2 from gromacs import TrajectoryAnalysis
3 from runner.pipeline import GromacsPipeline, runPipeline
5 class Test(TrajectoryAnalysis.TrajectoryAnalysisModule):
8 super(Test, self).__init__("test", "test")
10 def initOptions(self, options, settings):
11 settings.setHelpText(self.description())
17 return self.options[i]
19 def initAnalysis(self, settings, top):
22 def analyzeFrame(self, frnr, frame, pbc, data):
23 print("Analyzing frame in Test module")
25 def finishAnalysis(self, nframes):
28 def writeOutput(self):
32 ("Angle", "-group1 System -oav angles.xvg"),
34 (TrajectoryAnalysis.SasaInfo.create(), "-surface DNA"),
37 pipeline = runPipeline(name="Pipeline", modules=modules, keep_datasets=True)
38 dataset = pipeline.modules[0].datasetFromIndex(1)
39 for i in range(dataset.frameCount()):
40 print('frame =', i, ', columnCount =', dataset.columnCount(), ', y =', dataset.getDataFrame(i).y(0))