src/python/test.py

   1 import sys
   2 from gromacs import Options, TrajectoryAnalysis
   3
   4 class M(TrajectoryAnalysis.TrajectoryAnalysisModule):
   5     def __init__(self):
   6         super(M, self).__init__("a", "a")
   7
   8     def initOptions(self, options, settings):
   9         print('python: initOptions')
  10
  11         self.optionsHolder = Options.PyOptionsHolder()
  12
  13         options.setDescription('A stupid test module')
  14         options.addOption(self.optionsHolder.selectionOption('sel').required())
  15         options.addOption(self.optionsHolder.fileNameOption('file').defaultBasename('test').description('filename from python to rule them all').outputFile().required().filetype(Options.eftGenericData))
  16         settings.setFlag(TrajectoryAnalysis.TrajectoryAnalysisSettings.efRequireTop)
  17
  18         self.angle = TrajectoryAnalysis.AngleInfo.create()
  19
  20         print('python: inited')
  21
  22     def getBatch(self):
  23         print('python: getBatch')
  24         return [self.angle]
  25
  26     def getArgv(self, i):
  27         print('python: getArgv')
  28         if i == 0:
  29             #First element of list should be module name -- gets discarded by parser anyway
  30             return ["gangle", "-group1", "Backbone", "-oav", "angles.xvg"]
  31
  32     def initAnalysis(self, settings, top):
  33         print('python: initAnalysis')
  34         print('There are {} atoms'.format(top.topology().atoms.nr))
  35         print('Topology name: {}'.format(top.topology().name))
  36
  37         #Tell GROMACS to keep last frame in storage, required in analyzeFrame()
  38         self.angle.datasetFromIndex(1).requestStorage(1)
  39
  40     def analyzeFrame(self, frnr, frame, pbc, data):
  41         sel = self.optionsHolder['sel']
  42
  43         dataset = self.angle.datasetFromIndex(1)
  44
  45         print('frame =', frnr, ', columnCount =', dataset.columnCount(), ', y =', dataset.getDataFrame(frnr).y(0))
  46
  47     def finishAnalysis(self, nframes):
  48         print('python: Analyzed {} frames'.format(nframes))
  49
  50     def writeOutput(self):
  51         print('python: writeOutput')
  52         print('file = {}'.format(self.optionsHolder['file']))
  53
  54         fo = open(self.optionsHolder['file'], 'w')
  55         fo.write('Test output\n')
  56
  57 TrajectoryAnalysis.runAsMain(M(), sys.argv)