diff --git a/CHANGELOG b/CHANGELOG
index d3c472d6fbee538b8b947d7b2896a94eeebf0916..879c3a6ca5fe7c62c2a0760b5352336420d6fea9 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -8,6 +8,7 @@ Changelog
Release 1.3.0
--------------------------------------------------------------------------------
+* Apply Apache Version 2.0 License to the project
* 2010 Dunbrack rotamer library has been replaced by an own backbone dependent
rotamer library. All scripts required to reproduce the data are in
extras/data_generation/rotamer_library
diff --git a/COPYING.BSD b/COPYING.BSD
deleted file mode 100644
index 655966c9db44962696bd54dc2766a3f3626010e9..0000000000000000000000000000000000000000
--- a/COPYING.BSD
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- Copyright (c) 2011, Intel Corporation. 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 Intel Corporation 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 OWNER 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.
-*/
diff --git a/COPYING.README b/COPYING.README
deleted file mode 100644
index 74e3823187fd997f265bf17dfd0105ff0f9a548f..0000000000000000000000000000000000000000
--- a/COPYING.README
+++ /dev/null
@@ -1,2 +0,0 @@
-Some files contain third-party code under BSD licenses, whence the other
-COPYING.* files here.
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..c90fd010a07f1e1e6de3e5c1004a1bc2ffba9edf
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,210 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
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+ "Derivative Works" shall mean any work, whether in Source or Object
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+ "Contribution" shall mean any work of authorship, including
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+ communication on electronic mailing lists, source code control systems,
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+ "Contributor" shall mean Licensor and any individual or Legal Entity
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+ (b) You must cause any modified files to carry prominent notices
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+ (c) You must retain, in the Source form of any Derivative Works
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+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
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+
+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+
+ProMod3 bundles the file "FindEigen3.cmake", which is availabe under a
+"2-clause BSD" license. For details, see cmake_support/FindEigen3.cmake.
+
+ProMod3 bundles the file "cmake.py", which is available under a
+"3-clause BSD" license. For details, see doc/cmake.py and
+doc/Copyright_cmake.py.txt
diff --git a/NOTICE b/NOTICE
new file mode 100644
index 0000000000000000000000000000000000000000..adde9934022d9560b0d600e6028d4b878b9650a1
--- /dev/null
+++ b/NOTICE
@@ -0,0 +1,10 @@
+ProMod3 - A Versatile Homology Modelling Toolbox
+Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+ Biozentrum - University of Basel
+
+ProMod3 is developed in the Schwede Lab by Gabriel Studer, Gerardo Tauriello,
+Stefan Bienert, Marco Biasino, Niklaus Johner
+
+If you find this software useful, please cite:
+TO BE PUBLISHED
+
diff --git a/actions/pm-build-model b/actions/pm-build-model
index 6dfa741e6d95e09d48c89775af31a76205fcea65..4170252f5270c4a539423499dd9b8abc8756cbd6 100755
--- a/actions/pm-build-model
+++ b/actions/pm-build-model
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''
Automatically build a model from alignments and template structures.
diff --git a/actions/pm-build-rawmodel b/actions/pm-build-rawmodel
index 7b5260e39c6554e1765ac928033982afa375ac89..c86000142fc3983cf6ba665ff87e8ddf7231164b 100755
--- a/actions/pm-build-rawmodel
+++ b/actions/pm-build-rawmodel
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''
Create a very basic raw model from alignments and template structures.
Conserved parts are copied from the template and an incomplete pdb file is
diff --git a/actions/pm-build-sidechains b/actions/pm-build-sidechains
index c7ceb24428b799893f2be30ed23434f046d3ae50..72a0ddfc6a57d9bdca6fd07d70269d47f570abce 100644
--- a/actions/pm-build-sidechains
+++ b/actions/pm-build-sidechains
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''
Automatically (re-)construct sidechains in a protein model.
diff --git a/actions/pm-help b/actions/pm-help
index 274026ad1e9c616a8bee12fbbd03688f8b560c99..5c44cc63b796ff0e300f87f6e8468ac6f093b4cc 100755
--- a/actions/pm-help
+++ b/actions/pm-help
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''
Just list all actions (pm-.* files) available.
'''
diff --git a/actions/tests/test_action_build-model.py b/actions/tests/test_action_build-model.py
index a0889fd0c048c720c04d8ec7d4c07fba01f22047..a4b33c83f6a12a40c3432e34f50fc0db9835b46c 100644
--- a/actions/tests/test_action_build-model.py
+++ b/actions/tests/test_action_build-model.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for the 'build-model' action.
"""
diff --git a/actions/tests/test_action_build-rawmodel.py b/actions/tests/test_action_build-rawmodel.py
index 3f222c62a0644597920c1d7654764deb2e94a818..3f9af6d9762e9c893c5de5565ba0493be52c4b9c 100644
--- a/actions/tests/test_action_build-rawmodel.py
+++ b/actions/tests/test_action_build-rawmodel.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for the 'build-rawmodel' action.
"""
diff --git a/actions/tests/test_action_help.py b/actions/tests/test_action_help.py
index 74f24159ca4209d9211f6762a4c9279f9e9ce3cd..98309e33ea01711751e865279383e43146e2c3c9 100644
--- a/actions/tests/test_action_help.py
+++ b/actions/tests/test_action_help.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for the 'help' action.
diff --git a/actions/tests/test_actions.py b/actions/tests/test_actions.py
index 243d47b0d969ce518b7f7a552a8c62aa511ea9a2..f84622aae3cf8653e77d9db65ef24f93ee6e54ba 100644
--- a/actions/tests/test_actions.py
+++ b/actions/tests/test_actions.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
unittest.TestCase class providing common functionality for testing actions.
"""
diff --git a/config/src/config.hh.in b/config/src/config.hh.in
index d5fd0ccef3fb4510eae5051b87fa758eb9356295..b864eb0aaf25ac8b75030c3dbe9c0db27002392e 100644
--- a/config/src/config.hh.in
+++ b/config/src/config.hh.in
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/*
DO NOT EDIT the '.hh' file, it is processed from a template '.hh.in' by CMake.
*/
diff --git a/core/doc/geometry.rst b/core/doc/geometry.rst
index a17ed803c9741d48462b70316b702da726079eb7..1ac82fac9c1ecc650be29cd7a099f122ed7a6a5a 100644
--- a/core/doc/geometry.rst
+++ b/core/doc/geometry.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Geometry functions
================================================================================
diff --git a/core/doc/graph_minimizer.rst b/core/doc/graph_minimizer.rst
index fb8b8986cdb02ab1237e4fcfe6154a1472a371f1..a38bca5895963caf439339bf5e57af6459d10847 100644
--- a/core/doc/graph_minimizer.rst
+++ b/core/doc/graph_minimizer.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Graph Minimizer
================================================================================
diff --git a/core/doc/helper.rst b/core/doc/helper.rst
index 03d2cef127c61cb16af4680f5580673c34dae2e7..6684d1247ae7c8a53785187b4dd24a4b38737ac0 100644
--- a/core/doc/helper.rst
+++ b/core/doc/helper.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.core.helper` - Shared Functionality For the Everything
================================================================================
diff --git a/core/doc/index.rst b/core/doc/index.rst
index 2af5fca9cace92deef375d4857a1c9b55f9ec0d5..91b0d9c39c77212b3747e804b1a12191f422a213 100644
--- a/core/doc/index.rst
+++ b/core/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.core` - ProMod3 Core Functionality
================================================================================
diff --git a/core/doc/pm3argparse.rst b/core/doc/pm3argparse.rst
index 927faf547e89cc54e508fa38abfbf18b39fb217b..f6a048252ec82ce7dabbb48da87a242e26d82aa4 100644
--- a/core/doc/pm3argparse.rst
+++ b/core/doc/pm3argparse.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.core.pm3argparse` - Parsing Command Lines
================================================================================
diff --git a/core/doc/runtime_profiling.rst b/core/doc/runtime_profiling.rst
index 07c51ad5bb447b99aaf0335a1cd5f8e48d4a5c75..44bd8621a4ad7a5b77b185f5a9be069afbc9440c 100644
--- a/core/doc/runtime_profiling.rst
+++ b/core/doc/runtime_profiling.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Runtime profiling
================================================================================
diff --git a/core/doc/setcompoundschemlib.rst b/core/doc/setcompoundschemlib.rst
index fb0223432967ffc2ed53d542191c52fce4fb770b..2c6e660ffb8e1cf6d4d3df93a7f16fda04340724 100644
--- a/core/doc/setcompoundschemlib.rst
+++ b/core/doc/setcompoundschemlib.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:func:`~promod3.SetCompoundsChemlib`
================================================================================
diff --git a/core/init/__init__.py.in b/core/init/__init__.py.in
index 13cbe40a2ada8bb58cbb9a62a540424e485baf83..3be41dac459e2ba3cbeed1f8ae70cecb281470c9 100644
--- a/core/init/__init__.py.in
+++ b/core/init/__init__.py.in
@@ -1,3 +1,18 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
# enable access to loop and modelling via "import promod3"
import promod3.core
import promod3.sidechain
diff --git a/core/pymod/__init__.py b/core/pymod/__init__.py
index 4254903896c35f8649996983219c43382bb03390..1eac336f15bb63c7f87c2b62c281dbcb444572be 100644
--- a/core/pymod/__init__.py
+++ b/core/pymod/__init__.py
@@ -1,2 +1,18 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from _core import *
from _filecache import FileCache
diff --git a/core/pymod/_filecache.py b/core/pymod/_filecache.py
index 7fb9e5e2671124b914b2cec628ac91f50d8ffbd3..26b25b2484e3d0f5c428ad8452e0ae581b420c2d 100644
--- a/core/pymod/_filecache.py
+++ b/core/pymod/_filecache.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os
import shutil
diff --git a/core/pymod/export_geom.cc b/core/pymod/export_geom.cc
index c00233c513d754f8bfc31ec0b1aa105e3350e507..b26d5dba8f0bea9980182ac7804b461994ba9c5c 100644
--- a/core/pymod/export_geom.cc
+++ b/core/pymod/export_geom.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/core/message.hh>
diff --git a/core/pymod/export_graph_minimizer.cc b/core/pymod/export_graph_minimizer.cc
index bd301c84f7a3289d6ee1f3f9e91f8975be0718f7..a652c9a9ca37786161badd2e0acd1f0e63465414 100644
--- a/core/pymod/export_graph_minimizer.cc
+++ b/core/pymod/export_graph_minimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/graph_minimizer.hh>
diff --git a/core/pymod/export_runtime_profiling.cc b/core/pymod/export_runtime_profiling.cc
index 7386a4af9bc0e7f9aed7c0f61ed564cf0cc39ac7..aa61d4881968cafed2fdbb676567c72e29cd831e 100644
--- a/core/pymod/export_runtime_profiling.cc
+++ b/core/pymod/export_runtime_profiling.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/shared_ptr.hpp>
diff --git a/core/pymod/helper.py b/core/pymod/helper.py
index 91e9d6a5783805caca7b10f2ffe94dbdb01ef77f..3d6d6a09b58b8428804bf6c23f0017d620431e7f 100644
--- a/core/pymod/helper.py
+++ b/core/pymod/helper.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Uncategorised functions which may come handy at several places.
"""
diff --git a/core/pymod/pm3argparse.py b/core/pymod/pm3argparse.py
index 318d2230af86b81d54a3a1e1929267cbde054859..d4c9643f23532260f831e265e98178271792b129 100644
--- a/core/pymod/pm3argparse.py
+++ b/core/pymod/pm3argparse.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Extensions for the argparse module.
"""
diff --git a/core/pymod/wrap_core.cc b/core/pymod/wrap_core.cc
index ae1381eb24b990738ffa5c5751665f231856ff2f..8891cf7a2b2d814d96a36ce1cdce4fa0a7c852e4 100644
--- a/core/pymod/wrap_core.cc
+++ b/core/pymod/wrap_core.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_geom();
diff --git a/core/src/check_io.hh b/core/src/check_io.hh
index 8ddb610ad84e8a779eedd9725a38ddb071cec7bb..e4013eca3009ec9a26f0f77d912644c13dd954fc 100644
--- a/core/src/check_io.hh
+++ b/core/src/check_io.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines procedures to check validity of binary files.
/// (see portableIO doc for details)
diff --git a/core/src/cluster.cc b/core/src/cluster.cc
index 3c579730429acd631911538e2df574101ff955cf..d9bbd65e15696fe12875208f7d4d2c078956d786 100644
--- a/core/src/cluster.cc
+++ b/core/src/cluster.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/cluster.hh>
#include <promod3/core/message.hh>
diff --git a/core/src/cluster.hh b/core/src/cluster.hh
index 5c86bf02796e6566ba7fbcdbc3fef71ec655a46d..d9d475d35e921a5dbee3af30e9af51bb4394f00f 100644
--- a/core/src/cluster.hh
+++ b/core/src/cluster.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_CLUSTER_HH
#define PROMOD_LOOP_CLUSTER_HH
diff --git a/core/src/dynamic_spatial_organizer.hh b/core/src/dynamic_spatial_organizer.hh
index ca2b710dc288080681c89675fc6c20e63edb94e0..9565e49e3f1471e3f23d95bd9d74d5da6f988cf0 100644
--- a/core/src/dynamic_spatial_organizer.hh
+++ b/core/src/dynamic_spatial_organizer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_DYNAMIC_SPATIAL_ORGANIZER_HI
#define PROMOD3_DYNAMIC_SPATIAL_ORGANIZER_HI
diff --git a/core/src/eigen_types.hh b/core/src/eigen_types.hh
index 8eff20ee824802fee2c78246bcc9126a5fc48c47..773998c0c393179e37f0c9c89ce1804905217f53 100644
--- a/core/src/eigen_types.hh
+++ b/core/src/eigen_types.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_EIGEN_TYPES_HH
#define PROMOD3_EIGEN_TYPES_HH
diff --git a/core/src/enumerator.hh b/core/src/enumerator.hh
index 3fa65d54ca902e04f3ceee273fd0f98f2c4839ea..1eb1790e1e8124611c948c38757e2677b2ce9a5f 100644
--- a/core/src/enumerator.hh
+++ b/core/src/enumerator.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_CORE_ENUMERATOR_HH
#define PM3_CORE_ENUMERATOR_HH
diff --git a/core/src/export_helper.hh b/core/src/export_helper.hh
index 5f6bd0c89dd10beb34e6566d289348a19e39952d..9f86b080d6a26ed49e00f5024b41b2aa2a72c288 100644
--- a/core/src/export_helper.hh
+++ b/core/src/export_helper.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines helpers to convert STL objects to python objects
#ifndef PROMOD3_EXPORT_HELPERS_HH
diff --git a/core/src/geom_base.cc b/core/src/geom_base.cc
index 5b956ad31f6eb6513d7ccd9a9b9faeee6e2350b4..de84ef134953f7de798b4c678295cd2396479b23 100644
--- a/core/src/geom_base.cc
+++ b/core/src/geom_base.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <cmath>
#include <cassert>
#include <promod3/core/geom_base.hh>
diff --git a/core/src/geom_base.hh b/core/src/geom_base.hh
index 405907b704f2e4939db62e603d2da9421d61173e..8307a7192f797037943a9fa9d05fab5c85ba3911 100644
--- a/core/src/geom_base.hh
+++ b/core/src/geom_base.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_GEOM_BASE_HH
#define PROMOD3_GEOM_BASE_HH
diff --git a/core/src/geom_stems.cc b/core/src/geom_stems.cc
index b1bf3cf1978f6e43bab68cd05834e96e3614e9d8..2194e1a775ba7615297d9409e2320a2cb2e5544c 100644
--- a/core/src/geom_stems.cc
+++ b/core/src/geom_stems.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/geom_stems.hh>
#include <cmath>
#include <cassert>
diff --git a/core/src/geom_stems.hh b/core/src/geom_stems.hh
index 09069d8a1a3edb867fe1bf68f2aa12064071bc23..fc0128bf8d35f0a0b4cf4c318710870e0d4871b7 100644
--- a/core/src/geom_stems.hh
+++ b/core/src/geom_stems.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_GEOM_STEMS_HH
#define PROMOD3_GEOM_STEMS_HH
diff --git a/core/src/graph.cc b/core/src/graph.cc
index 995a6517eb9705e6099bce090b0636fa86dbd741..90082ccaaec1a7d08db9674088b1ef596b3d6866 100644
--- a/core/src/graph.cc
+++ b/core/src/graph.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/graph.hh>
#include <promod3/core/message.hh>
#include <algorithm>
diff --git a/core/src/graph.hh b/core/src/graph.hh
index 2638e8276cd7dc03e4352d7021b4d7047256217c..7187be85c776c451610ccab47aedbc916fbe168c 100644
--- a/core/src/graph.hh
+++ b/core/src/graph.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_GRAPH_HH
#define PROMOD3_GRAPH_HH
diff --git a/core/src/graph_minimizer.cc b/core/src/graph_minimizer.cc
index e524efc2fb53447967c9c37b2f9fc985072b1b00..0f9bd8fd05d25610376ffa6087b1418ad25fd0ee 100644
--- a/core/src/graph_minimizer.cc
+++ b/core/src/graph_minimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <algorithm>
#include <queue>
#include <limits>
diff --git a/core/src/graph_minimizer.hh b/core/src/graph_minimizer.hh
index 410cc21d0eb4664f1b6c8ef70e4b7caf6ec6535b..28e9df7b9324a7d81845d39e321cb843b99f30a6 100644
--- a/core/src/graph_minimizer.hh
+++ b/core/src/graph_minimizer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_GRAPH_MINIMIZER_HH
#define PROMOD3_GRAPH_MINIMIZER_HH
diff --git a/core/src/message.hh b/core/src/message.hh
index f0d4368ed6bba7588f2d1483f38e6d177207f9f6..c652f2bab02703d4edc0635aec78856b54b4bbad 100644
--- a/core/src/message.hh
+++ b/core/src/message.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MESSAGE_HH
#define PROMOD3_MESSAGE_HH
diff --git a/core/src/portable_binary_data_sink.hh b/core/src/portable_binary_data_sink.hh
index 40e3fdab7809ffd7a6cb824ae4a4525ef4537f78..c3c8c9e93e1013747f0981862882a98ded0124e2 100644
--- a/core/src/portable_binary_data_sink.hh
+++ b/core/src/portable_binary_data_sink.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines a portable binary data sink.
