From: Alexey Shvetsov Date: Tue, 28 Jul 2015 17:03:39 +0000 (+0300) Subject: Update headers, fix style for some py files X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?p=alexxy%2Fgromacs.git;a=commitdiff_plain;h=0595b4a4c763a0bc574658992081abf8b0abc3fe Update headers, fix style for some py files Change-Id: Iee373c180a280c5842ac5cee78cf47f3838c3a6d Signed-off-by: Alexey Shvetsov --- diff --git a/cmake/PythonCompile.py b/cmake/PythonCompile.py index e7cc17ee6f..4b12c13da9 100644 --- a/cmake/PythonCompile.py +++ b/cmake/PythonCompile.py @@ -1,5 +1,6 @@ # By Simon Edwards # This file is in the public domain. -import py_compile, sys +import sys +import py_compile sys.exit(py_compile.main()) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index d2f779eb45..8ca514b9c6 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2014, by the GROMACS development team, led by +# Copyright (c) 2014,2015, 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. @@ -31,7 +31,6 @@ # # To help us fund GROMACS development, we humbly ask that you cite # the research papers on the package. Check out http://www.gromacs.org. -# find_package(PythonLibrary REQUIRED) find_package(NumPy REQUIRED) diff --git a/src/python/__init__.py b/src/python/__init__.py index e69de29bb2..7af993abf7 100644 --- a/src/python/__init__.py +++ b/src/python/__init__.py @@ -0,0 +1,34 @@ +# +# 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. + diff --git a/src/python/include/numpy_conv.h b/src/python/include/numpy_conv.h index 67d04da321..3c7c5674ca 100644 --- a/src/python/include/numpy_conv.h +++ b/src/python/include/numpy_conv.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/pipeline_test.py b/src/python/pipeline_test.py index 8e2124453b..7c28ab414a 100644 --- 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): diff --git a/src/python/runner/__init__.py b/src/python/runner/__init__.py index e69de29bb2..7af993abf7 100644 --- a/src/python/runner/__init__.py +++ b/src/python/runner/__init__.py @@ -0,0 +1,34 @@ +# +# 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. + diff --git a/src/python/runner/pipeline.py b/src/python/runner/pipeline.py index 2ea912df68..48106cbb3f 100644 --- a/src/python/runner/pipeline.py +++ b/src/python/runner/pipeline.py @@ -1,6 +1,41 @@ - -from gromacs import Options, TrajectoryAnalysis -import sys, shlex +# +# 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 +import shlex +from gromacs import Options +from gromacs import TrajectoryAnalysis class GromacsPipeline(TrajectoryAnalysis.TrajectoryAnalysisModule): diff --git a/src/python/sip/definitions.sip b/src/python/sip/definitions.sip index e06e1da296..5e3a395b8a 100644 --- a/src/python/sip/definitions.sip +++ b/src/python/sip/definitions.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/options/Options.sip b/src/python/sip/options/Options.sip index f70db48284..77da1cdb24 100644 --- a/src/python/sip/options/Options.sip +++ b/src/python/sip/options/Options.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/options/abstractoption.sip b/src/python/sip/options/abstractoption.sip index 0861e92491..1723663680 100644 --- a/src/python/sip/options/abstractoption.sip +++ b/src/python/sip/options/abstractoption.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/options/basicoptions.sip b/src/python/sip/options/basicoptions.sip index d69697b5d3..91d56c9980 100644 --- a/src/python/sip/options/basicoptions.sip +++ b/src/python/sip/options/basicoptions.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/options/filenameoption.sip b/src/python/sip/options/filenameoption.sip index c3a76ab8d0..7151480d6d 100644 --- a/src/python/sip/options/filenameoption.sip +++ b/src/python/sip/options/filenameoption.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/options/ioptionscontainer.sip b/src/python/sip/options/ioptionscontainer.sip index c1c88e35f5..0d392e619e 100644 --- a/src/python/sip/options/ioptionscontainer.sip +++ b/src/python/sip/options/ioptionscontainer.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015 by the GROMACS development team, led by + * 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. diff --git a/src/python/sip/options/options.sip b/src/python/sip/options/options.sip index 115760eee3..c899989e8f 100644 --- a/src/python/sip/options/options.sip +++ b/src/python/sip/options/options.