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.doubleOption('py').description('option added from python just to check').required())
  15         options.addOption(self.optionsHolder.selectionOption('sel').description('selection option from python').required())
  16         options.addOption(self.optionsHolder.booleanOption('fail').description('fail :)'))
  17         settings.setFlag(TrajectoryAnalysis.TrajectoryAnalysisSettings.efRequireTop)
  18         print('python: inited')
  19
  20     def initAnalysis(self, settings, top):
  21         print('python: initAnalysis')
  22         print('There are {} atoms'.format(top.topology().atoms.nr))
  23         print('Topology name: {}'.format(top.topology().name))
  24
  25     def analyzeFrame(self, frnr, frame, pbc, data):
  26         sel = self.optionsHolder['sel']
  27         print('selected atoms {}, {}'.format(sel.atomCount(), sel.coordinates()[0]))
  28         print('ids: {}'.format(sel.mappedIds()[:5]))
  29         return
  30         print('python: Analyzing frame {}, {} atoms'.format(frnr, frame.natoms))
  31         print(frame.box[0], frame.box[1], frame.box[2])
  32         print(frame.x[0], frame.v[0], frame.f[0])
  33
  34     def finishAnalysis(self, nframes):
  35         print('python: Analyzed {} frames'.format(nframes))
  36
  37     def writeOutput(self):
  38         print('python: writeOutput')
  39         print('py = {}'.format(self.optionsHolder['py']))
  40         print('sel = {}'.format(self.optionsHolder['sel']))
  41
  42 TrajectoryAnalysis.runAsMain(M(), sys.argv)