/// This generates files to be read by PortableBinaryDataSink.
/// The interface is compatible with ost-like data sinks.
diff --git a/core/src/portable_binary_data_source.hh b/core/src/portable_binary_data_source.hh
index b97491520197be70645d6c2b796b9c318bd00c17..00d80a50d5c1ea69ce48f68fab080c82d0124e57 100644
--- a/core/src/portable_binary_data_source.hh
+++ b/core/src/portable_binary_data_source.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines a portable binary data source.
/// This works with files dumped by PortableBinaryDataSink.
/// The interface is compatible with ost-like data sources.
diff --git a/core/src/portable_binary_serializer.hh b/core/src/portable_binary_serializer.hh
index 8c5a570cd784c210784b6a91892c411c6157dd49..4a5b52efab05161da16c1bf30c66828e81eb4f5a 100644
--- a/core/src/portable_binary_serializer.hh
+++ b/core/src/portable_binary_serializer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Define everything needed for portable I/O.
/// Here we include any custom Serialize function.
/// Main classes are PortableBinaryDataSink and PortableBinaryDataSource.
diff --git a/core/src/runtime_profiling.hh b/core/src/runtime_profiling.hh
index 379b6e40c5febcf5c0c003d327f5c5b5b51f36ee..343666befacf48c27eb5b1b7f27e300aea93864c 100644
--- a/core/src/runtime_profiling.hh
+++ b/core/src/runtime_profiling.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality for runtime profiling.
/// All profiling can be completely turned off by setting
/// PM3_RUNTIME_PROFILING_LEVEL=0
diff --git a/core/src/superpose.cc b/core/src/superpose.cc
index 717b9de6b7fb06794fa42412ce072d3d69c93a9a..0e06a6e6994588fd83c925f26cabe64b05d5dc4f 100644
--- a/core/src/superpose.cc
+++ b/core/src/superpose.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/superpose.hh>
#include <Eigen/SVD>
#include <Eigen/Geometry>
diff --git a/core/src/superpose.hh b/core/src/superpose.hh
index 8a3fdcec3b0c4d4e8e3ce13c7bdce1ef286304d1..2fd82314a9fbeb3ab2510ba478963793f4490dfd 100644
--- a/core/src/superpose.hh
+++ b/core/src/superpose.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SUPERPOSE_HH
#define PROMOD3_SUPERPOSE_HH
diff --git a/core/src/tetrahedral_polytope.cc b/core/src/tetrahedral_polytope.cc
index 576ab1fd82093f5c4c0c8cc6a18f8c987577796d..40bf460479765da8c31d5451a3b14f28fea49154 100644
--- a/core/src/tetrahedral_polytope.cc
+++ b/core/src/tetrahedral_polytope.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/tetrahedral_polytope.hh>
#include <limits>
diff --git a/core/src/tetrahedral_polytope.hh b/core/src/tetrahedral_polytope.hh
index 3a2863b2854aaca9f2eee184c5fa9a8260d3125e..31c88a77d99719ddd68e1da69d51dc0201ed9275 100644
--- a/core/src/tetrahedral_polytope.hh
+++ b/core/src/tetrahedral_polytope.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_CORE_TETRAHEDRAL_POLYTOPE_HH
#define PROMOD3_CORE_TETRAHEDRAL_POLYTOPE_HH
diff --git a/core/src/tree.cc b/core/src/tree.cc
index 4bf941d486b4583a2d6b9ea8cc8e22bbad364236..8e32afb18e0f80d14e1337b544015efe29a7b464 100644
--- a/core/src/tree.cc
+++ b/core/src/tree.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/tree.hh>
#include <promod3/core/message.hh>
#include <stack>
diff --git a/core/src/tree.hh b/core/src/tree.hh
index c8a1628c78cfeb609a7fd3063bf6ff86476fa9d9..dd45dc327e907021c6176a14e8fc09bced8fe2b2 100644
--- a/core/src/tree.hh
+++ b/core/src/tree.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_TREE_HH
#define PROMOD3_TREE_HH
diff --git a/core/tests/test_check_io.cc b/core/tests/test_check_io.cc
index 742694b3df2ccf4d57b840f408f3aca287d54b04..87a951d780c0ed7850e659f39ff0f9729bdc93c7 100644
--- a/core/tests/test_check_io.cc
+++ b/core/tests/test_check_io.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/check_io.hh>
#include <promod3/core/portable_binary_serializer.hh>
#define BOOST_TEST_DYN_LINK
diff --git a/core/tests/test_graph_minimizer.cc b/core/tests/test_graph_minimizer.cc
index 7a52ae53b6e1cc49eab7cab236c3a9b304c9b589..c5737eb86718c4856f35e8c3d72e870c3952c8fd 100644
--- a/core/tests/test_graph_minimizer.cc
+++ b/core/tests/test_graph_minimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/eigen_types.hh>
#include <promod3/core/graph_minimizer.hh>
#define BOOST_TEST_DYN_LINK
diff --git a/core/tests/test_helper.py b/core/tests/test_helper.py
index 9005334a502988f194c650fa776c416ebf2060b7..eb82be1d97daed11716f60332cf080886099a1f1 100644
--- a/core/tests/test_helper.py
+++ b/core/tests/test_helper.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import unittest
import ost
from promod3.core import helper
diff --git a/core/tests/test_pm3argparse.py b/core/tests/test_pm3argparse.py
index 0b2310e8cf0db4494185ac68bf521e6a7b7fb681..a9626bf498adda61f58388636cfbdbd74fd08430 100644
--- a/core/tests/test_pm3argparse.py
+++ b/core/tests/test_pm3argparse.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Testing our own little argument parser.
"""
diff --git a/core/tests/test_portable_binary.cc b/core/tests/test_portable_binary.cc
index 31102f39f1c5401ed2d9fc3c6b65dd2b0b93ed9c..0cadce21d330ade13fe2a620915712672030a395 100644
--- a/core/tests/test_portable_binary.cc
+++ b/core/tests/test_portable_binary.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/portable_binary_serializer.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
diff --git a/core/tests/test_setcompoundschemlib.py b/core/tests/test_setcompoundschemlib.py
index 8f90d569b4e802974429034b424f675d0233aa07..2da5ead8d841146fb9bcdc57f4dfc5652dde157f 100644
--- a/core/tests/test_setcompoundschemlib.py
+++ b/core/tests/test_setcompoundschemlib.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import unittest
import os
from ost import conop
diff --git a/core/tests/tests.cc b/core/tests/tests.cc
index f3c1473f9e8e9e8e759cb7e2a590870dedbd4b69..723aa61416a8bb5d5eb9935903958c1ffba5f12f 100644
--- a/core/tests/tests.cc
+++ b/core/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_core
#define BOOST_AUTO_TEST_MAIN
diff --git a/doc/buildsystem.rst b/doc/buildsystem.rst
index a601d619b695a46a2f15352e312e4bdaf91ab90f..1143070094fc23525a08ced74fe8f91915e7d27c 100644
--- a/doc/buildsystem.rst
+++ b/doc/buildsystem.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
.. _building-promod:
Building |project|
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 394831ba4302622ad01e13edc68eb9aa29e15de5..713d4a748c49463ee41f7f27ef33e0f620478468 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -59,7 +59,7 @@ master_doc = 'index'
# General information about the project.
project = u'ProMod3'
-copyright = u'2018, ProMod3 authors'# pylint: disable=redefined-builtin
+copyright = u'2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
diff --git a/doc/container/docker.rst b/doc/container/docker.rst
index 57cc2ab1d61ed32c98c9768516a60e17d994a34e..cc5faaa095f903fc4f5a68ba776b5b8b144874ff 100644
--- a/doc/container/docker.rst
+++ b/doc/container/docker.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Docker
======
diff --git a/doc/container/index.rst b/doc/container/index.rst
index 9fac38710ca915c70ec599d2018f697740c2c018..9cf79e23f891def49bfd42346f0e31c027838b79 100644
--- a/doc/container/index.rst
+++ b/doc/container/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
ProMod3 and Containers
======================
diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst
index 7b4bb4dd4e997d404509c32ccf5c21860cb9a4ca..ede88ddb3845154c24ea1534d96ebc6bb964b02a 100644
--- a/doc/container/singularity.rst
+++ b/doc/container/singularity.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Singularity
===========
diff --git a/doc/contributing.rst b/doc/contributing.rst
index feb1f033e1d7cd6d6ccf256983e320262ca3cca7..3a261b411ab249a578a79cf8c0760ef1deb68150 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Contributing
================================================================================
diff --git a/doc/dev_setup.rst b/doc/dev_setup.rst
index 3b450accf0a5cb18ada95e2e7b1ab6d0e35799dd..91909c30154907dcbb269a4d5cb805ef6af9d1bf 100644
--- a/doc/dev_setup.rst
+++ b/doc/dev_setup.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
|project| Setup
================================================================================
diff --git a/doc/developers.rst b/doc/developers.rst
index 3955c47c1cab44e3274e54919b0b0d949299c0f6..f15f85db820e896de015b614c871d0317030dc38 100644
--- a/doc/developers.rst
+++ b/doc/developers.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Documentation For Developers
===============================================================================
diff --git a/doc/gettingstarted.rst b/doc/gettingstarted.rst
index 9b2b8024b6cb6e7cd2e98aa10c3c86df5754f645..2bed4049fe4de07f7fafe0994c1867fd40f5be61 100644
--- a/doc/gettingstarted.rst
+++ b/doc/gettingstarted.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Getting Started
================================================================================
diff --git a/doc/index.rst b/doc/index.rst
index 27f2e9e87b5c2a1e40e25a6b3a83c29263981c8a..0b5ab1314219903ed06d88d5a3bd1ddd13af9387 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
ProMod3
=======
diff --git a/doc/licence.rst b/doc/licence.rst
index a8efd73cfa54657a7ef295a3e5a38ab67297ba88..90469d5a56d3aa18c459294299293ef2c22b1bdb 100644
--- a/doc/licence.rst
+++ b/doc/licence.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Licence
=======
diff --git a/doc/portableIO.rst b/doc/portableIO.rst
index 5c30639815477b7b579aa873361c3efa3d630795..a548e3c86400f7e09a9c7cc65c9c2fd7de19e8ce 100644
--- a/doc/portableIO.rst
+++ b/doc/portableIO.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
.. _portableIO:
Using Binary Files In |project|
diff --git a/doc/references.rst b/doc/references.rst
index c12f301e35b331745c20084b6d024c4e3bdaae61..927de6ddbad6c032f0f760c17384e977d1ed31e9 100644
--- a/doc/references.rst
+++ b/doc/references.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
References
==========
diff --git a/doc/tests/scripts/action_test.py b/doc/tests/scripts/action_test.py
index d0fafdf37da2b15c9d88187bfe76b409a00d3ea8..b304223211bde3783962c2f3dd8313b135af5fc2 100644
--- a/doc/tests/scripts/action_test.py
+++ b/doc/tests/scripts/action_test.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import sys
# this is needed so there will be no test_actions.pyc created in the source
diff --git a/doc/tests/scripts/action_test_verbose.py b/doc/tests/scripts/action_test_verbose.py
index f00a803cc438710ae071e2fd1280fbb86dc7526f..c290afe5579706c140a4cd3ad7670b173e15952e 100644
--- a/doc/tests/scripts/action_test_verbose.py
+++ b/doc/tests/scripts/action_test_verbose.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import sys
# this is needed so there will be no test_actions.pyc created in the source
diff --git a/doc/tests/scripts/core_file_checks.py b/doc/tests/scripts/core_file_checks.py
index 004e8c2655f50f473a44a2f25f969bc727a42932..037917e7e8fe7c86213ed6c9211f0009dcfd57e5 100644
--- a/doc/tests/scripts/core_file_checks.py
+++ b/doc/tests/scripts/core_file_checks.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Test for file reading."""
from promod3.core import helper
from promod3.core import pm3argparse
diff --git a/doc/tests/scripts/core_msg_error.py b/doc/tests/scripts/core_msg_error.py
index d8c3940c01b7c1ae118ea71f3877ca743aa0011c..959fe4790abdb74a1e85ad9ad0e319c138901bac 100644
--- a/doc/tests/scripts/core_msg_error.py
+++ b/doc/tests/scripts/core_msg_error.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3.core import helper
helper.MsgErrorAndExit("Something failed!", 1)
diff --git a/doc/tests/scripts/core_pm3argparse.py b/doc/tests/scripts/core_pm3argparse.py
index e177cb4c61e8141514fa0253de1b73dbae9457e7..106d2545702390c43e243694d4a08d8913fc2f18 100644
--- a/doc/tests/scripts/core_pm3argparse.py
+++ b/doc/tests/scripts/core_pm3argparse.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Place the description of your script right in the file and import
it via '__doc__' as description to the parser ('-h', '--help').