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/options/pyoptionsholder.sip b/src/python/sip/options/pyoptionsholder.sip index 0f775761d2..0b4e57412d 100644 --- a/src/python/sip/options/pyoptionsholder.sip +++ b/src/python/sip/options/pyoptionsholder.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/options/selectionoption.sip b/src/python/sip/options/selectionoption.sip index fad72544e2..40daf4abdd 100644 --- a/src/python/sip/options/selectionoption.sip +++ b/src/python/sip/options/selectionoption.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/selection/Selection.sip b/src/python/sip/selection/Selection.sip index 68592fbc49..e99dde2eb1 100644 --- a/src/python/sip/selection/Selection.sip +++ b/src/python/sip/selection/Selection.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/selection/selection.sip b/src/python/sip/selection/selection.sip index cbcc95aebc..1dafb43d92 100644 --- a/src/python/sip/selection/selection.sip +++ b/src/python/sip/selection/selection.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/string.sip b/src/python/sip/string.sip index f9a0326001..76c96c8965 100644 --- a/src/python/sip/string.sip +++ b/src/python/sip/string.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/topology/Topology.sip b/src/python/sip/topology/Topology.sip index 9c57b4d44d..2e466d47e7 100644 --- a/src/python/sip/topology/Topology.sip +++ b/src/python/sip/topology/Topology.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/topology/atoms.sip b/src/python/sip/topology/atoms.sip index 752ccb48a7..3f97896d93 100644 --- a/src/python/sip/topology/atoms.sip +++ b/src/python/sip/topology/atoms.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/topology/pstringlistwrapper.sip b/src/python/sip/topology/pstringlistwrapper.sip index 665fa3eb41..330aaaf67f 100644 --- a/src/python/sip/topology/pstringlistwrapper.sip +++ b/src/python/sip/topology/pstringlistwrapper.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/topology/topology.sip b/src/python/sip/topology/topology.sip index 1ce94d4f33..34c38b0bd9 100644 --- a/src/python/sip/topology/topology.sip +++ b/src/python/sip/topology/topology.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/trajectoryanalysis/TrajectoryAnalysis.sip b/src/python/sip/trajectoryanalysis/TrajectoryAnalysis.sip index 94c9a901e2..cbcd919b4e 100644 --- a/src/python/sip/trajectoryanalysis/TrajectoryAnalysis.sip +++ b/src/python/sip/trajectoryanalysis/TrajectoryAnalysis.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/trajectoryanalysis/analysisdata.sip b/src/python/sip/trajectoryanalysis/analysisdata.sip index 5eb1effcba..c8e0144bd0 100644 --- a/src/python/sip/trajectoryanalysis/analysisdata.sip +++ b/src/python/sip/trajectoryanalysis/analysisdata.sip @@ -1,4 +1,37 @@ - +/* + * 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. + */ class AbstractAnalysisData /NoDefaultCtors/ { %TypeHeaderCode #include diff --git a/src/python/sip/trajectoryanalysis/analysismodule.sip b/src/python/sip/trajectoryanalysis/analysismodule.sip index 504b6e38b2..cd5c65628d 100644 --- a/src/python/sip/trajectoryanalysis/analysismodule.sip +++ b/src/python/sip/trajectoryanalysis/analysismodule.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/trajectoryanalysis/analysissettings.sip b/src/python/sip/trajectoryanalysis/analysissettings.sip index 3e29c100c1..f45fed1b1c 100644 --- a/src/python/sip/trajectoryanalysis/analysissettings.sip +++ b/src/python/sip/trajectoryanalysis/analysissettings.sip @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2014, by the GROMACS development team, led by + * Copyright (c) 2014,2015, 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. diff --git a/src/python/sip/trajectoryanalysis/modules.sip b/src/python/sip/trajectoryanalysis/modules.sip index f724ef1f20..83c31f202d 100644 --- a/src/python/sip/trajectoryanalysis/modules.sip +++ b/src/python/sip/trajectoryanalysis/modules.sip @@ -1,4 +1,37 @@ - +/* + * 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. + */ template class shared_ptr /NoDefaultCtors/ { %TypeHeaderCode #include diff --git a/src/python/sip/vector.sip b/src/python/sip/vector.sip index f19846e88b..eb8f1e51be 100644 --- a/src/python/sip/vector.sip +++ b/src/python/sip/vector.sip @@ -1,3 +1,37 @@ +/* + * 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. + */ // SIP support for std::vector // by Giovanni Bajo develer.com> // Public domain diff --git a/src/python/test.py b/src/python/test.py index 67e6ecc48a..ac91337f08 100644 --- 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):