Add example and install for them

Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5d7a1c2807b3d84c294943646079cdbedbfb1fcc..92784e7b121ff7ee4d4d40b6287ae12a7cb2c841 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -26,7 +26,6 @@ list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 project(GROMACS-PyAPI)
 
-
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
@@ -36,4 +35,9 @@ find_package(GROMACS 2016)
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
 include_directories(${CMAKE_SOURCE_DIR}/stub_headers)
 
+file(GLOB GROMACS_PYAPI_MISC README COPYING)
+install(FILES ${GROMACS_PYAPI_MISC}
+       DESTINATION ${CMAKE_INSTALL_PREFIX}/share/gromacs-pyapi)
+
 add_subdirectory(src)
+add_subdirectory(examples)

diff --git a/README b/README
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
new file mode 100644 (file)
index 0000000..b0e29a5
--- /dev/null
+++ b/examples/CMakeLists.txt
@@ -0,0 +1,26 @@
+#
+# This file is part of the GROMACS-PyAPI package.
+#
+# Copyright (c) 2014,2015,
+# by Maks Koltsov <maks@omrb.pnpi.spb.ru> and
+# by Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
+#
+# GROMACS-PyAPI 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-PyAPI 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.
+
+file(GLOB GROMACS_PYAPI_EXAMPLES *.py)
+install(FILES ${GROMACS_PYAPI_EXAMPLES}
+       DESTINATION ${CMAKE_INSTALL_PREFIX}/share/gromacs-pyapi)
+

diff --git a/examples/example_pyapi.py b/examples/example_pyapi.py
new file mode 100755 (executable)
index 0000000..16720b0
--- /dev/null
+++ b/examples/example_pyapi.py
@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2015,2016, 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__()
+
+    def initOptions(self, options, settings):
+        print('python: initOptions')
+
+        settings.setHelpText('A stupid test module')
+
+        self.optionsHolder = Options.PyOptionsHolder()
+
+        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 :)'))
+        settings.setFlag(TrajectoryAnalysis.TrajectoryAnalysisSettings.efRequireTop)
+        print('python: inited')
+
+    def initAnalysis(self, settings, top):
+        print('python: initAnalysis')
+        print('There are {} atoms'.format(top.topology().atoms.nr))
+        print('Topology name: {}'.format(top.topology().name))
+
+    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])
+
+    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']))
+
+if __name__ == '__main__':
+    TrajectoryAnalysis.TrajectoryAnalysisCommandLineRunner.runAsMain(M(), sys.argv)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index aecdfeeaf6e3ae88f1be40856997b2add0d6d850..8523674c700cfab413653572231659d1ba02a9e0 100644 (file)
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS-PyAPI package.
 #
-# Copyright (c) 2014,2015,2016,2014,2015,
+# Copyright (c) 2014,2015,
 # by Maks Koltsov <maks@omrb.pnpi.spb.ru> and
 # by Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
 #