diff --git a/doc/tests/scripts/hello_world.py b/doc/tests/scripts/hello_world.py
index 1cac861a81712eadda4cb47260e6882545feac01..6073d3adf4dda4b62d784ef7ec5ee24af49cf7eb 100644
--- a/doc/tests/scripts/hello_world.py
+++ b/doc/tests/scripts/hello_world.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io
from promod3 import loop
diff --git a/doc/tests/scripts/loop_all_atom.py b/doc/tests/scripts/loop_all_atom.py
index d491873f1cd5db0cdc0d855c6eacf55d43034662..2e340ee67290c94140084792112e55339d5aeb44 100644
--- a/doc/tests/scripts/loop_all_atom.py
+++ b/doc/tests/scripts/loop_all_atom.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, geom
from promod3 import loop
diff --git a/doc/tests/scripts/loop_backbone.py b/doc/tests/scripts/loop_backbone.py
index 79901d51689acc3de66d12f05f0130a7554fe400..ea4c2ef8611ea1cec4cc8c3e197b596477978203 100644
--- a/doc/tests/scripts/loop_backbone.py
+++ b/doc/tests/scripts/loop_backbone.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io
from ost import conop
from promod3 import loop
diff --git a/doc/tests/scripts/loop_frag_db.py b/doc/tests/scripts/loop_frag_db.py
index 0efd8226859dbfc115f5973d3d456b6e1b88bfed..fbc0601cc1b502b12ac12ceb0d5a7c6a2685c9e8 100644
--- a/doc/tests/scripts/loop_frag_db.py
+++ b/doc/tests/scripts/loop_frag_db.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io
from promod3 import loop
diff --git a/doc/tests/scripts/loop_fragger.py b/doc/tests/scripts/loop_fragger.py
index c61d634127143ba8b57a72eeee85bb05d8505db5..73241c8894d14e75b7de0b39cc379c55e06a635e 100644
--- a/doc/tests/scripts/loop_fragger.py
+++ b/doc/tests/scripts/loop_fragger.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, seq
from promod3 import loop
diff --git a/doc/tests/scripts/loop_main.py b/doc/tests/scripts/loop_main.py
index 6e4f4f45cb419e8607f5a8e2f965c934cf9e4e2a..dc1d95a0811afe474b228fbf66c227160166daeb 100644
--- a/doc/tests/scripts/loop_main.py
+++ b/doc/tests/scripts/loop_main.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, seq
from promod3 import loop
diff --git a/doc/tests/scripts/loop_mm_sys_creation.py b/doc/tests/scripts/loop_mm_sys_creation.py
index 642c4dac3b7403b5eb7a389608c6b28eeaa5336c..fb975fe88cfc609bf0dc0803448018b9a3ba7305 100644
--- a/doc/tests/scripts/loop_mm_sys_creation.py
+++ b/doc/tests/scripts/loop_mm_sys_creation.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, geom
from promod3 import loop
diff --git a/doc/tests/scripts/loop_structure_db.py b/doc/tests/scripts/loop_structure_db.py
index 09258a9236b4c8dc6e27dfb866c83df17c6067e4..05bc3e7c8acdfdd129a57fb2dc854552f6c3453d 100644
--- a/doc/tests/scripts/loop_structure_db.py
+++ b/doc/tests/scripts/loop_structure_db.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
from ost import io, seq
import os
diff --git a/doc/tests/scripts/loop_torsion_sampler.py b/doc/tests/scripts/loop_torsion_sampler.py
index 95ee3e78c50cd8e78dac49767e7c2ea4f966f65f..a075872ed0d96f40176f6ff447bbb8dc46999550 100644
--- a/doc/tests/scripts/loop_torsion_sampler.py
+++ b/doc/tests/scripts/loop_torsion_sampler.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
from ost import conop
# this requires matplotlib and numpy
diff --git a/doc/tests/scripts/modelling_all.py b/doc/tests/scripts/modelling_all.py
index ae0d12ccde3bdd7869d7b2a69a2f8836874f606f..b24447307d8d5f2a2e654b26a782af01d49cc858 100644
--- a/doc/tests/scripts/modelling_all.py
+++ b/doc/tests/scripts/modelling_all.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io
from promod3 import modelling
diff --git a/doc/tests/scripts/modelling_allatomrelaxer.py b/doc/tests/scripts/modelling_allatomrelaxer.py
index c99244bcdd68e64d1cfb81cf6d717b1c44562e18..4d6d70e3bb5d19360e342ba93979b73b10af71a4 100644
--- a/doc/tests/scripts/modelling_allatomrelaxer.py
+++ b/doc/tests/scripts/modelling_allatomrelaxer.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io
from promod3 import modelling, loop
diff --git a/doc/tests/scripts/modelling_close_small_deletions.py b/doc/tests/scripts/modelling_close_small_deletions.py
index 80e8c3e590b9bd3d4d80449ee34bb7eac4c68263..0bd80b51c4781d0f42684ee8b4061828a16e6303 100644
--- a/doc/tests/scripts/modelling_close_small_deletions.py
+++ b/doc/tests/scripts/modelling_close_small_deletions.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, seq
from promod3 import modelling
diff --git a/doc/tests/scripts/modelling_fill_loops_by_database.py b/doc/tests/scripts/modelling_fill_loops_by_database.py
index d7126b079f38a1c6ae54f82394e770202d27acb4..d3297ede7269b8fc35c9da7a3d0da60cddccaa9d 100644
--- a/doc/tests/scripts/modelling_fill_loops_by_database.py
+++ b/doc/tests/scripts/modelling_fill_loops_by_database.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, seq
from promod3 import modelling, loop
diff --git a/doc/tests/scripts/modelling_fill_loops_by_monte_carlo.py b/doc/tests/scripts/modelling_fill_loops_by_monte_carlo.py
index daa860909ec68c0bbd9c2129b3856f20381a58b1..acd0cfe36b81109bce0376241d2ff32831ebc10d 100644
--- a/doc/tests/scripts/modelling_fill_loops_by_monte_carlo.py
+++ b/doc/tests/scripts/modelling_fill_loops_by_monte_carlo.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, seq
from promod3 import modelling, loop
diff --git a/doc/tests/scripts/modelling_loop_candidates.py b/doc/tests/scripts/modelling_loop_candidates.py
index 60d4abeb8836fd3e035c877bfe1c09982958fa67..8e2df1d1b89bed2e436156294e93eb4e0815edd7 100644
--- a/doc/tests/scripts/modelling_loop_candidates.py
+++ b/doc/tests/scripts/modelling_loop_candidates.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io
from promod3 import loop, scoring, modelling
diff --git a/doc/tests/scripts/modelling_loop_scoring.py b/doc/tests/scripts/modelling_loop_scoring.py
index b6456842b3765897d54c6fd9bb5060a142604291..5358f875ce119b1d96790e978fa95ada39efd90d 100644
--- a/doc/tests/scripts/modelling_loop_scoring.py
+++ b/doc/tests/scripts/modelling_loop_scoring.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, seq
from promod3 import modelling, loop
diff --git a/doc/tests/scripts/modelling_merge_gaps_by_distance.py b/doc/tests/scripts/modelling_merge_gaps_by_distance.py
index 1606d30d3813c3f67c6e1ee3caf70e3a0ec84e7e..3324d698d033388955826b37e92492259ff46352 100644
--- a/doc/tests/scripts/modelling_merge_gaps_by_distance.py
+++ b/doc/tests/scripts/modelling_merge_gaps_by_distance.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, seq
from promod3 import modelling
diff --git a/doc/tests/scripts/modelling_model_termini.py b/doc/tests/scripts/modelling_model_termini.py
index 3b312a7625b94f6813ef0572de95e1d47eb533a6..f79e196332bfed8cd7570d1e0eb695c6b5bf19b1 100644
--- a/doc/tests/scripts/modelling_model_termini.py
+++ b/doc/tests/scripts/modelling_model_termini.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, seq
from promod3 import modelling, loop
diff --git a/doc/tests/scripts/modelling_monte_carlo.py b/doc/tests/scripts/modelling_monte_carlo.py
index b3d7d07b76016f7f9f3746a5ea683a4dd9630165..b55b9a5390214ce93fab2a055523b1ee8d0c99e7 100644
--- a/doc/tests/scripts/modelling_monte_carlo.py
+++ b/doc/tests/scripts/modelling_monte_carlo.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io
from promod3 import loop, scoring, modelling
import numpy as np
diff --git a/doc/tests/scripts/modelling_reconstruct_sidechains.py b/doc/tests/scripts/modelling_reconstruct_sidechains.py
index de157d80189522346e502e0c4b3d8f985c0b995f..fb5e1fefcf5ad48ebc68a274415eff36fc40528e 100644
--- a/doc/tests/scripts/modelling_reconstruct_sidechains.py
+++ b/doc/tests/scripts/modelling_reconstruct_sidechains.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, mol
from promod3 import modelling
diff --git a/doc/tests/scripts/modelling_sidechain_reconstructor.py b/doc/tests/scripts/modelling_sidechain_reconstructor.py
index a39d3bf6afee1b33048dac47a473daf822f6e978..cc691d1e02166fe3c8b9a18a1792884e13663923 100644
--- a/doc/tests/scripts/modelling_sidechain_reconstructor.py
+++ b/doc/tests/scripts/modelling_sidechain_reconstructor.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io
from promod3 import loop, modelling
diff --git a/doc/tests/scripts/modelling_steps.py b/doc/tests/scripts/modelling_steps.py
index f557c28fb7710a161f699821260bafad86c18bc3..6e9f935cd630fa4e197357848c69500277cf3eab 100644
--- a/doc/tests/scripts/modelling_steps.py
+++ b/doc/tests/scripts/modelling_steps.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io
from promod3 import modelling, loop
diff --git a/doc/tests/scripts/scoring_main.py b/doc/tests/scripts/scoring_main.py
index a5bb94771e369e18b2f14720e4c312689386e566..058b2b29e7f5f3d4e77f03844c7ae8b6dfd138a9 100644
--- a/doc/tests/scripts/scoring_main.py
+++ b/doc/tests/scripts/scoring_main.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io, seq
from promod3 import loop, scoring
diff --git a/doc/tests/scripts/sidechain_steps.py b/doc/tests/scripts/sidechain_steps.py
index 854ff709f9b88187d7db704bc681a2132740a6df..6b152ee5b1b9e515d25cee41e0d3e38877701ff5 100644
--- a/doc/tests/scripts/sidechain_steps.py
+++ b/doc/tests/scripts/sidechain_steps.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import io,mol
from promod3 import sidechain
diff --git a/doc/tests/scripts/unittest_sidechain_reconstruction.py b/doc/tests/scripts/unittest_sidechain_reconstruction.py
index 083416eb7b838380f457bf217d1d53a8dbea4494..068d6bafe1118a0ecf8badd42fa11d2ccf716cc7 100644
--- a/doc/tests/scripts/unittest_sidechain_reconstruction.py
+++ b/doc/tests/scripts/unittest_sidechain_reconstruction.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import unittest
from promod3 import modelling
from ost import io,mol
diff --git a/doc/tests/test_doctests.py b/doc/tests/test_doctests.py
index bd9d89a001f8f883e1804a08bf7dd3d48dbbf009..42d8071136c6a94d82d91cdcaded36bdcf36d819 100644
--- a/doc/tests/test_doctests.py
+++ b/doc/tests/test_doctests.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Test example codes from documentation.
Each example code is given as a python script in scripts-folder and may use
diff --git a/doc/users.rst b/doc/users.rst
index 893af45f801380c0f846fa328fc518a4caeaacb5..3b11ff195d4009fcf10bea662e5f54367150d90c 100644
--- a/doc/users.rst
+++ b/doc/users.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Documentation For Users
=======================
diff --git a/extras/code_generation/amino_acid_atoms.py b/extras/code_generation/amino_acid_atoms.py
index 87e562d73a9b9cd27f82450886aae3c2eec842d6..be8d8cfce8ec1cd7fe33a4ebba96c5a0b09f4161 100644
--- a/extras/code_generation/amino_acid_atoms.py
+++ b/extras/code_generation/amino_acid_atoms.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Code generation of code snippets for heavy atom part of amino_acid_atoms."""
from ost import conop
diff --git a/extras/code_generation/amino_acid_atoms_hydrogens.py b/extras/code_generation/amino_acid_atoms_hydrogens.py
index 5150f3576e808d326656240b6072326c62179718..52c8c6cc44179b6adb4c9863d18f5b723d7918ad 100644
--- a/extras/code_generation/amino_acid_atoms_hydrogens.py
+++ b/extras/code_generation/amino_acid_atoms_hydrogens.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Code generation of code snippets for hydrogen part of amino_acid_atoms."""
import promod3
diff --git a/extras/code_generation/backbone_score_unittest.py b/extras/code_generation/backbone_score_unittest.py
index fd66538682832f42877ac54d2db4037504e9bc62..67b0af45a8ad03f558b75dd3a5859cb218d04704 100644
--- a/extras/code_generation/backbone_score_unittest.py
+++ b/extras/code_generation/backbone_score_unittest.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from qmean import *
import os
from promod3 import loop
diff --git a/extras/code_generation/hydrogen_rules.py b/extras/code_generation/hydrogen_rules.py
index 1142ebb3266ab194d57c53181fc23e7a2f929928..cdcac7e2f869b0b598c3d97d9c56b3916173349e 100644
--- a/extras/code_generation/hydrogen_rules.py
+++ b/extras/code_generation/hydrogen_rules.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Code generation of code snippets for hydrogen_constructor."""
from promod3 import loop
diff --git a/extras/code_generation/ideal_bb_param.py b/extras/code_generation/ideal_bb_param.py
index 348519eae01252878ab2e76275e4bc5042e68d03..b9ceef405a54ca9f8169e0506a4606170c8d8fd2 100644
--- a/extras/code_generation/ideal_bb_param.py
+++ b/extras/code_generation/ideal_bb_param.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import conop
import numpy as np
diff --git a/extras/code_generation/sidechain_atom_rule_lookup.py b/extras/code_generation/sidechain_atom_rule_lookup.py
index fe4ba9157cb27c4457c1890f50c23f91e78b161b..684d9682f2368be99359bd3ea5f6aec78c392dd4 100644
--- a/extras/code_generation/sidechain_atom_rule_lookup.py
+++ b/extras/code_generation/sidechain_atom_rule_lookup.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
from ost import conop
from ost.mol import mm
diff --git a/extras/data_generation/all_atom_scorer/create_default_aa_scorer.py b/extras/data_generation/all_atom_scorer/create_default_aa_scorer.py
index 9f390f8531c2dff964ec13578ae732c28c134614..92c786e6c5bfe5bab02bea88d33938afb2c7ecd4 100644
--- a/extras/data_generation/all_atom_scorer/create_default_aa_scorer.py
+++ b/extras/data_generation/all_atom_scorer/create_default_aa_scorer.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import ost
from qmean import *
from promod3 import scoring, loop
diff --git a/extras/data_generation/backbone_scorer/create_default_scorer.py b/extras/data_generation/backbone_scorer/create_default_scorer.py
index 8ffd8de2ca2fe8f24dc99d2b5a07dcb91d8a74fb..585e00c93837fd21e9d9e8b9a82c8bfdd13c6db9 100644
--- a/extras/data_generation/backbone_scorer/create_default_scorer.py
+++ b/extras/data_generation/backbone_scorer/create_default_scorer.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import ost
from qmean import *
from promod3 import scoring
diff --git a/extras/data_generation/force_field/create_charmm_force_field.py b/extras/data_generation/force_field/create_charmm_force_field.py
index 1ba4b09ca9e5ac84c8f27fe5bfc68d4be52b6eb9..8ec3d23813a77ee30603529bb08fd29d76931412 100644
--- a/extras/data_generation/force_field/create_charmm_force_field.py
+++ b/extras/data_generation/force_field/create_charmm_force_field.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
from ost import conop, io
from ost.mol import mm
diff --git a/extras/data_generation/frag_db/build_frag_db.py b/extras/data_generation/frag_db/build_frag_db.py
index 5faa5ad22d6b209846544ddbc1900aa43e5c7b36..b58530ad80e3569d08dec153693d96e84110ece9 100644
--- a/extras/data_generation/frag_db/build_frag_db.py
+++ b/extras/data_generation/frag_db/build_frag_db.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
diff --git a/extras/data_generation/portable_binaries/convert_data.cc b/extras/data_generation/portable_binaries/convert_data.cc
index 20c0144cac447d21b360ba860fd67862eafc42b5..4b0e3483003b8e1187078457955f83e28e2e1795 100644
--- a/extras/data_generation/portable_binaries/convert_data.cc
+++ b/extras/data_generation/portable_binaries/convert_data.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
// Test code for promod3
#include <promod3/loop/loop_object_loader.hh>
diff --git a/extras/data_generation/rotamer_library/CreateDunbrackLibrary.py b/extras/data_generation/rotamer_library/CreateDunbrackLibrary.py
index 7d3d65c805aa106f455412a9a61b0ccbe19eb175..7b2a53ada798b63e6f42c8cef8e67183794320b7 100644
--- a/extras/data_generation/rotamer_library/CreateDunbrackLibrary.py
+++ b/extras/data_generation/rotamer_library/CreateDunbrackLibrary.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import sidechain
# the file is available here: http://dunbrack.fccc.edu/bbdep2010/
diff --git a/extras/data_generation/rotamer_library/README b/extras/data_generation/rotamer_library/README
index 4c90c94f656d79db65e5909edaab59941453ae57..a387512ede267d0ec674f34a9765e6f9b5001d4e 100644
--- a/extras/data_generation/rotamer_library/README
+++ b/extras/data_generation/rotamer_library/README
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
You can get rotamer libraries from several sources.
#############################
diff --git a/extras/data_generation/rotamer_library/do_bbdep_lib.py b/extras/data_generation/rotamer_library/do_bbdep_lib.py
index 48c1789ee8339a6aada4d20dea0afa6b52d5690d..9dab196e971b33a3677160cf42fbe11cd894a4c0 100644
--- a/extras/data_generation/rotamer_library/do_bbdep_lib.py
+++ b/extras/data_generation/rotamer_library/do_bbdep_lib.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os, math, sys
import numpy as np
from scipy.ndimage import gaussian_filter
diff --git a/extras/data_generation/rotamer_library/do_lib.py b/extras/data_generation/rotamer_library/do_lib.py
index 70a7a9e4ad8ead6df8cebb5ca672ed8c8081d9a7..abb4ce3aa993f99454f851c26366eccf72076431 100644
--- a/extras/data_generation/rotamer_library/do_lib.py
+++ b/extras/data_generation/rotamer_library/do_lib.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os, math, sys
import numpy as np
from scipy.ndimage import gaussian_filter
diff --git a/extras/data_generation/rotamer_library/fetch_data.py b/extras/data_generation/rotamer_library/fetch_data.py
index 8a45c6a5b0851be70f16cda953ca34a0f6c5ba21..97ad79363270fe540dacdaab3b1f5f7ed69647ab 100644
--- a/extras/data_generation/rotamer_library/fetch_data.py
+++ b/extras/data_generation/rotamer_library/fetch_data.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os
from promod3 import sidechain
import numpy as np
diff --git a/extras/data_generation/structure_db/README b/extras/data_generation/structure_db/README
index f86fa19e8c37a82083e61ecc780679ff606a4dbb..2286f335b4c01c5f7b6350327db905617bc151d7 100644
--- a/extras/data_generation/structure_db/README
+++ b/extras/data_generation/structure_db/README
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
We provide several scripts to obtain a StructureDB.
