.py

   1
   2 from gromacs import TrajectoryAnalysis
   3 from runner.pipeline import GromacsPipeline, runPipeline
   4
   5 class Test(TrajectoryAnalysis.TrajectoryAnalysisModule):
   6
   7     def __init__(self):
   8         super(Test, self).__init__("test", "test")
   9
  10     def initOptions(self, options, settings):
  11         options.setDescription(self.description())
  12
  13     def getBatch(self):
  14         return self.modules
  15
  16     def getArgv(self, i):
  17         return self.options[i]
  18
  19     def initAnalysis(self, settings, top):
  20         pass
  21
  22     def analyzeFrame(self, frnr, frame, pbc, data):
  23         print("Analyzing frame in Test module")
  24
  25     def finishAnalysis(self, nframes):
  26         pass
  27
  28     def writeOutput(self):
  29         pass
  30
  31 modules = [
  32     ("Angle", "-group1 System -oav angles.xvg"),
  33     (Test(), ""),
  34     (TrajectoryAnalysis.SasaInfo.create(), "-surface DNA"),
  35 ]
  36
  37 runPipeline(name="Pipeline", modules=modules)
  38