Merge 6fa907b into 26fa6ab

AUTHORS

@@ -0,0 +1,10 @@
+Longbow was originally created by:
+
+Dr James T. Gebbie-Rayet (STFC - Daresbury Lab)
+Dr Gareth B. Shannon (University of Nottingham)
+Prof Charles A. Laughton (University of Nottingham)
+
+
+Contributors:
+
+Developers with accepted contributions should include their name below.

LICENSE

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 2017, Science and Technology Facilities Council and
+The University of Nottingham
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -1,8 +1,8 @@
-# Include the copying file
-include COPYING.txt
+# Include AUTHORS file
+include AUTHORS
 
 # Include the license file
-include LICENSE.txt
+include LICENSE
 
 # Include the readme file
 include README.rst

README.rst

@@ -38,8 +38,8 @@ supports.
 Licensing
 =========
 
-Longbow is released under the GNU GPLv2 license. A copy of this license will
-be provided with the Longbow application when it is downloaded and installed.
+Longbow is released under the BSD 3-clause license. A copy of this license is
+provided when Longbow is downloaded and installed.
 
 
 Citing

examples/README

@@ -15,13 +15,8 @@
 
 
 
-LongbowExamples contains a set of Molecular Dynamics input files users can use to learn how to use Longbow*. In LongbowExamples/how-to-run there is a list of the commands that will submit jobs on an external resource (HPC) using these files.
+LongbowExamples contains a set of Molecular Dynamics input files users can use
+to learn how to use Longbow.
 
-
-* Longbow is Copyright (C) of James T Gebbie-Rayet and Gareth B Shannon 2015.
-
-Longbow is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
-
-Longbow 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 General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with Longbow.  If not, see http://www.gnu.org/licenses/.
+In longbow-examples/how-to-run there is a list of the commands that will submit
+jobs on an external resource (HPC) using these files.

examples/how-to-run

@@ -50,7 +50,9 @@ longbow --job job.conf --verbose
 ################################################################################
 LongbowExamples/CondorSubmission
 
-In this directory, users can learn how to submit Longbow jobs to a local batch system - in this case Condor. Execute the below command on a desktop if using Condor:
+In this directory, users can learn how to submit Longbow jobs to a local batch
+system - in this case Condor. Execute the below command on a desktop if using
+Condor:
 
 condor_submit condor_desc
 

longbow/__init__.py

@@ -1,22 +1,34 @@
-# Longbow is Copyright (C) of James T Gebbie-Rayet and Gareth B Shannon 2015.
+# BSD 3-Clause License
 #
-# This file is part of the Longbow software which was developed as part of the
-# HECBioSim project (http://www.hecbiosim.ac.uk/).
+# Copyright (c) 2017, Science and Technology Facilities Council and
+# The University of Nottingham
+# All rights reserved.
 #
-# HECBioSim facilitates and supports high-end computing within the UK
-# biomolecular simulation community on resources such as ARCHER.
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
 #
-# Longbow is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 2 of the License, or (at your option) any later
-# version.
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
 #
-# Longbow 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 General Public License for more details.
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
 #
-# You should have received a copy of the GNU General Public License along with
-# Longbow.  If not, see <http://www.gnu.org/licenses/>.
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
 
 """Longbow package."""
 

longbow/apps/__init__.py

@@ -1,22 +1,34 @@
-# Longbow is Copyright (C) of James T Gebbie-Rayet and Gareth B Shannon 2015.
+# BSD 3-Clause License
 #
-# This file is part of the Longbow software which was developed as part of the
-# HECBioSim project (http://www.hecbiosim.ac.uk/).
+# Copyright (c) 2017, Science and Technology Facilities Council and
+# The University of Nottingham
+# All rights reserved.
 #
-# HECBioSim facilitates and supports high-end computing within the UK
-# biomolecular simulation community on resources such as ARCHER.
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
 #
-# Longbow is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 2 of the License, or (at your option) any later
-# version.
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
 #
-# Longbow 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 General Public License for more details.
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
 #
-# You should have received a copy of the GNU General Public License along with
-# Longbow.  If not, see <http://www.gnu.org/licenses/>.
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
 
 """This module contains the import logic for the application plugins.
 

longbow/apps/amber.py

@@ -1,22 +1,34 @@
-# Longbow is Copyright (C) of James T Gebbie-Rayet and Gareth B Shannon 2015.
+# BSD 3-Clause License
 #
-# This file is part of the Longbow software which was developed as part of the
-# HECBioSim project (http://www.hecbiosim.ac.uk/).
+# Copyright (c) 2017, Science and Technology Facilities Council and
+# The University of Nottingham
+# All rights reserved.
 #
-# HECBioSim facilitates and supports high-end computing within the UK
-# biomolecular simulation community on resources such as ARCHER.
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
 #
-# Longbow is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 2 of the License, or (at your option) any later
-# version.
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
 #
-# Longbow 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 General Public License for more details.
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
 #
-# You should have received a copy of the GNU General Public License along with
-# Longbow.  If not, see <http://www.gnu.org/licenses/>.
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
 
 """This is the AMBER plugin module.
 

longbow/apps/charmm.py

@@ -1,22 +1,34 @@
-# Longbow is Copyright (C) of James T Gebbie-Rayet and Gareth B Shannon 2015.
+# BSD 3-Clause License
 #
-# This file is part of the Longbow software which was developed as part of the
-# HECBioSim project (http://www.hecbiosim.ac.uk/).
+# Copyright (c) 2017, Science and Technology Facilities Council and
+# The University of Nottingham
+# All rights reserved.
 #
-# HECBioSim facilitates and supports high-end computing within the UK
-# biomolecular simulation community on resources such as ARCHER.
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
 #
-# Longbow is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 2 of the License, or (at your option) any later
-# version.
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
 #
-# Longbow 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 General Public License for more details.
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
 #
-# You should have received a copy of the GNU General Public License along with
-# Longbow.  If not, see <http://www.gnu.org/licenses/>.
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
 
 """This is the CHARMM plugin module.
 

longbow/apps/desmond.py

@@ -1,22 +1,34 @@
-# Longbow is Copyright (C) of James T Gebbie-Rayet and Gareth B Shannon 2015.
+# BSD 3-Clause License
 #
-# This file is part of the Longbow software which was developed as part of the
-# HECBioSim project (http://www.hecbiosim.ac.uk/).
+# Copyright (c) 2017, Science and Technology Facilities Council and
+# The University of Nottingham
+# All rights reserved.
 #
-# HECBioSim facilitates and supports high-end computing within the UK
-# biomolecular simulation community on resources such as ARCHER.
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
 #
-# Longbow is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 2 of the License, or (at your option) any later
-# version.
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
 #
-# Longbow 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 General Public License for more details.
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
 #
-# You should have received a copy of the GNU General Public License along with
-# Longbow.  If not, see <http://www.gnu.org/licenses/>.
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
 
 """This is the DESMOND plugin module.