More information regarding the different steps you'll find in the comments
in the corresponding scripts.
diff --git a/extras/data_generation/structure_db/assign_structure_profiles.py b/extras/data_generation/structure_db/assign_structure_profiles.py
index 2c14c44087fbd2a84be740c1f626565cfae81dd4..ed1b57098a16902876dc0085fc08d1e8f3f05f3b 100644
--- a/extras/data_generation/structure_db/assign_structure_profiles.py
+++ b/extras/data_generation/structure_db/assign_structure_profiles.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os
from promod3 import loop
from ost import seq
diff --git a/extras/data_generation/structure_db/build_structure_db.py b/extras/data_generation/structure_db/build_structure_db.py
index 450899c4e2d2f9e95ee001cbaf19f6e2032543e5..a4b6252a1f68498713bee4d127b227a9d0051f1a 100644
--- a/extras/data_generation/structure_db/build_structure_db.py
+++ b/extras/data_generation/structure_db/build_structure_db.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
import os
import traceback
diff --git a/extras/data_generation/structure_db/create_structure_profiles.py b/extras/data_generation/structure_db/create_structure_profiles.py
index a0e335925a4ed4fa5ced2e07a44bd0b379da4bb8..eb00492e24de84e80509522a402a7f57aaf20997 100644
--- a/extras/data_generation/structure_db/create_structure_profiles.py
+++ b/extras/data_generation/structure_db/create_structure_profiles.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os
import sys
from promod3 import loop
diff --git a/extras/data_generation/structure_db/get_data_from_smtl.py b/extras/data_generation/structure_db/get_data_from_smtl.py
index 7965046a728bd55260ab275073d7449ce7147db7..48806e713c9677b8ff8c4c35761f141793cdece3 100644
--- a/extras/data_generation/structure_db/get_data_from_smtl.py
+++ b/extras/data_generation/structure_db/get_data_from_smtl.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import time
import os
import pickle
diff --git a/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py b/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py
index d982a468161a2ccfbcceb994961f4f7e706f543d..d0e195c9555dbcea76b74d0e1fbcb4a4ec0bea86 100644
--- a/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py
+++ b/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
import os
diff --git a/extras/data_generation/torsion_sampler/train_torsion_sampler.py b/extras/data_generation/torsion_sampler/train_torsion_sampler.py
index 1c6eb9d809068664075f554c9aa8a1dde93db2f1..5e1181b51a80ab88bfee2b020a7ceffd52bfd1cc 100644
--- a/extras/data_generation/torsion_sampler/train_torsion_sampler.py
+++ b/extras/data_generation/torsion_sampler/train_torsion_sampler.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
from ost import mol
import os
diff --git a/extras/pre_commit/pm3_csc/__init__.py b/extras/pre_commit/pm3_csc/__init__.py
index 5c7540fe7a00cb9de5098adefb7e591f53f77673..d526e2ccc561f65cb13374753646fb3b92a63d0e 100644
--- a/extras/pre_commit/pm3_csc/__init__.py
+++ b/extras/pre_commit/pm3_csc/__init__.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Module to enforce ProMod3's coding policy.
"""
diff --git a/extras/pre_commit/pm3_csc/base.py b/extras/pre_commit/pm3_csc/base.py
index 4b0bc2efaf2f57f9b6e089a38006a6b96c5989ad..17a763716534776a87b9463189a966a0ec0875e7 100644
--- a/extras/pre_commit/pm3_csc/base.py
+++ b/extras/pre_commit/pm3_csc/base.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
This is a bunch of default functions for the coding style checker.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/__init__.py b/extras/pre_commit/pm3_csc/filecheck/__init__.py
index 5ba0033bb887a15c1215a16c3588dcfed4ffb9a8..1d614bb5528fbe5dd31812b610874762f48b3943 100644
--- a/extras/pre_commit/pm3_csc/filecheck/__init__.py
+++ b/extras/pre_commit/pm3_csc/filecheck/__init__.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Module hosting the code/ file check system.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/base.py b/extras/pre_commit/pm3_csc/filecheck/base.py
index 134a5069a9cdd868b2d190555411f84381b5dd72..95ab2274f992a4e2b9322eb87db537431dbd55a1 100644
--- a/extras/pre_commit/pm3_csc/filecheck/base.py
+++ b/extras/pre_commit/pm3_csc/filecheck/base.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Generic class for checking code from files.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/ccode.py b/extras/pre_commit/pm3_csc/filecheck/ccode.py
index 6ac3e170c696cac9fed2f8809fa7410a1aa95a33..e5bfe8be8a20cbd45e975be1fdf79e43eb9225ed 100644
--- a/extras/pre_commit/pm3_csc/filecheck/ccode.py
+++ b/extras/pre_commit/pm3_csc/filecheck/ccode.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking C/ C++ code.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/cmake.py b/extras/pre_commit/pm3_csc/filecheck/cmake.py
index 9bc06c24f7c5315da19f9ce9f17896929ea7538f..fde92de2138f904f40e9ce3d5a333942ebdae0de 100644
--- a/extras/pre_commit/pm3_csc/filecheck/cmake.py
+++ b/extras/pre_commit/pm3_csc/filecheck/cmake.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking CMake files.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/python.py b/extras/pre_commit/pm3_csc/filecheck/python.py
index b307d84acd15b0479697dc3b10cd0654e517a7b8..692c42e03cd1621966938b9df5788caab116f49c 100644
--- a/extras/pre_commit/pm3_csc/filecheck/python.py
+++ b/extras/pre_commit/pm3_csc/filecheck/python.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking Python code.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/rest.py b/extras/pre_commit/pm3_csc/filecheck/rest.py
index 315c2f86dfde1eb55012e147454bf298adcb6391..a3e5a4c62e0e6101da5cb7f47d3d8dfb3f47e0a2 100644
--- a/extras/pre_commit/pm3_csc/filecheck/rest.py
+++ b/extras/pre_commit/pm3_csc/filecheck/rest.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking reStructuredText docmentation files.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/shellscript.py b/extras/pre_commit/pm3_csc/filecheck/shellscript.py
index 0175f25c0d8bee28783b851f441c99f37e938a7e..73a958957c95817d0d0f7c98a97c7b3a3c1f2f95 100644
--- a/extras/pre_commit/pm3_csc/filecheck/shellscript.py
+++ b/extras/pre_commit/pm3_csc/filecheck/shellscript.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking shell code files.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/text.py b/extras/pre_commit/pm3_csc/filecheck/text.py
index 5ff81c3233f77677cc83cc759733dc1afb4b7a5f..d4b59f3721589d10b424f232e7897e24bff9aae3 100644
--- a/extras/pre_commit/pm3_csc/filecheck/text.py
+++ b/extras/pre_commit/pm3_csc/filecheck/text.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking just text.
"""
diff --git a/extras/pre_commit/pm3_csc/git.py b/extras/pre_commit/pm3_csc/git.py
index cba5c9c5f91667483144c0354737533470b9e0fe..cebe8327860f2dbffff7541d141ce816db0fd25d 100644
--- a/extras/pre_commit/pm3_csc/git.py
+++ b/extras/pre_commit/pm3_csc/git.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Keep all the functions calling git in one place.
"""
diff --git a/extras/pre_commit/pre-commit b/extras/pre_commit/pre-commit
index 1c216048ca4d9596f273ae5bcdd5c38414d1ad52..df8eb506803ee6c928d7451a5e359cd30fe95925 100644
--- a/extras/pre_commit/pre-commit
+++ b/extras/pre_commit/pre-commit
@@ -1,6 +1,22 @@
#!/usr/bin/env python
# pylint: disable=invalid-name
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import subprocess, sys, re, os, difflib
# prevent creating .pyc files in the source directory
diff --git a/extras/sanity_checks/Makefile b/extras/sanity_checks/Makefile
index 454cab058d2dafb2d214cbdc1dc5f96382581e81..79d2b5862144b7926d6ba11628ad060085e67d85 100644
--- a/extras/sanity_checks/Makefile
+++ b/extras/sanity_checks/Makefile
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
########
# SETUP
########
diff --git a/extras/sanity_checks/README b/extras/sanity_checks/README
index 28977485bcb889baf193bd940597244513fdbec4..81bbd702a922c5ba1504ec3ab355ca54b25265e4 100644
--- a/extras/sanity_checks/README
+++ b/extras/sanity_checks/README
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
Check installation of PM3:
==========================
diff --git a/extras/sanity_checks/run_pipeline.py b/extras/sanity_checks/run_pipeline.py
index 4fd77a97db72a32b82ede9b5a164b121cf69f1a7..556ea8f82304f97e6172d9302ece99e87cd4a893 100644
--- a/extras/sanity_checks/run_pipeline.py
+++ b/extras/sanity_checks/run_pipeline.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import ost
from ost import io, mol
from promod3 import modelling
diff --git a/extras/sanity_checks/test_all.py b/extras/sanity_checks/test_all.py
index 73161a29ac9406235f447b77b25dac9717beadd1..d528c7a0acd0e7c826688bcd73c1b86cc6969b62 100644
--- a/extras/sanity_checks/test_all.py
+++ b/extras/sanity_checks/test_all.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os
import sys
import unittest
diff --git a/extras/sanity_checks/test_cpp.cc b/extras/sanity_checks/test_cpp.cc
index 1d4a18c232ca7e8b4aa1fb2f4a7337d5546e038b..9c8e3365517e69d0dcf73637e9308cf2b4b8a6fe 100644
--- a/extras/sanity_checks/test_cpp.cc
+++ b/extras/sanity_checks/test_cpp.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
// Test code for low-level ProMod3 features
#include <ost/base.hh>
diff --git a/extras/sanity_checks/test_module.py b/extras/sanity_checks/test_module.py
index 78437c9e362c62d8852d3bd4a0a0b21e36369fe8..db97a6d249431ce36feb6f82e0fa32d7a7c4a661 100644
--- a/extras/sanity_checks/test_module.py
+++ b/extras/sanity_checks/test_module.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import promod3
print "ProMod3-version =", promod3.__version__
diff --git a/extras/scoring_weight_training/README b/extras/scoring_weight_training/README
index 523a8ecd3bc4c03f70ce43b2a2d4b7885b3c0004..3c6db6b77663e2fe55690fe2586d0d444eb758a6 100644
--- a/extras/scoring_weight_training/README
+++ b/extras/scoring_weight_training/README
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
This folder contains scripts that were used to train weights for the scoring
functions used in loop selection in the pipeline. You need a compiled and
working version of ProMod3 to run these scripts. Scripts are provided as-is!
diff --git a/extras/scoring_weight_training/analyze_bft_candidates.py b/extras/scoring_weight_training/analyze_bft_candidates.py
index 27a12999478a9c75aba44878f20e02f187ba654f..1c1d28690117b22c9320356ef0d9b66fbbd48a4f 100644
--- a/extras/scoring_weight_training/analyze_bft_candidates.py
+++ b/extras/scoring_weight_training/analyze_bft_candidates.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: analyze number of loop candidates in BFT (also considering within_bounds)
IN:
diff --git a/extras/scoring_weight_training/analyze_bft_score_correlations.py b/extras/scoring_weight_training/analyze_bft_score_correlations.py
index c066cdbc6fdee0ba5be883529f91ad2a22d68cfc..a399df014ca329be042963d464bed0afa88833af 100644
--- a/extras/scoring_weight_training/analyze_bft_score_correlations.py
+++ b/extras/scoring_weight_training/analyze_bft_score_correlations.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: analyze correlation of scores to ca_rmsd
IN:
diff --git a/extras/scoring_weight_training/analyze_bft_scores.py b/extras/scoring_weight_training/analyze_bft_scores.py
index 423f9d92b3a08ea45ff92406368dc5097a4d64b0..a8abdf597f7ea63cbbc0db5fddb494f3d67f77c6 100644
--- a/extras/scoring_weight_training/analyze_bft_scores.py
+++ b/extras/scoring_weight_training/analyze_bft_scores.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: analyze performance of single scores and effect of within_bounds
-> need to manually tune wb_mode variable below to check within_bounds
diff --git a/extras/scoring_weight_training/analyze_weights.py b/extras/scoring_weight_training/analyze_weights.py
index 719bdc7354bdb2ef9ff122efda90ad5be1c61219..d04d40a776bdcec8ef8bd921cff45cf7b24452f9 100644
--- a/extras/scoring_weight_training/analyze_weights.py
+++ b/extras/scoring_weight_training/analyze_weights.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: analyze optimized scoring weights
IN:
diff --git a/extras/scoring_weight_training/collect_optimized_weights.py b/extras/scoring_weight_training/collect_optimized_weights.py
index 66c0dfba8b32d90d5e64641441c47977cf4c3f10..02544620abec130adbf7f33310a271a3f81c25bc 100644
--- a/extras/scoring_weight_training/collect_optimized_weights.py
+++ b/extras/scoring_weight_training/collect_optimized_weights.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: collect optimized weights from run_all_optimizations*.py
IN:
diff --git a/extras/scoring_weight_training/common.py b/extras/scoring_weight_training/common.py
index a46c419d7b54d331265e7a6040c52fdbee9f2135..f0bcf55b2a0c8e0a167907ee7528693962fdf91f 100644
--- a/extras/scoring_weight_training/common.py
+++ b/extras/scoring_weight_training/common.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Common functionality for analysis scripts.'''
import json, random
diff --git a/extras/scoring_weight_training/generate_bft.py b/extras/scoring_weight_training/generate_bft.py
index f7ae946a07b6c3fedd151dcd3f95d712fae25d8d..1687e0e24f9653fee838b68017c088ccb3393004 100644
--- a/extras/scoring_weight_training/generate_bft.py
+++ b/extras/scoring_weight_training/generate_bft.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: combine chunks into a single BFT
IN:
diff --git a/extras/scoring_weight_training/generate_bft_chunks.py b/extras/scoring_weight_training/generate_bft_chunks.py
index c31ca52f887e7e6704e7a053a67d2ef4102cf17f..ef0bcdf35e0e7878feae0af1a52f67a46a06e000 100644
--- a/extras/scoring_weight_training/generate_bft_chunks.py
+++ b/extras/scoring_weight_training/generate_bft_chunks.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: extract a chunk of the BFT
IN:
diff --git a/extras/scoring_weight_training/generate_bft_dbs.py b/extras/scoring_weight_training/generate_bft_dbs.py
index f6f931b357207094a059f8e42e70c8b7c99b90a5..863f922125b1a2b80d1aef301462b3ca83697be4 100644
--- a/extras/scoring_weight_training/generate_bft_dbs.py
+++ b/extras/scoring_weight_training/generate_bft_dbs.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: extract subset of DBs for clean scoring
IN: fragments.json from generate_bft_testset.py
diff --git a/extras/scoring_weight_training/generate_bft_testset.py b/extras/scoring_weight_training/generate_bft_testset.py
index d7fc423f3eba8c0bb8b908ed2bd9268def37a135..ac46ce477ced492e7964d76e6844631dbbc6ee7c 100644
--- a/extras/scoring_weight_training/generate_bft_testset.py
+++ b/extras/scoring_weight_training/generate_bft_testset.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: extract loop examples from structure DB
OUT: fragments.json: list of fragment infos ([chain_idx, offset, length])
diff --git a/extras/scoring_weight_training/generate_training_bft.py b/extras/scoring_weight_training/generate_training_bft.py
index bf46da2c4eb1390c01aeb10e6e665d3a37f9a40c..3d4b5984321db8a0bb54c73ee7167a34227f0e71 100644
--- a/extras/scoring_weight_training/generate_training_bft.py
+++ b/extras/scoring_weight_training/generate_training_bft.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: split BFT into training and test data
IN:
diff --git a/extras/scoring_weight_training/get_weights_code.py b/extras/scoring_weight_training/get_weights_code.py
index d83bf463e77f272b7c053a48294b197a21759f7d..1716a2c340b8a848ba0e3b58acc5a66be53d8134 100644
--- a/extras/scoring_weight_training/get_weights_code.py
+++ b/extras/scoring_weight_training/get_weights_code.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: get code snippets for weights of interest
IN:
diff --git a/extras/scoring_weight_training/optimize_weights.py b/extras/scoring_weight_training/optimize_weights.py
index 06ab7039bd71ecd10ae38db2fb4be8efa0b54973..e6c339c8f31aad2514edf2b251770bcf5902de4d 100644
--- a/extras/scoring_weight_training/optimize_weights.py
+++ b/extras/scoring_weight_training/optimize_weights.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: optimize weights for best possible AUC using Nelder-Mead method
IN:
diff --git a/extras/scoring_weight_training/optimize_weights_cma.py b/extras/scoring_weight_training/optimize_weights_cma.py
index a1372aec26d59a02ef05e2700a458f7f897d6ff3..88870e37cf908fb163582d1540718256e0a1326d 100644
--- a/extras/scoring_weight_training/optimize_weights_cma.py
+++ b/extras/scoring_weight_training/optimize_weights_cma.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: optimize weights for best possible AUC using CMA-ES
IN:
diff --git a/extras/scoring_weight_training/run_all_optimizations.py b/extras/scoring_weight_training/run_all_optimizations.py
index 50d186251a41835ac948824572169b707c657e00..e979fc6d4e01a214a6f163da03817e6817adbbe2 100644
--- a/extras/scoring_weight_training/run_all_optimizations.py
+++ b/extras/scoring_weight_training/run_all_optimizations.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os, json
###############################################################################
diff --git a/extras/test_code/test.cc b/extras/test_code/test.cc
index 59d7963bd48741d4c57b693d97ca869db0b36f19..7920788f06cdfa792e9a8ece3ac9d212a3c26083 100644
--- a/extras/test_code/test.cc
+++ b/extras/test_code/test.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
// Test code for low-level ProMod3 features
#include <ost/base.hh>
diff --git a/loop/data/convert_binaries.py b/loop/data/convert_binaries.py
index 8c2653f6abbf7f3b4fa759d22829cb8ebcb43b31..57171075c54e59cc990517f200765c43ee95a347 100644
--- a/loop/data/convert_binaries.py
+++ b/loop/data/convert_binaries.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Convert files from portable to raw.'''
