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 5c01936423f86ae9f99eaf3117adcfb8486eb1b2..ac91337f085c25e3f99b6ad2e1c82c6c96495f6a 100644 (file)
--- a/src/python/test.py
+++ b/src/python/test.py
@@ -1,31 +1,93 @@
+#
+# 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
 from gromacs import TrajectoryAnalysis
 
 class M(TrajectoryAnalysis.TrajectoryAnalysisModule):
     def __init__(self):
-        super(M, self).__init__(b"a", b"a")
+        super(M, self).__init__("a", "a")
 
     def initOptions(self, options, settings):
         print('python: initOptions')
-        options.setDescription(b'A stupid test module')
-        #settings.setFlag(TrajectoryAnalysis.TrajectoryAnalysisSettings.efRequireTop)
+
+        settings.setHelpText('A stupid test module')
+
+        self.optionsHolder = Options.PyOptionsHolder()
+
+        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):
-        print('python: Analyzing frame {}, {} atoms'.format(frnr, frame.natoms))
-        #print(frame.box[0,0], frame.box[0,1], frame.box[0,2])
-        print(pbc.box[0], pbc.box[1], pbc.box[2])
+        sel = self.optionsHolder['sel']
+
+        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('file = {}'.format(self.optionsHolder['file']))
 
-m = M()
+        fo = open(self.optionsHolder['file'], 'w')
+        fo.write('Test output\n')
 
-runner = TrajectoryAnalysis.TrajectoryAnalysisCommandLineRunner(m)
-print(runner.run(sys.argv))
+TrajectoryAnalysis.runAsMain(M(), sys.argv)