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     ):
  12         super(GromacsPipeline, self).__init__(name, description)
  13
  14         self.optionsHolder = Options.PyOptionsHolder()
  15
  16         self.modules = []
  17         self.options = []
  18
  19         for module, options in modules:
  20             if not isinstance(module, TrajectoryAnalysis.TrajectoryAnalysisModule):
  21                 info_name = module + "Info"
  22                 if not hasattr(TrajectoryAnalysis, info_name):
  23                     raise ValueError("There is no module named {}".format(name))
  24
  25                 module = getattr(TrajectoryAnalysis, info_name).create()
  26
  27             options_list = [name] + shlex.split(options)
  28
  29             self.modules.append(module)
  30             self.options.append(options_list)
  31
  32     def initOptions(self, options, settings):
  33         options.setDescription(self.description())
  34
  35     def getBatch(self):
  36         return self.modules
  37
  38     def getArgv(self, i):
  39         return self.options[i]
  40
  41     def initAnalysis(self, settings, top):
  42         pass
  43
  44     def analyzeFrame(self, frnr, frame, pbc, data):
  45         pass
  46
  47     def finishAnalysis(self, nframes):
  48         pass
  49
  50     def writeOutput(self):
  51         pass
  52
  53     def run(self, argv):
  54         if argv is None:
  55             argv = sys.argv
  56
  57         TrajectoryAnalysis.runAsMain(self, argv)
  58
  59 def runPipeline(name="PythonPipeline", description="Pipeline of modules created with Python", modules=[], argv=None):
  60     pipeline = GromacsPipeline(name, description, modules)
  61     pipeline.run(argv)