import sys
import os
diff --git a/loop/doc/all_atom.rst b/loop/doc/all_atom.rst
index b2f19a81997933e3ac1815f2a7759cb0f8b06613..eaeb294774c88c8f4c239fc493e2eb641ee7408f 100644
--- a/loop/doc/all_atom.rst
+++ b/loop/doc/all_atom.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Handling All Atom Positions
================================================================================
diff --git a/loop/doc/backbone.rst b/loop/doc/backbone.rst
index 90209e98f296298e9b260ee6db19f0f2956c8253..3acc2f8e1a2b74a97e559c050e71eb97c777802e 100644
--- a/loop/doc/backbone.rst
+++ b/loop/doc/backbone.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Representing Loops
================================================================================
diff --git a/loop/doc/index.rst b/loop/doc/index.rst
index f60393092beaea6d8315036c82ee7dfb02b267d7..1b4199c068f6532d019465b011fb112ef140443f 100644
--- a/loop/doc/index.rst
+++ b/loop/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.loop` - Loop Handling
================================================================================
diff --git a/loop/doc/load_loop_objects.rst b/loop/doc/load_loop_objects.rst
index 07596175fde261f02781b8f5afbbd8ac09ff2e83..a8410bea4fa9ec2f5a7ff3ac96ed26d06f707aea 100644
--- a/loop/doc/load_loop_objects.rst
+++ b/loop/doc/load_loop_objects.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Loading Precomputed Objects
================================================================================
diff --git a/loop/doc/mm_system_creation.rst b/loop/doc/mm_system_creation.rst
index 7ad0c03a88e75d071685fbee47a3d5f88dcc6530..87b6fb05808a9d70e5e489638d087cd99d95c46c 100644
--- a/loop/doc/mm_system_creation.rst
+++ b/loop/doc/mm_system_creation.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Generate :mod:`ost.mol.mm` systems
================================================================================
diff --git a/loop/doc/structure_db.rst b/loop/doc/structure_db.rst
index a5152b7be20a3ff0ebb4645e2d2b10a16c5073e1..b3089c7248bc40d5f4bd292125795b2edde82204 100644
--- a/loop/doc/structure_db.rst
+++ b/loop/doc/structure_db.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Structural Data
================================================================================
diff --git a/loop/doc/torsion_sampler.rst b/loop/doc/torsion_sampler.rst
index 0962c3563d62638c5948f7d6f08189b2fcf6a95b..8344079a5065f12c19e844f50be70636032ba365 100644
--- a/loop/doc/torsion_sampler.rst
+++ b/loop/doc/torsion_sampler.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Sampling Dihedral Angles
================================================================================
diff --git a/loop/pymod/__init__.py b/loop/pymod/__init__.py
index fc70505fd93e0ec4f2cfe0b6286935732beb3457..3d3a8d1f0794350f978d5a05ca341d721d226018 100644
--- a/loop/pymod/__init__.py
+++ b/loop/pymod/__init__.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Initialise the loop module."""
# geom needed for export_backbone
from ost import geom
diff --git a/loop/pymod/export_all_atom_env.cc b/loop/pymod/export_all_atom_env.cc
index 8ebdf1229c8137bf69435b1c65b38f409c016c4c..552bc6135a4b9d328d13f7f6809b8f254245b3cd 100644
--- a/loop/pymod/export_all_atom_env.cc
+++ b/loop/pymod/export_all_atom_env.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_all_atom_positions.cc b/loop/pymod/export_all_atom_positions.cc
index d161f4b05551ca743457a978735e2d363d96dcf4..143020cdec7b2291c50c6e337e3ecfbfc47967e0 100644
--- a/loop/pymod/export_all_atom_positions.cc
+++ b/loop/pymod/export_all_atom_positions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_amino_acid_atoms.cc b/loop/pymod/export_amino_acid_atoms.cc
index 5efcbd77c6b95be25b330f9dda5687a59b98934a..bd163ca2698cf0365de13dbd1fd9a14fb31e8c96 100644
--- a/loop/pymod/export_amino_acid_atoms.cc
+++ b/loop/pymod/export_amino_acid_atoms.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/message.hh>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_backbone.cc b/loop/pymod/export_backbone.cc
index 6d97c8a7eddf9dc0544697e1e00c486e58d323b5..61265152fa088f9c7a2b91c633b8485f32a93c4c 100644
--- a/loop/pymod/export_backbone.cc
+++ b/loop/pymod/export_backbone.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
diff --git a/loop/pymod/export_forcefield_lookup.cc b/loop/pymod/export_forcefield_lookup.cc
index e1405f83bcbe27c0c3329726a3cd330be90c8847..7d56ce4239db3cbb8e9207bf5e4f2dc0a450edda 100644
--- a/loop/pymod/export_forcefield_lookup.cc
+++ b/loop/pymod/export_forcefield_lookup.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/message.hh>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_frag_db.cc b/loop/pymod/export_frag_db.cc
index c4fc17f0fcf24c15a2e25c78483095c1c0d0bee0..c5b7c59925cec905fc7e1e2c0ba2869a5b34db9e 100644
--- a/loop/pymod/export_frag_db.cc
+++ b/loop/pymod/export_frag_db.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_fragger.cc b/loop/pymod/export_fragger.cc
index 4c4f8b5903eefddfaddefa6f7696de4a26c45f31..d6afcf0f9f0d07785046f02de58510865395dcb3 100644
--- a/loop/pymod/export_fragger.cc
+++ b/loop/pymod/export_fragger.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
diff --git a/loop/pymod/export_loop_object_loader.cc b/loop/pymod/export_loop_object_loader.cc
index fb6cb09087e4950cb473d4255fd2dc1ad5731ccb..48dcf12c5cb99e4e4d62390d6861ad30ea062285 100644
--- a/loop/pymod/export_loop_object_loader.cc
+++ b/loop/pymod/export_loop_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/loop/loop_object_loader.hh>
diff --git a/loop/pymod/export_mm_system_creator.cc b/loop/pymod/export_mm_system_creator.cc
index a4f316c01ff0cc4ec4d1daed11625cb0e4cfb3c9..cffb7509271404be2fb8d39a9a83819da368fc02 100644
--- a/loop/pymod/export_mm_system_creator.cc
+++ b/loop/pymod/export_mm_system_creator.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_psipred_prediction.cc b/loop/pymod/export_psipred_prediction.cc
index fcdbb64b959b90b964898583d634ae54dba3b5a0..18eca538596823bd5ebe1bc3d6e5fc24c24e1a3d 100644
--- a/loop/pymod/export_psipred_prediction.cc
+++ b/loop/pymod/export_psipred_prediction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
diff --git a/loop/pymod/export_structure_db.cc b/loop/pymod/export_structure_db.cc
index 954614498a7b99168f1c1598211a7be1e7a86889..a9f96d4629a10e8f32dbbc2915a63b94012f7c02 100644
--- a/loop/pymod/export_structure_db.cc
+++ b/loop/pymod/export_structure_db.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_torsion_sampler.cc b/loop/pymod/export_torsion_sampler.cc
index 286a70302f7be6f0c4ad3f350b078db0fb39fb6f..ead2f96d30e09d41df6ce5e14a86a11d228b3f27 100644
--- a/loop/pymod/export_torsion_sampler.cc
+++ b/loop/pymod/export_torsion_sampler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
diff --git a/loop/pymod/wrap_loop.cc b/loop/pymod/wrap_loop.cc
index fd8a344e9450630fc028a11bb8d589996e2fb6a8..39aa16aeaa5ac7ada91bc8dc37904ccddad25c41 100644
--- a/loop/pymod/wrap_loop.cc
+++ b/loop/pymod/wrap_loop.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_FragDB();
diff --git a/loop/src/all_atom_env.cc b/loop/src/all_atom_env.cc
index cef7b4eca18ebfd5ada74f84012cfd95807185f2..991e90c777445cdc80dd3328c1f41bf55a41a614 100644
--- a/loop/src/all_atom_env.cc
+++ b/loop/src/all_atom_env.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/all_atom_env.hh>
#include <promod3/core/message.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/loop/src/all_atom_env.hh b/loop/src/all_atom_env.hh
index 66ead82b0d564e81dcf86b571823d6fbf5486080..f39cf74347df2bf7c99f104721f1e45470f79ed9 100644
--- a/loop/src/all_atom_env.hh
+++ b/loop/src/all_atom_env.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_LOOP_ALL_ATOM_ENV_HH
#define PROMOD3_LOOP_ALL_ATOM_ENV_HH
diff --git a/loop/src/all_atom_positions.cc b/loop/src/all_atom_positions.cc
index 2dad21d0e0c802bd81cc771af31c4de0127a6db5..38976fed98a1016fc5cfd77397a1680bf1497c17 100644
--- a/loop/src/all_atom_positions.cc
+++ b/loop/src/all_atom_positions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/all_atom_positions.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/geom_base.hh>
diff --git a/loop/src/all_atom_positions.hh b/loop/src/all_atom_positions.hh
index 3947d788eb5a91ad70927955eea94dc01f236b3f..03a2c2c9c952326b5629a8a269afc0943c6a1fba 100644
--- a/loop/src/all_atom_positions.hh
+++ b/loop/src/all_atom_positions.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_LOOP_ALL_ATOM_POSITIONS_HH
#define PROMOD3_LOOP_ALL_ATOM_POSITIONS_HH
diff --git a/loop/src/amino_acid_atoms.cc b/loop/src/amino_acid_atoms.cc
index 9924dbbaa67cf73e7b83212aad05a2d1170c0590..66e5c3364e3f6739052cd60b30de3dd46a9cbc5c 100644
--- a/loop/src/amino_acid_atoms.cc
+++ b/loop/src/amino_acid_atoms.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/amino_acid_atoms.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/message.hh>
diff --git a/loop/src/amino_acid_atoms.hh b/loop/src/amino_acid_atoms.hh
index 7de3f538be80ba8100911f3719d3c19e562f0397..44b32de1d16f15f5f298dabd718fc906b965e0e2 100644
--- a/loop/src/amino_acid_atoms.hh
+++ b/loop/src/amino_acid_atoms.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality to deal with all atoms of amino acids.
///
/// - ...AtomIndex are used to index atoms of each amino acid. The backbone atom
diff --git a/loop/src/backbone.cc b/loop/src/backbone.cc
index edb4dd63c7dbbf09997f30d0395166e21a9104ad..35bc7e86a0de04cdf761e2fc71c3ec5057aea6d7 100644
--- a/loop/src/backbone.cc
+++ b/loop/src/backbone.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/backbone.hh>
#include <promod3/loop/density_creator.hh>
#include <ost/conop/processor.hh>
diff --git a/loop/src/backbone.hh b/loop/src/backbone.hh
index 70e3cb15fe838860bc2d5a4ad506475dc376c4b8..253bcd429305548c0c58b728921c43141eab658f 100644
--- a/loop/src/backbone.hh
+++ b/loop/src/backbone.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_BACKBONE_HH
#define PM3_BACKBONE_HH
diff --git a/loop/src/bb_trace_param.cc b/loop/src/bb_trace_param.cc
index aa8dabef0de6ad1fb1db65f05ef9ba19a62ab748..9a3fa35e869e729da119fa9c7d13e76f756f3439 100644
--- a/loop/src/bb_trace_param.cc
+++ b/loop/src/bb_trace_param.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/bb_trace_param.hh>
#include <promod3/core/message.hh>
diff --git a/loop/src/bb_trace_param.hh b/loop/src/bb_trace_param.hh
index 392eb19657c5682efbc799fab50293cccff4912e..821e1ea7fefa7761ce36cb26164cd473dca52ca5 100644
--- a/loop/src/bb_trace_param.hh
+++ b/loop/src/bb_trace_param.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_BB_TRACE_PARAM_HH
#define PM3_BB_TRACE_PARAM_HH
diff --git a/loop/src/data_bag.hh b/loop/src/data_bag.hh
index f6fa5919024bdcfa32dc9a54e896b85ca66ba1ad..f9926a483b11cb740bcc685e818b8df2a88ad4aa 100644
--- a/loop/src/data_bag.hh
+++ b/loop/src/data_bag.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_CORE_DATA_BAG_HH
#define PM3_CORE_DATA_BAG_HH
diff --git a/loop/src/dense_hash_table.hh b/loop/src/dense_hash_table.hh
index 884c7c3fa5ae9831dd4a2052cca832f9f047c046..ec9f573a09688bcf7f69dcd5ee0e204f360e2bc6 100644
--- a/loop/src/dense_hash_table.hh
+++ b/loop/src/dense_hash_table.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_DENSE_HASH_TABLE_HH
#define PROMOD_LOOP_DENSE_HASH_TABLE_HH
diff --git a/loop/src/dense_map.hh b/loop/src/dense_map.hh
index 189c688cd1a76f70da9fa2a4e0a89c68306a15fb..b0ab0c0fd1fea31ce879553b158c404aa9f2fa10 100644
--- a/loop/src/dense_map.hh
+++ b/loop/src/dense_map.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_DENSE_MAP_HH
#define PROMOD_LOOP_DENSE_MAP_HH
diff --git a/loop/src/density_creator.cc b/loop/src/density_creator.cc
index 6e6d8575159c876b2a3faef9f3c851689f3af3f8..48ba28c5d3e3759b6a5472399b9cc237e41b8343 100644
--- a/loop/src/density_creator.cc
+++ b/loop/src/density_creator.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/density_creator.hh>
#include <promod3/core/message.hh>
diff --git a/loop/src/density_creator.hh b/loop/src/density_creator.hh
index e317ef62d0c819c237c91e210d947c722989fd74..c65a8742bf00bcf8854818076cea9b8fe796a19d 100644
--- a/loop/src/density_creator.hh
+++ b/loop/src/density_creator.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_LOOP_DENSITY_CREATOR_HH
#define PM3_LOOP_DENSITY_CREATOR_HH
diff --git a/loop/src/forcefield_lookup.cc b/loop/src/forcefield_lookup.cc
index e662afe4e529d2f6da17487e95290e40a5ea2062..0dbf5a57ec8d04dffaeef4df4cdde807d11356bf 100644
--- a/loop/src/forcefield_lookup.cc
+++ b/loop/src/forcefield_lookup.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <fstream>
#include <promod3/loop/forcefield_lookup.hh>
#include <promod3/core/portable_binary_serializer.hh>
diff --git a/loop/src/forcefield_lookup.hh b/loop/src/forcefield_lookup.hh
index f0d08b8975d0483c75dc36654cd6a769c0ca87eb..cf043ace433fd53e548bee7d244d1e334ed0dece 100644
--- a/loop/src/forcefield_lookup.hh
+++ b/loop/src/forcefield_lookup.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality to deal with force fields.
