Update headers, fix style for some py files

[alexxy/gromacs.git] / src / python / test.py

diff --git a/src/python/test.py b/src/python/test.py
index 24a17e5cab4d96b33a60312932b4f4e0a4edef18..ac91337f085c25e3f99b6ad2e1c82c6c96495f6a 100644 (file)
--- a/src/python/test.py
+++ b/src/python/test.py
@@ -1,5 +1,40 @@
+#
+# 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
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
 import sys
-from gromacs import Options, TrajectoryAnalysis
+from gromacs import Options
+from gromacs import TrajectoryAnalysis
 
 class M(TrajectoryAnalysis.TrajectoryAnalysisModule):
     def __init__(self):
@@ -8,35 +43,51 @@ class M(TrajectoryAnalysis.TrajectoryAnalysisModule):
     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)