Update headers, fix style for some py files

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

diff --git a/src/python/pipeline_test.py b/src/python/pipeline_test.py
index 1aaedd57bf15d15b12af25ff816713f942a45539..7c28ab414ac8c6a0c1cc4a07d29b9cccc2a098b5 100644 (file)
--- a/src/python/pipeline_test.py
+++ b/src/python/pipeline_test.py
@@ -1,6 +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.
 
 from gromacs import TrajectoryAnalysis
-from runner.pipeline import GromacsPipeline, runPipeline
+from runner.pipeline import GromacsPipeline
+from runner.pipeline import runPipeline
 
 class Test(TrajectoryAnalysis.TrajectoryAnalysisModule):
 
@@ -8,7 +42,7 @@ class Test(TrajectoryAnalysis.TrajectoryAnalysisModule):
         super(Test, self).__init__("test", "test")
 
     def initOptions(self, options, settings):
-        options.setDescription(self.description())
+        settings.setHelpText(self.description())
 
     def getBatch(self):
         return self.modules
@@ -34,5 +68,7 @@ modules = [
     (TrajectoryAnalysis.SasaInfo.create(), "-surface DNA"),
 ]
 
-runPipeline(name="Pipeline", modules=modules)
-
+pipeline = runPipeline(name="Pipeline", modules=modules, keep_datasets=True)
+dataset = pipeline.modules[0].datasetFromIndex(1)
+for i in range(dataset.frameCount()):
+    print('frame =', i, ', columnCount =', dataset.columnCount(), ', y =', dataset.getDataFrame(i).y(0))