///
/// Here, we define:
diff --git a/loop/src/frag_db.cc b/loop/src/frag_db.cc
index 73f75b903efc17f72edbf402f63acd58e989ec9c..8bbe44523a4b37d6c73b555d1d4f084f79d4c25a 100644
--- a/loop/src/frag_db.cc
+++ b/loop/src/frag_db.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <fstream>
#include <limits>
#include <ost/mol/mol.hh>
diff --git a/loop/src/frag_db.hh b/loop/src/frag_db.hh
index 6bb3134df3e2084734a02dd8b5b27573ffa5b120..8df2c8b4cc3c76ee78d2388bb816b5d03053a198 100644
--- a/loop/src/frag_db.hh
+++ b/loop/src/frag_db.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_FRAG_DB_HH
#define PROMOD_LOOP_FRAG_DB_HH
diff --git a/loop/src/fragger.cc b/loop/src/fragger.cc
index aa6bc18dd72ad8699eddf2493eac9dfc2353ef48..e9db9731f8d5c171005b5665763f509ce8980fd5 100644
--- a/loop/src/fragger.cc
+++ b/loop/src/fragger.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/fragger.hh>
// for raw serialization
diff --git a/loop/src/fragger.hh b/loop/src/fragger.hh
index b109770cc5d2ace6a75d4da6d08e24d8355a8c04..c83d7df913459205c33a3aa8a68973363fef04e2 100644
--- a/loop/src/fragger.hh
+++ b/loop/src/fragger.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_FRAGGER_HH
#define PROMOD_LOOP_FRAGGER_HH
diff --git a/loop/src/hydrogen_constructor.cc b/loop/src/hydrogen_constructor.cc
index 27718a746a1f408dcf3158e99da99ba779034114..3df6326d6a173e8a0b30049c29688ae5a694c76a 100644
--- a/loop/src/hydrogen_constructor.cc
+++ b/loop/src/hydrogen_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/hydrogen_constructor.hh>
namespace promod3 { namespace loop {
diff --git a/loop/src/hydrogen_constructor.hh b/loop/src/hydrogen_constructor.hh
index 966a3a2064b19cfd258f6a67594aaee29d5d18b8..3ad2d3a97d28c712dab8c1c969d40887fff2dc9a 100644
--- a/loop/src/hydrogen_constructor.hh
+++ b/loop/src/hydrogen_constructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality to construct hydrogens for amino acids.
#ifndef PROMOD3_HYDROGEN_CONSTRUCTOR_HH
diff --git a/loop/src/hydrogen_rule_lookup.cc b/loop/src/hydrogen_rule_lookup.cc
index f1201c9f9b227a53df5517cb5c52eac0b44ba670..af209a9058eb8cd8e7307de287db4f5979424f9d 100644
--- a/loop/src/hydrogen_rule_lookup.cc
+++ b/loop/src/hydrogen_rule_lookup.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/hydrogen_rule_lookup.hh>
namespace promod3 { namespace loop {
diff --git a/loop/src/hydrogen_rule_lookup.hh b/loop/src/hydrogen_rule_lookup.hh
index 43300434aeadc64c94725f152a28cb62b2fb8275..1114e3554f89812893b0c2237d6c332568ccc8fb 100644
--- a/loop/src/hydrogen_rule_lookup.hh
+++ b/loop/src/hydrogen_rule_lookup.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines rules to construct hydrogens for amino acids.
#ifndef PROMOD3_HYDROGEN_RULE_LOOKUP_HH
diff --git a/loop/src/idx_handler.cc b/loop/src/idx_handler.cc
index dfc50c26c159112638e248fde20750fa17ba362c..688fdbbeb2104c7368a8e1f9effab2c9643ab78e 100644
--- a/loop/src/idx_handler.cc
+++ b/loop/src/idx_handler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/idx_handler.hh>
#include <promod3/core/message.hh>
#include <ost/log.hh>
diff --git a/loop/src/idx_handler.hh b/loop/src/idx_handler.hh
index 193520286029bdf138bbd6c738a37405ef905d27..9cecb881e5f8f2338b03710371afb296d0117a31 100644
--- a/loop/src/idx_handler.hh
+++ b/loop/src/idx_handler.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_LOOP_IDX_HANDLER_HH
#define PROMOD3_LOOP_IDX_HANDLER_HH
diff --git a/loop/src/loop_object_loader.cc b/loop/src/loop_object_loader.cc
index 4eeff56860e15a6603312f8fa62104ad1e3f87af..f05bd9dbc45bfb244fb1b5538daa3acd5198fb9a 100644
--- a/loop/src/loop_object_loader.cc
+++ b/loop/src/loop_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/loop_object_loader.hh>
#include <promod3/config.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/loop/src/loop_object_loader.hh b/loop/src/loop_object_loader.hh
index 0b89e68a50ba2f96e453d3a3d1aab52b2fbe6d21..b42a2ffe249c768fcc422391b3e76ab3f4954f68 100644
--- a/loop/src/loop_object_loader.hh
+++ b/loop/src/loop_object_loader.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_LOOP_OBJECT_LOADER_HH
#define PROMOD3_LOOP_OBJECT_LOADER_HH
diff --git a/loop/src/mm_system_creator.cc b/loop/src/mm_system_creator.cc
index fdda4908ddbd0edaede2c01afc5e69f8caeb0f0b..6bdc36a4dd64e6b9407a81ac515ddfaeb975aa1e 100644
--- a/loop/src/mm_system_creator.cc
+++ b/loop/src/mm_system_creator.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/mm_system_creator.hh>
#include <promod3/loop/hydrogen_constructor.hh>
diff --git a/loop/src/mm_system_creator.hh b/loop/src/mm_system_creator.hh
index 2602a27e8f752223f2aedc905a3b7b9f80d07318..dd4a41713e3d6103b3a275f14c1baf1cd5283913 100644
--- a/loop/src/mm_system_creator.hh
+++ b/loop/src/mm_system_creator.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MM_SYSTEM_CREATOR_HH
#define PROMOD3_MM_SYSTEM_CREATOR_HH
diff --git a/loop/src/paged_array.hh b/loop/src/paged_array.hh
index 3591e2915fb9b3acc07ce9ffd10720860ada420c..21c2cce8418d50494075cb01eb507e229876e13b 100644
--- a/loop/src/paged_array.hh
+++ b/loop/src/paged_array.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef OST_PAGED_ARRAY_HH
#define OST_PAGED_ARRAY_HH
diff --git a/loop/src/psipred_prediction.cc b/loop/src/psipred_prediction.cc
index 00b3f460be3e9564c5d7eda160cbc9b31440ccb3..08251013ca1bebf8cbf3f112388d6e6f9ad405c0 100644
--- a/loop/src/psipred_prediction.cc
+++ b/loop/src/psipred_prediction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/psipred_prediction.hh>
namespace promod3{ namespace loop{
diff --git a/loop/src/psipred_prediction.hh b/loop/src/psipred_prediction.hh
index 31ff335c15ee553b6443a44f1b3addd75fb9276d..1b32ef591b21412aef43c05540b445d1ba5a262a 100644
--- a/loop/src/psipred_prediction.hh
+++ b/loop/src/psipred_prediction.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_PSIPRED_PREDICTION_HH
#define PROMOD_LOOP_PSIPRED_PREDICTION_HH
diff --git a/loop/src/sidechain_atom_constructor.cc b/loop/src/sidechain_atom_constructor.cc
index 0fb09cefbb5367fd9b24103448f62ee32a3db2dc..e1832ae3bb90d43df3acd79cfe118ee53a30aea9 100644
--- a/loop/src/sidechain_atom_constructor.cc
+++ b/loop/src/sidechain_atom_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/sidechain_atom_constructor.hh>
#include <promod3/core/geom_base.hh>
diff --git a/loop/src/sidechain_atom_constructor.hh b/loop/src/sidechain_atom_constructor.hh
index 92b97f100d88fecb35447b9354991b2daaa0a9a9..0c6679e3a8d8e56623b383995db2275562eba768 100644
--- a/loop/src/sidechain_atom_constructor.hh
+++ b/loop/src/sidechain_atom_constructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality to construct sidechain heavy atoms based on
/// dihedral angles for amino acids.
diff --git a/loop/src/sidechain_atom_rule_lookup.cc b/loop/src/sidechain_atom_rule_lookup.cc
index 27d0b4f86b16d6eafd758e87bc4760c170e9bb56..70afd99afd898359ab34c39fd9780c8a2bced0aa 100644
--- a/loop/src/sidechain_atom_rule_lookup.cc
+++ b/loop/src/sidechain_atom_rule_lookup.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/sidechain_atom_rule_lookup.hh>
#include <promod3/loop/amino_acid_atoms.hh>
#include <ost/conop/amino_acids.hh>
diff --git a/loop/src/sidechain_atom_rule_lookup.hh b/loop/src/sidechain_atom_rule_lookup.hh
index 71805709bdccb274bf9a2c9d77f8f93ac785102d..38a35491938c689a1ee8ce69bbd93e9d7c50379a 100644
--- a/loop/src/sidechain_atom_rule_lookup.hh
+++ b/loop/src/sidechain_atom_rule_lookup.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines rules to construct sidechain heavy atoms from dihedral angles.
#ifndef PROMOD3_SIDECHAIN_ATOM_RULE_LOOKUP_HH
diff --git a/loop/src/stem_geom.hh b/loop/src/stem_geom.hh
index a1d123c5375634eef346ea388a2e357ed8587441..b29565dacfa02f04db8e3fb982e76e3ed203d1a5 100644
--- a/loop/src/stem_geom.hh
+++ b/loop/src/stem_geom.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MELD_FRAGMENT_HH
#define PM3_MELD_FRAGMENT_HH
diff --git a/loop/src/structure_db.cc b/loop/src/structure_db.cc
index 5758c3a3be818fa75060416afb31a5afe1b383ac..b78558c11193b8b0af934e3183c26c7ee7afa71a 100644
--- a/loop/src/structure_db.cc
+++ b/loop/src/structure_db.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/structure_db.hh>
#include <promod3/core/portable_binary_serializer.hh>
#include <promod3/core/check_io.hh>
diff --git a/loop/src/structure_db.hh b/loop/src/structure_db.hh
index a11db69ef12d31a3669ea5c986933ebadd94e640..228785d6c19ab6084783272cd5f9fff86deffefd 100644
--- a/loop/src/structure_db.hh
+++ b/loop/src/structure_db.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_STRUCTURE_DB_HH
#define PROMOD_LOOP_STRUCTURE_DB_HH
diff --git a/loop/src/structure_db_custom_types.hh b/loop/src/structure_db_custom_types.hh
index d636c7dbd21edb8a335fb91f51f4d2003a064548..49ec68b4867e0a95382d14fa83b09c37bf606c01 100644
--- a/loop/src/structure_db_custom_types.hh
+++ b/loop/src/structure_db_custom_types.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_STRUCTURE_DB_CUSTOM_TYPES
#define PROMOD_LOOP_STRUCTURE_DB_CUSTOM_TYPES
diff --git a/loop/src/torsion_sampler.cc b/loop/src/torsion_sampler.cc
index 11ee9137e8e5cd8d1af6b493d5f5f380bf28cb65..70d32064a3c7638d394b25209cbdb0ba670fc2d1 100644
--- a/loop/src/torsion_sampler.cc
+++ b/loop/src/torsion_sampler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/torsion_sampler.hh>
#include <promod3/core/check_io.hh>
#include <promod3/core/portable_binary_serializer.hh>
diff --git a/loop/src/torsion_sampler.hh b/loop/src/torsion_sampler.hh
index d489e35c5fba307bf1fcb21bd92dba6c98d19bd3..4e5c9fd2f10fb3f5062319eac1f018e5ee32f759 100644
--- a/loop/src/torsion_sampler.hh
+++ b/loop/src/torsion_sampler.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_TORSION_SAMPLER_HH
#define PROMOD_LOOP_TORSION_SAMPLER_HH
diff --git a/loop/src/ushort_vec.hh b/loop/src/ushort_vec.hh
index 9016eff2fcdf4cc8d9c6e6ff2581542f4320ae65..6339c2ce524570f8b57b9c01afc4e2db3d7da30a 100644
--- a/loop/src/ushort_vec.hh
+++ b/loop/src/ushort_vec.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_USHORT_VEC_HH
#define PROMOD_USHORT_VEC_HH
diff --git a/loop/tests/test_all_atom_env.cc b/loop/tests/test_all_atom_env.cc
index a3ecc8205a1916fee6c43c010102248c5128c706..0c2a45d3c4c1a7f2fc1965c4aec7e0922dbacabe 100644
--- a/loop/tests/test_all_atom_env.cc
+++ b/loop/tests/test_all_atom_env.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/all_atom_env.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_all_atom_positions.cc b/loop/tests/test_all_atom_positions.cc
index 14a21edaf8b21eb69c372bec36a20722c8880a6a..f50d5c5b40ee476385049e66059eca9857a1d71d 100644
--- a/loop/tests/test_all_atom_positions.cc
+++ b/loop/tests/test_all_atom_positions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/all_atom_positions.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_amino_acid_atoms.cc b/loop/tests/test_amino_acid_atoms.cc
index a8b55b9d4829bb8cb54823816f66ac01ed4ecf7e..d4723925bbd0510426e36bf78a66ffea69145bf6 100644
--- a/loop/tests/test_amino_acid_atoms.cc
+++ b/loop/tests/test_amino_acid_atoms.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/amino_acid_atoms.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_backbone.cc b/loop/tests/test_backbone.cc
index 4b82781ca072c3ebd504f4a502a59e13a30a4958..8b7e31c938c78d32ce1d9d336436776960f1661f 100644
--- a/loop/tests/test_backbone.cc
+++ b/loop/tests/test_backbone.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/backbone.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_forcefield.cc b/loop/tests/test_forcefield.cc
index 1c7c54b9bf830681165657207ffb161522893fad..8c0722a397b01412f1413b52d43d3095836b25c2 100644
--- a/loop/tests/test_forcefield.cc
+++ b/loop/tests/test_forcefield.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/forcefield_lookup.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_hydrogens.cc b/loop/tests/test_hydrogens.cc
index 5d24f74da614f648defab26a9998fe61042263a1..523d10128b8df758752d9809dee468c4e2ffbeb9 100644
--- a/loop/tests/test_hydrogens.cc
+++ b/loop/tests/test_hydrogens.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/hydrogen_rule_lookup.hh>
#include <promod3/loop/hydrogen_constructor.hh>
diff --git a/loop/tests/test_idx_handler.cc b/loop/tests/test_idx_handler.cc
index 1ae50995d44229053a85ea9c7280fef941d13726..a726fc2be0e34be231d4b60e6eed1b53d44121dd 100644
--- a/loop/tests/test_idx_handler.cc
+++ b/loop/tests/test_idx_handler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/idx_handler.hh>
#include <promod3/loop/backbone.hh>
diff --git a/loop/tests/test_mm_system_creator.cc b/loop/tests/test_mm_system_creator.cc
index b02651f48ec964ad680fda776d40e02125d595c1..0077c2a900b6d35f51ed7ec7ee2c95acfcd99d38 100644
--- a/loop/tests/test_mm_system_creator.cc
+++ b/loop/tests/test_mm_system_creator.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/mm_system_creator.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_psipred_prediction.cc b/loop/tests/test_psipred_prediction.cc
index 7053e5a1dc6eaf2f60ab062fca6765b0d13e632e..5dbc83c7ba8d5a08970886598342c328b733aa32 100644
--- a/loop/tests/test_psipred_prediction.cc
+++ b/loop/tests/test_psipred_prediction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/psipred_prediction.hh>
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
diff --git a/loop/tests/test_sidechain_construction.cc b/loop/tests/test_sidechain_construction.cc
index 70c4ea2eaaff04530ffe3fdc2c613abc3a43d46b..2e65c53c7d40efce1db613e4d2836969429d6421 100644
--- a/loop/tests/test_sidechain_construction.cc
+++ b/loop/tests/test_sidechain_construction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/sidechain_atom_rule_lookup.hh>
#include <promod3/loop/sidechain_atom_constructor.hh>
diff --git a/loop/tests/test_structuredb.cc b/loop/tests/test_structuredb.cc
index 01cf26055402ab8a89363d2426287329d48a3dff..69715800d0b4bcbda3a3c70fef82a4d162cce1eb 100644
--- a/loop/tests/test_structuredb.cc
+++ b/loop/tests/test_structuredb.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/structure_db.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_torsion_sampler.cc b/loop/tests/test_torsion_sampler.cc
index e956f094da3786b7a783e34f1d057e97598af5d6..af517a90beb8e9c6d989083895e71239757c4f6d 100644
--- a/loop/tests/test_torsion_sampler.cc
+++ b/loop/tests/test_torsion_sampler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/torsion_sampler.hh>
#include <promod3/core/message.hh>
#include <promod3/loop/loop_object_loader.hh>
diff --git a/loop/tests/tests.cc b/loop/tests/tests.cc
index 1ba3edee29d4c0accae2178df7e5dc482f294322..5757e0a2c6da50f5d690c41365dbb0913543503e 100644
--- a/loop/tests/tests.cc
+++ b/loop/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_loop
#define BOOST_AUTO_TEST_MAIN
diff --git a/modelling/doc/algorithms.rst b/modelling/doc/algorithms.rst
index 7ff5ae3a33e08ccccdf6d98f87abe2748e1d0d19..51357bc0615a49e58f2ef12f3efad67eeb3b003d 100644
--- a/modelling/doc/algorithms.rst
+++ b/modelling/doc/algorithms.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Modelling Algorithms
================================================================================
diff --git a/modelling/doc/gap_handling.rst b/modelling/doc/gap_handling.rst
index e939f9f60fa779b43bfdb196e0649ebd28306a08..b70d39a57558559a9ee4f6240384ffdbeb4df34c 100644
--- a/modelling/doc/gap_handling.rst
+++ b/modelling/doc/gap_handling.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Handling Gaps
================================================================================
diff --git a/modelling/doc/index.rst b/modelling/doc/index.rst
index 27ed61013a17190ebef7f0afb0027241c0e19294..ce9be313f8c26c747a5e1d711c9bf44751ac8587 100644
--- a/modelling/doc/index.rst
+++ b/modelling/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.modelling` - Protein Modelling
================================================================================
diff --git a/modelling/doc/loop_candidates.rst b/modelling/doc/loop_candidates.rst
index d0711c5a7c89292a61e3f1547ed28af62841382b..927107a0ddaa78b2bb6efe78b80c0f1dbc5aae1e 100644
--- a/modelling/doc/loop_candidates.rst
+++ b/modelling/doc/loop_candidates.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Handling Loop Candidates
================================================================================
diff --git a/modelling/doc/loop_closing.rst b/modelling/doc/loop_closing.rst
index 5290137a9ad5e531abbd6aa67170604c6f7b2405..21b842f5d1e25b00dc2f2cb863bf8124ccfb8f81 100644
--- a/modelling/doc/loop_closing.rst
+++ b/modelling/doc/loop_closing.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Fitting Loops Into Gaps
================================================================================
diff --git a/modelling/doc/model_checking.rst b/modelling/doc/model_checking.rst
index 97d7f69a83735d2757ede0afee224f181afdd6d5..03763e178971929ce13573f5ac8d72dc6624434d 100644
--- a/modelling/doc/model_checking.rst
+++ b/modelling/doc/model_checking.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Model Checking
================================================================================
diff --git a/modelling/doc/monte_carlo.rst b/modelling/doc/monte_carlo.rst
index 4040c723bac575c4d216d1ee149866bc369b24ca..1cb924b406ab017598f909d34872c0394697cb72 100644
--- a/modelling/doc/monte_carlo.rst
+++ b/modelling/doc/monte_carlo.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Generating Loops De Novo
================================================================================
diff --git a/modelling/doc/pipeline.rst b/modelling/doc/pipeline.rst
index 175b65c5d6554d15f76076e3bd3c530595a7cf64..54d86037d316ed87434fea7ae1cca2e3a2ae11d0 100644
--- a/modelling/doc/pipeline.rst
+++ b/modelling/doc/pipeline.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Modelling Pipeline
================================================================================
diff --git a/modelling/doc/sidechain_reconstruction.rst b/modelling/doc/sidechain_reconstruction.rst
index c6e933f4a65043446a3ef51b7423ae3370509e3d..f6a076c6b780c809d729bf52882d7e7e1fc04cb0 100644
--- a/modelling/doc/sidechain_reconstruction.rst
+++ b/modelling/doc/sidechain_reconstruction.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Sidechain Reconstruction
================================================================================
diff --git a/modelling/pymod/__init__.py b/modelling/pymod/__init__.py
index 70ccfbb88eb891f54d21a19f01f99425b49d7f49..d81fc6ee63f97c01c6810036749a957c53f35205 100644
--- a/modelling/pymod/__init__.py
+++ b/modelling/pymod/__init__.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Initialise the modelling module."""
