src/python/runner/pipeline.py

   1
   2 from gromacs import Options, TrajectoryAnalysis
   3 import sys, shlex
   4
   5 class GromacsPipeline(TrajectoryAnalysis.TrajectoryAnalysisModule):
   6
   7     def __init__(self,
   8         name="PythonPipeline",
   9         description="Pipeline of modules created with Python",
  10         modules=[],
  11         keep_datasets=False,
  12     ):
  13         super(GromacsPipeline, self).__init__(name, description)
  14
  15         self.optionsHolder = Options.PyOptionsHolder()
  16
  17         self.modules = []
  18         self.options = []
  19
  20         for module, options in modules:
  21             if not isinstance(module, TrajectoryAnalysis.TrajectoryAnalysisModule):
  22                 info_name = module + "Info"
  23                 if not hasattr(TrajectoryAnalysis, info_name):
  24                     raise ValueError("There is no module named {}".format(name))
  25
  26                 module = getattr(TrajectoryAnalysis, info_name).create()
  27
  28             options_list = [name] + shlex.split(options)
  29
  30             if keep_datasets:
  31                 for i in range(module.datasetCount()):
  32                     module.datasetFromIndex(i).requestStorage(-1)
  33
  34             self.modules.append(module)
  35             self.options.append(options_list)
  36
  37     def initOptions(self, options, settings):
  38         settings.setHelpText(self.description())
  39
  40     def getBatch(self):
  41         return self.modules
  42
  43     def getArgv(self, i):
  44         return self.options[i]
  45
  46     def initAnalysis(self, settings, top):
  47         pass
  48
  49     def analyzeFrame(self, frnr, frame, pbc, data):
  50         pass
  51
  52     def finishAnalysis(self, nframes):
  53         pass
  54
  55     def writeOutput(self):
  56         pass
  57
  58     def run(self, argv):
  59         if argv is None:
  60             argv = sys.argv
  61
  62         TrajectoryAnalysis.runAsMain(self, argv)
  63
  64 def runPipeline(argv=None, *args, **kwargs):
  65     pipeline = GromacsPipeline(*args, **kwargs)
  66     pipeline.run(argv)
  67
  68     return pipeline