+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2015, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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+
import sys
-from gromacs import Options, TrajectoryAnalysis
+from gromacs import Options
+from gromacs import TrajectoryAnalysis
class M(TrajectoryAnalysis.TrajectoryAnalysisModule):
def __init__(self):
def initOptions(self, options, settings):
print('python: initOptions')
+ settings.setHelpText('A stupid test module')
+
self.optionsHolder = Options.PyOptionsHolder()
- options.setDescription('A stupid test module')
- options.addOption(self.optionsHolder.doubleOption('py').description('option added from python just to check').required())
- options.addOption(self.optionsHolder.selectionOption('sel').description('selection option from python').required())
- options.addOption(self.optionsHolder.booleanOption('fail').description('fail :)'))
+ options.addOption(self.optionsHolder.selectionOption('sel').required())
+ options.addOption(self.optionsHolder.fileNameOption('file').defaultBasename('test').description('filename from python to rule them all').outputFile().required().filetype(Options.eftGenericData))
settings.setFlag(TrajectoryAnalysis.TrajectoryAnalysisSettings.efRequireTop)
+
+ self.angle = TrajectoryAnalysis.AngleInfo.create()
+
print('python: inited')
+ def getBatch(self):
+ print('python: getBatch')
+ return [self.angle]
+
+ def getArgv(self, i):
+ print('python: getArgv')
+ if i == 0:
+ #First element of list should be module name -- gets discarded by parser anyway
+ return ["gangle", "-group1", "Backbone", "-oav", "angles.xvg"]
+
def initAnalysis(self, settings, top):
print('python: initAnalysis')
print('There are {} atoms'.format(top.topology().atoms.nr))
print('Topology name: {}'.format(top.topology().name))
+ #Tell GROMACS to keep last frame in storage, required in analyzeFrame()
+ self.angle.datasetFromIndex(1).requestStorage(1)
+
def analyzeFrame(self, frnr, frame, pbc, data):
sel = self.optionsHolder['sel']
- print('selected atoms {}, {}'.format(sel.atomCount(), sel.coordinates()[0]))
- print('ids: {}'.format(sel.mappedIds()[:5]))
- return
- print('python: Analyzing frame {}, {} atoms'.format(frnr, frame.natoms))
- print(frame.box[0], frame.box[1], frame.box[2])
- print(frame.x[0], frame.v[0], frame.f[0])
+
+ dataset = self.angle.datasetFromIndex(1)
+
+ print('frame =', frnr, ', columnCount =', dataset.columnCount(), ', y =', dataset.getDataFrame(frnr).y(0))
def finishAnalysis(self, nframes):
print('python: Analyzed {} frames'.format(nframes))
def writeOutput(self):
print('python: writeOutput')
- print('py = {}'.format(self.optionsHolder['py']))
- print('sel = {}'.format(self.optionsHolder['sel']))
+ print('file = {}'.format(self.optionsHolder['file']))
+
+ fo = open(self.optionsHolder['file'], 'w')
+ fo.write('Test output\n')
TrajectoryAnalysis.runAsMain(M(), sys.argv)