from _modelling import *
from _closegaps import *
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index aa857023be8b7543a56670d0b8db6e340a4edcf1..167379a70fa81bbfaa400f65050d617655b0664b 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''High-level functionality for modelling module to close gaps. Added in the
__init__.py file. To be used directly by passing a ModellingHandle instance
as argument.
diff --git a/modelling/pymod/_denovo.py b/modelling/pymod/_denovo.py
index 51dd26d0ca0b540c9b6523c66337f5aa0a96fa52..445c9574c829b4bc02f3eed107e68586bacdff34 100644
--- a/modelling/pymod/_denovo.py
+++ b/modelling/pymod/_denovo.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import scoring, loop
from _modelling import *
diff --git a/modelling/pymod/_fragger_handle.py b/modelling/pymod/_fragger_handle.py
index 95dee6db0f9c33dcdaf0bd3f5e78ba31c5202487..50ba6e50e6f3c7f000b90c0687cfcf83d864c79c 100644
--- a/modelling/pymod/_fragger_handle.py
+++ b/modelling/pymod/_fragger_handle.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Python functionality to generate fraggers.'''
from promod3.loop import *
diff --git a/modelling/pymod/_molprobity.py b/modelling/pymod/_molprobity.py
index ad431058365f6a80c702a9518fe237e2ac860adb..8f583e6ee2e90a2741c20d21394fa23d0a0a0ddb 100644
--- a/modelling/pymod/_molprobity.py
+++ b/modelling/pymod/_molprobity.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Binding to external MolProbity tool to get scores.'''
import ost
diff --git a/modelling/pymod/_monte_carlo.py b/modelling/pymod/_monte_carlo.py
index 7c284aed00a979441c76a938f8282a0484cfb4aa..13a085ccac3c4cac8b8727540f62671f0bfc43f9 100644
--- a/modelling/pymod/_monte_carlo.py
+++ b/modelling/pymod/_monte_carlo.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import random
import math
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 4beb438b967693edccf160cc48404a5df9bc2b47..56cc847c61da1238af93114613208ab3061fe2a6 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''High-level functionality for modelling module to build pipelines. Added in
the __init__.py file. To be used directly by passing a ModellingHandle instance
as argument.
diff --git a/modelling/pymod/_reconstruct_sidechains.py b/modelling/pymod/_reconstruct_sidechains.py
index 37deb4901ee0310b0d59000cc0b0bc6a5fcdddcb..d9a7dbd5541b9e7ca3102bf9e8cc78bda4b8f1e6 100644
--- a/modelling/pymod/_reconstruct_sidechains.py
+++ b/modelling/pymod/_reconstruct_sidechains.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import geom, mol, conop
from promod3 import core, sidechain
import traceback
diff --git a/modelling/pymod/_ring_punches.py b/modelling/pymod/_ring_punches.py
index 969aca39d8b7daabb2dc354350314bc18ac13f80..2efed0c1cd7c479abc6c397ea2ab141d0b8301ae 100644
--- a/modelling/pymod/_ring_punches.py
+++ b/modelling/pymod/_ring_punches.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Helper functions to deal with ring punchings.'''
import ost
from ost import geom
diff --git a/modelling/pymod/export_extension_scheme.cc b/modelling/pymod/export_extension_scheme.cc
index 56e96be00216cd1a66c624fdd95accf7325dadd1..26298341987427308fb16d1f70a2503c561ad6fd 100644
--- a/modelling/pymod/export_extension_scheme.cc
+++ b/modelling/pymod/export_extension_scheme.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <promod3/modelling/extension_scheme.hh>
diff --git a/modelling/pymod/export_gap.cc b/modelling/pymod/export_gap.cc
index d2c8d07ff216564bb8e71d33c823a4399b095654..de39d2c23324a7d0c0d3fd2724272600ae7d454d 100644
--- a/modelling/pymod/export_gap.cc
+++ b/modelling/pymod/export_gap.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <promod3/modelling/gap.hh>
diff --git a/modelling/pymod/export_gap_extender.cc b/modelling/pymod/export_gap_extender.cc
index 5c27c41b33ea38fbc8fa4789ebef5cc9ca093b35..3d530e190333a71ae9d1cdd01bed9ba059350596 100644
--- a/modelling/pymod/export_gap_extender.cc
+++ b/modelling/pymod/export_gap_extender.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/modelling/gap_extender.hh>
#include <promod3/core/export_helper.hh>
diff --git a/modelling/pymod/export_loop_candidate.cc b/modelling/pymod/export_loop_candidate.cc
index 7bb657db9d310ff2319217e054fa184b6f2df44d..564395002d68cfbf3699526ef35e0cfa10b08611 100644
--- a/modelling/pymod/export_loop_candidate.cc
+++ b/modelling/pymod/export_loop_candidate.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
diff --git a/modelling/pymod/export_loop_closure.cc b/modelling/pymod/export_loop_closure.cc
index a6aa1a0da761152f0fab494f034725b1746c7205..0a28b6bea9201f6e848a5493c2d88f4135c69330 100644
--- a/modelling/pymod/export_loop_closure.cc
+++ b/modelling/pymod/export_loop_closure.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
diff --git a/modelling/pymod/export_model.cc b/modelling/pymod/export_model.cc
index db325e3d416a5b436da212f4ee0f550ac222a106..589242c563e995db7f7d96dd55f90e6c1ecf34b6 100644
--- a/modelling/pymod/export_model.cc
+++ b/modelling/pymod/export_model.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <promod3/modelling/model.hh>
diff --git a/modelling/pymod/export_monte_carlo.cc b/modelling/pymod/export_monte_carlo.cc
index 1cbf251a6f3114dc5f3c0cddd9b509b0dc1eb987..32950cdbb17e2ada13c0772bfdb72ec50d5bcb62 100644
--- a/modelling/pymod/export_monte_carlo.cc
+++ b/modelling/pymod/export_monte_carlo.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/python/raw_function.hpp>
diff --git a/modelling/pymod/export_rigid_blocks.cc b/modelling/pymod/export_rigid_blocks.cc
index 3c7584d80b6f39ca036dfe616d15f86a6ed59274..36763f3a089dc775e3cdbe21f5091dc1e3c0b7c7 100644
--- a/modelling/pymod/export_rigid_blocks.cc
+++ b/modelling/pymod/export_rigid_blocks.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/modelling/pymod/export_score_container.cc b/modelling/pymod/export_score_container.cc
index 237e1d415f0dc52125c369ad2b5aebbde1c5d6ad..4afef319bfd48498b6929b542a1afd561b893066 100644
--- a/modelling/pymod/export_score_container.cc
+++ b/modelling/pymod/export_score_container.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/message.hh>
#include <promod3/core/export_helper.hh>
diff --git a/modelling/pymod/export_scoring_weights.cc b/modelling/pymod/export_scoring_weights.cc
index 11e3c18eb54a48f5162e88bab3c0286d4f8aca55..c100ec806c7ae8a888b567d526729b75696a345e 100644
--- a/modelling/pymod/export_scoring_weights.cc
+++ b/modelling/pymod/export_scoring_weights.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/message.hh>
#include <promod3/core/export_helper.hh>
diff --git a/modelling/pymod/export_sidechain_reconstructor.cc b/modelling/pymod/export_sidechain_reconstructor.cc
index 5c8306f3becb3f13b9c99b3ac0e5906ebf7895a9..0d270147df0de325c646d536ca627b307476ac9b 100644
--- a/modelling/pymod/export_sidechain_reconstructor.cc
+++ b/modelling/pymod/export_sidechain_reconstructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/modelling/sidechain_reconstructor.hh>
diff --git a/modelling/pymod/wrap_modelling.cc b/modelling/pymod/wrap_modelling.cc
index 72125d290d12735a145389f9d47b30a9eca7366e..7e4affa848f8deca25c2f428db14751cc328d533 100644
--- a/modelling/pymod/wrap_modelling.cc
+++ b/modelling/pymod/wrap_modelling.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_gap();
diff --git a/modelling/src/all_atom_relaxer.cc b/modelling/src/all_atom_relaxer.cc
index 9fe1dc51136b70c71d5b4945978375c06f00d0e5..a7dd1ab6922425971a8afe85a1f20ace74b4e3e8 100644
--- a/modelling/src/all_atom_relaxer.cc
+++ b/modelling/src/all_atom_relaxer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/all_atom_relaxer.hh>
#include <promod3/loop/hydrogen_constructor.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/modelling/src/all_atom_relaxer.hh b/modelling/src/all_atom_relaxer.hh
index 9235a13f7980d05b37a06d51ef09c41637bd39ed..1e594df529d38a0a9656e4fd9d5d7ddae72d0ce8 100644
--- a/modelling/src/all_atom_relaxer.hh
+++ b/modelling/src/all_atom_relaxer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MODELLING_ALL_ATOM_RELAXER_HH
#define PROMOD3_MODELLING_ALL_ATOM_RELAXER_HH
diff --git a/modelling/src/backbone_relaxer.cc b/modelling/src/backbone_relaxer.cc
index ded52f6a222d2cf2135de02027563fdc94ce9a13..c2212c9289fd13882973879164ab080461b883d2 100644
--- a/modelling/src/backbone_relaxer.cc
+++ b/modelling/src/backbone_relaxer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/backbone_relaxer.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/loop/amino_acid_atoms.hh>
diff --git a/modelling/src/backbone_relaxer.hh b/modelling/src/backbone_relaxer.hh
index 78d142e43c207597bf9e7fb127ffe3706ebda1cd..0d5499a3e2403536537ae8e373872646270320e3 100644
--- a/modelling/src/backbone_relaxer.hh
+++ b/modelling/src/backbone_relaxer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_BACKBONE_RELAXER_HH
#define PROMOD_MODELLING_BACKBONE_RELAXER_HH
diff --git a/modelling/src/ccd.cc b/modelling/src/ccd.cc
index bc913bba3f4b76fec10cc5f2a3fd513d6acbc006..10ffafaed32c2ff836f26c1cbaee253149e7152a 100644
--- a/modelling/src/ccd.cc
+++ b/modelling/src/ccd.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/ccd.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/geom_base.hh>
diff --git a/modelling/src/ccd.hh b/modelling/src/ccd.hh
index 344228a1391ee488b43d1e1a595e36dd332638f1..4d82a32f07e3a58b6aa2ea6d19fbfda348a1fbdd 100644
--- a/modelling/src/ccd.hh
+++ b/modelling/src/ccd.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_CCD_HH
#define PROMOD_MODELLING_CCD_HH
diff --git a/modelling/src/extension_scheme.cc b/modelling/src/extension_scheme.cc
index da4fd528548047fc800ade063867ff3850557d89..5e3535a83815df1fa3b6735f1a0b23e26fe86e1c 100644
--- a/modelling/src/extension_scheme.cc
+++ b/modelling/src/extension_scheme.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/extension_scheme.hh>
namespace promod3 { namespace modelling{
diff --git a/modelling/src/extension_scheme.hh b/modelling/src/extension_scheme.hh
index c9f183ded6c881c67757a5812b13dde3232f02f6..46de03491585b5bf5db1203bb50709d807eb5ecc 100644
--- a/modelling/src/extension_scheme.hh
+++ b/modelling/src/extension_scheme.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_EXTENSION_SCHEME_HH
#define PROMOD_MODELLING_EXTENSION_SCHEME_HH
diff --git a/modelling/src/gap.cc b/modelling/src/gap.cc
index df052586abaab7fa9dea6db806a4f713647a4ed8..5c13071eaff51ce8f8dd708f17feb17fdf11a78e 100644
--- a/modelling/src/gap.cc
+++ b/modelling/src/gap.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <ost/log.hh>
#include <promod3/modelling/gap.hh>
diff --git a/modelling/src/gap.hh b/modelling/src/gap.hh
index 4bbe3347fb9819619e4f9c09661c35a63c232919..b8bb9d5ec0ccfcbc616b2ef1e33a1b99a78263a5 100644
--- a/modelling/src/gap.hh
+++ b/modelling/src/gap.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MODELLING_GAP_HH
#define PM3_MODELLING_GAP_HH
diff --git a/modelling/src/gap_extender.cc b/modelling/src/gap_extender.cc
index 02492976d7c358524506d21166eee585647b6272..2d723c4a5a31476c9814fdcee3a3cb789f43f003 100644
--- a/modelling/src/gap_extender.cc
+++ b/modelling/src/gap_extender.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/gap_extender.hh>
#include <algorithm>
diff --git a/modelling/src/gap_extender.hh b/modelling/src/gap_extender.hh
index 63217f96e04ee0042b54052c35c69b69fdc70d48..625b6f5877bff9d0aece6039d1a06d042c25cf2d 100644
--- a/modelling/src/gap_extender.hh
+++ b/modelling/src/gap_extender.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MODELLING_GAP_EXTENDER_HH
#define PM3_MODELLING_GAP_EXTENDER_HH
diff --git a/modelling/src/kic.cc b/modelling/src/kic.cc
index fb7005aedd659dd59c21dbb7513657945e62726a..8571fa0759d1e63ef531b5ebd7b535ba0d017e79 100644
--- a/modelling/src/kic.cc
+++ b/modelling/src/kic.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/kic.hh>
#include <promod3/core/eigen_types.hh>
#include <promod3/core/message.hh>
diff --git a/modelling/src/kic.hh b/modelling/src/kic.hh
index 367e7969828f5fc8bccb8b86ef3ce75a79e05dcc..02166346104e1a054768c06664839d921cc8d457 100644
--- a/modelling/src/kic.hh
+++ b/modelling/src/kic.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_KIC_HH
#define PROMOD_MODELLING_KIC_HH
diff --git a/modelling/src/loop_candidate.cc b/modelling/src/loop_candidate.cc
index 5aa7cccee59836bc3589f851f741bf1e158c6a4e..8539705677d6bec217f1d4869f8ef662fc2768b1 100644
--- a/modelling/src/loop_candidate.cc
+++ b/modelling/src/loop_candidate.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/loop_candidate.hh>
#include <promod3/modelling/kic.hh>
#include <promod3/modelling/scoring_weights.hh>
diff --git a/modelling/src/loop_candidate.hh b/modelling/src/loop_candidate.hh
index 0b30ecf4bf2b51c2422ca0b26ec7607d805be3e0..14c6accf2145747158a2bad14165b1ac98e7d8bf 100644
--- a/modelling/src/loop_candidate.hh
+++ b/modelling/src/loop_candidate.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MODELLING_LOOP_CANDIDATE_HH
#define PM3_MODELLING_LOOP_CANDIDATE_HH
diff --git a/modelling/src/model.cc b/modelling/src/model.cc
index 57f4965af95dd426efff9481ba2f4b93f078fbb5..a4ef588ead11793811ba8b82a636adf7271c888f 100644
--- a/modelling/src/model.cc
+++ b/modelling/src/model.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <ctype.h>
#include <ost/log.hh>
#include <ost/dyn_cast.hh>
diff --git a/modelling/src/model.hh b/modelling/src/model.hh
index e42a2c8db6ee029ad4f7547faf6511b9f5be4fd2..e7503d8a3bbac7a73579d55b477eb8aaa63c03db 100644
--- a/modelling/src/model.hh
+++ b/modelling/src/model.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MODELLING_MODEL_HH
#define PM3_MODELLING_MODEL_HH
diff --git a/modelling/src/monte_carlo.cc b/modelling/src/monte_carlo.cc
index dab1adef2b9248065f687d1fbe60cff20afac5df..3c9782d12104409fedb32ff17ad2784c69f31cac 100644
--- a/modelling/src/monte_carlo.cc
+++ b/modelling/src/monte_carlo.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo.hh>
namespace promod3 { namespace modelling {
diff --git a/modelling/src/monte_carlo.hh b/modelling/src/monte_carlo.hh
index d25464b12dc9fdc0eaf5d78bcfc8256eed627329..1e573957efa0ace1aa8fcd4c999e89a4ed5a686a 100644
--- a/modelling/src/monte_carlo.hh
+++ b/modelling/src/monte_carlo.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_HH
#define PROMOD_MODELLING_MONTE_CARLO_HH
diff --git a/modelling/src/monte_carlo_closer.cc b/modelling/src/monte_carlo_closer.cc
index 3d3090efb57e5cb1b63841523bc5e2edc7b82516..02d20b40c2d288eb4463852b8af83bf8df38fd07 100644
--- a/modelling/src/monte_carlo_closer.cc
+++ b/modelling/src/monte_carlo_closer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo_closer.hh>
#include <promod3/modelling/kic.hh>
#include <promod3/modelling/ccd.hh>
diff --git a/modelling/src/monte_carlo_closer.hh b/modelling/src/monte_carlo_closer.hh
index 239f11c93701ec2947f7084aed5bb7e8dadcbf0c..28feb029c3e847bc1018553f06aa4e7b99699de9 100644
--- a/modelling/src/monte_carlo_closer.hh
+++ b/modelling/src/monte_carlo_closer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_CLOSER_HH
#define PROMOD_MODELLING_MONTE_CARLO_CLOSER_HH
diff --git a/modelling/src/monte_carlo_cooler.cc b/modelling/src/monte_carlo_cooler.cc
index 1a99a55d1281b031ae61858f952b9c98ffae31a0..1b50af2133687bd419a3c3c00a6c6594d0b61005 100644
--- a/modelling/src/monte_carlo_cooler.cc
+++ b/modelling/src/monte_carlo_cooler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo_cooler.hh>
namespace promod3 { namespace modelling {
diff --git a/modelling/src/monte_carlo_cooler.hh b/modelling/src/monte_carlo_cooler.hh
index acf12e5f2e7573b824ec8bffa706152c52046390..8906e454ec90c02fb9dfab4747103298431aa45d 100644
--- a/modelling/src/monte_carlo_cooler.hh
+++ b/modelling/src/monte_carlo_cooler.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_COOLER_HH
#define PROMOD_MODELLING_MONTE_CARLO_COOLER_HH
diff --git a/modelling/src/monte_carlo_sampler.cc b/modelling/src/monte_carlo_sampler.cc
index e2d69b7675523fa369504003e2a9e12e25385393..31e398be7b38a72144447a14908d89705b2748e8 100644
--- a/modelling/src/monte_carlo_sampler.cc
+++ b/modelling/src/monte_carlo_sampler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo_sampler.hh>
diff --git a/modelling/src/monte_carlo_sampler.hh b/modelling/src/monte_carlo_sampler.hh
index e80478fd2e9629e8a26e485df6d90bd628f85781..e3e7223c9f2f229b858672ce6ffed92f769322d3 100644
--- a/modelling/src/monte_carlo_sampler.hh
+++ b/modelling/src/monte_carlo_sampler.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_SAMPLER_HH
#define PROMOD_MODELLING_MONTE_CARLO_SAMPLER_HH
diff --git a/modelling/src/monte_carlo_scorer.cc b/modelling/src/monte_carlo_scorer.cc
index ba536e7d772fc8b8d506c8375269e4d9fb528da1..e13fb44305136f832ec8b885b4ab80cfdbe18029 100644
--- a/modelling/src/monte_carlo_scorer.cc
+++ b/modelling/src/monte_carlo_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo_scorer.hh>
namespace promod3 { namespace modelling {
diff --git a/modelling/src/monte_carlo_scorer.hh b/modelling/src/monte_carlo_scorer.hh
index a6707b359e0a138f296120815e524bfd9f4488b8..b478805833423e8246510fd02a2de3b1a08b87ec 100644
--- a/modelling/src/monte_carlo_scorer.hh
+++ b/modelling/src/monte_carlo_scorer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_SCORER_HH
#define PROMOD_MODELLING_MONTE_CARLO_SCORER_HH
diff --git a/modelling/src/rigid_blocks.cc b/modelling/src/rigid_blocks.cc
index df46c90fc4195cf3c47b6f4bb09a2b9ec5301e7f..d334a932ce55795573d6a857d9da314ac5710910 100644
--- a/modelling/src/rigid_blocks.cc
+++ b/modelling/src/rigid_blocks.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/rigid_blocks.hh>
#include <promod3/core/cluster.hh>
diff --git a/modelling/src/rigid_blocks.hh b/modelling/src/rigid_blocks.hh
index a210c6e77ab0e4b9aba403f09420d37145b2561d..9cddf9254d38c8a4bd11ebdfdcd1609da244f131 100644
--- a/modelling/src/rigid_blocks.hh
+++ b/modelling/src/rigid_blocks.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_RIGID_BLOCKS_HH
#define PROMOD_MODELLING_RIGID_BLOCKS_HH
diff --git a/modelling/src/score_container.cc b/modelling/src/score_container.cc
index 5cbaf767239e742459ba58096debc49ee7113ca3..0a707265a03cae4f76d129685f7c52cedb85c385 100644
--- a/modelling/src/score_container.cc
+++ b/modelling/src/score_container.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/score_container.hh>
namespace promod3 { namespace modelling {
diff --git a/modelling/src/score_container.hh b/modelling/src/score_container.hh
index cd5b235b6c8b15966eb2cb971785955ecdd95d56..08ba76781e32113371941d02731ef68d1070a4a4 100644
--- a/modelling/src/score_container.hh
+++ b/modelling/src/score_container.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MODELLING_SCORE_CONTAINER_HH
#define PROMOD3_MODELLING_SCORE_CONTAINER_HH
diff --git a/modelling/src/scoring_weights.cc b/modelling/src/scoring_weights.cc
index ac8ad4f8fd8408a604842f5c54744ed6a1e50f05..aa484910b25a2926bbef7775795e5c61191c9864 100644
--- a/modelling/src/scoring_weights.cc
+++ b/modelling/src/scoring_weights.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/scoring_weights.hh>
#include <promod3/core/message.hh>
diff --git a/modelling/src/scoring_weights.hh b/modelling/src/scoring_weights.hh
index b51158e330ef1f476c266751f4cdbf9a9f872406..72f59dc84b018be59b454c40c26822ddb78093cc 100644
--- a/modelling/src/scoring_weights.hh
+++ b/modelling/src/scoring_weights.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MODELLING_SCORING_WEIGHTS_HH
#define PROMOD3_MODELLING_SCORING_WEIGHTS_HH
diff --git a/modelling/src/sidechain_env_listener.cc b/modelling/src/sidechain_env_listener.cc
index 74eb4c58226b3db4f1350db728363b369e316b51..19d97aa12f345b8c6b81bc184457b9c7cb7e7226 100644
--- a/modelling/src/sidechain_env_listener.cc
+++ b/modelling/src/sidechain_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/sidechain_env_listener.hh>
#include <promod3/sidechain/sidechain_object_loader.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/modelling/src/sidechain_env_listener.hh b/modelling/src/sidechain_env_listener.hh
index 2f8c14a1349f80b6d36464debc298b7aa3161d01..309930e65e0b0db0469a36c1338e7c39db22a118 100644
--- a/modelling/src/sidechain_env_listener.hh
+++ b/modelling/src/sidechain_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SIDECHAIN_ENV_LISTENER_HH
#define PM3_SIDECHAIN_ENV_LISTENER_HH
diff --git a/modelling/src/sidechain_reconstructor.cc b/modelling/src/sidechain_reconstructor.cc
index 9bc1dabac79df3bc9474f41108bf61e1ac12f887..3e63c3221e189cb5cca392298fcc34545581e971 100644
--- a/modelling/src/sidechain_reconstructor.cc
+++ b/modelling/src/sidechain_reconstructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/sidechain_reconstructor.hh>
#include <promod3/sidechain/disulfid.hh>
#include <promod3/sidechain/rotamer_graph.hh>
diff --git a/modelling/src/sidechain_reconstructor.hh b/modelling/src/sidechain_reconstructor.hh
index 6c1a4ac06e05a0683a960579b39883d7007c39e4..167493b0ecae058728ba4a02ce9584658d6e4d96 100644
--- a/modelling/src/sidechain_reconstructor.hh
+++ b/modelling/src/sidechain_reconstructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SIDECHAIN_RECONSTRUCTOR_HH
#define PM3_SIDECHAIN_RECONSTRUCTOR_HH
diff --git a/modelling/tests/test_close_gaps.py b/modelling/tests/test_close_gaps.py
index 988cb6078aac2da0ad8a19ba9441ce4fbe2c8aec..43a2e2d599f62613f9f8379f996112b2f9242627 100644
--- a/modelling/tests/test_close_gaps.py
+++ b/modelling/tests/test_close_gaps.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for modelling components to close gaps.
"""
diff --git a/modelling/tests/test_gap_extension.py b/modelling/tests/test_gap_extension.py
index a5504bc191c8b534112c47444a6ae217b2fe8618..2c7b5d93665cfbf7ac70df1b741d3f374ad2fcd6 100644
--- a/modelling/tests/test_gap_extension.py
+++ b/modelling/tests/test_gap_extension.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import unittest
from promod3 import modelling
from ost import io,seq
diff --git a/modelling/tests/test_loop_candidates.cc b/modelling/tests/test_loop_candidates.cc
index 70c92d55fb35c002c0d3077aaaa1c334b9df29b5..f82acf29f4c931c589960898fa936d53c5fdf290 100644
--- a/modelling/tests/test_loop_candidates.cc
+++ b/modelling/tests/test_loop_candidates.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/loop_candidate.hh>
diff --git a/modelling/tests/test_loop_closing.cc b/modelling/tests/test_loop_closing.cc
index 5a7b9d475f651dd39a955400f2fb8264e3c3c555..7d1c163f405f0a512ced58284e38f92ba90858d5 100644
--- a/modelling/tests/test_loop_closing.cc
+++ b/modelling/tests/test_loop_closing.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/kic.hh>
#include <promod3/modelling/ccd.hh>
diff --git a/modelling/tests/test_modelling.py b/modelling/tests/test_modelling.py
index 5ca41eabe0b8fa0467bc609e9acd60d1d6061658..f7169d4d60577dddc3fd54429d67627e49765343 100644
--- a/modelling/tests/test_modelling.py
+++ b/modelling/tests/test_modelling.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for modelling.
"""
diff --git a/modelling/tests/test_pipeline.py b/modelling/tests/test_pipeline.py
index df74384274f06a5a9c8f59f05c8cd2ecc9a1f447..0ae2afaa810a1a8ff936315448b6a26401771ef1 100644
--- a/modelling/tests/test_pipeline.py
+++ b/modelling/tests/test_pipeline.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for modelling pipeline components.
We go from a fake cut in crambin to reconstruct that same protein.
diff --git a/modelling/tests/test_ring_punches.py b/modelling/tests/test_ring_punches.py
index 901cfbc04e10a7dedbb7e7ebb3f5e1e738cacd2a..64d1b1b80cbd8a6bfda65f14f6d051366f939cc4 100644
--- a/modelling/tests/test_ring_punches.py
+++ b/modelling/tests/test_ring_punches.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests to detect ring punchings.
"""
diff --git a/modelling/tests/test_sidechain_reconstruction.py b/modelling/tests/test_sidechain_reconstruction.py
index 8daf328aa0594275dd407f8bf012d29e3ff7b5a6..7b5a988ff484b7513187db97dc4e00da246c7d86 100644
--- a/modelling/tests/test_sidechain_reconstruction.py
+++ b/modelling/tests/test_sidechain_reconstruction.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import unittest
from ost import io, mol, geom
from promod3 import loop, sidechain, modelling
diff --git a/modelling/tests/test_sidechain_reconstructor.cc b/modelling/tests/test_sidechain_reconstructor.cc
index e6f9a9a2ee5f6e5ead668361f4e00857e284feca..7e730c697d6401bc8170bac20f3bdea6f33cd573 100644
--- a/modelling/tests/test_sidechain_reconstructor.cc
+++ b/modelling/tests/test_sidechain_reconstructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/sidechain_reconstructor.hh>
#include <promod3/core/message.hh>
diff --git a/modelling/tests/tests.cc b/modelling/tests/tests.cc
index 956b0f2712eee2fcb1cc6ae9b9f183a4caa360cb..b497ab9838fe7aeeb97fcc164d0fa443164c0a06 100644
--- a/modelling/tests/tests.cc
+++ b/modelling/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_modelling
#define BOOST_AUTO_TEST_MAIN
diff --git a/scoring/data/convert_binaries.py b/scoring/data/convert_binaries.py
index d7b5ff7c2978492f5bc0902ce706ac32921e4ae5..4a6210bf1a76efad00ab6768f686166e1515ec87 100644
--- a/scoring/data/convert_binaries.py
+++ b/scoring/data/convert_binaries.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Convert files from portable to raw.'''
import sys
import os
diff --git a/scoring/doc/all_atom_scorers.rst b/scoring/doc/all_atom_scorers.rst
index 0a1b39b1613522dd671df0b73b32e98dcaac55eb..bcb3cdc43ed0e78becf8a07467928571d60bf604 100644
--- a/scoring/doc/all_atom_scorers.rst
+++ b/scoring/doc/all_atom_scorers.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
All Atom Scorers
================================================================================
diff --git a/scoring/doc/backbone_score_env.rst b/scoring/doc/backbone_score_env.rst
index fa9eb8f41810d125d2e81ad3a7e11c75a09a0159..11ea33ce9e947a60b120cc82e658231249e48082 100644
--- a/scoring/doc/backbone_score_env.rst
+++ b/scoring/doc/backbone_score_env.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Backbone Score Environment
================================================================================
diff --git a/scoring/doc/backbone_scorers.rst b/scoring/doc/backbone_scorers.rst
index c9cf4a44973fa6d5df86ce4ec0ee06d35be8fae3..68a45cab6d736cc1963c245bb0c5cf1e0e140e08 100644
--- a/scoring/doc/backbone_scorers.rst
+++ b/scoring/doc/backbone_scorers.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Backbone Scorers
================================================================================
diff --git a/scoring/doc/index.rst b/scoring/doc/index.rst
index e09b7bce0b1ed731d7b3e325f18420906441e922..d21154f06951fcdb6bbbe1c11f329f69f24bd57c 100644
--- a/scoring/doc/index.rst
+++ b/scoring/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.scoring` - Loop Scoring
================================================================================
diff --git a/scoring/doc/other_scoring_functions.rst b/scoring/doc/other_scoring_functions.rst
index 95e0eb49480797cc94ee856bad95b0b78e2efe8a..80487531f986d6004e6764b8a8575be11b8bf6de 100644
--- a/scoring/doc/other_scoring_functions.rst
+++ b/scoring/doc/other_scoring_functions.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Other Scoring Functions
================================================================================
diff --git a/scoring/pymod/__init__.py b/scoring/pymod/__init__.py
index 9a977e84016d8b94a0396beac02175298fa2cbb8..e00f68205fd1fecacb0edb1d4e8582ca3323e9c5 100644
--- a/scoring/pymod/__init__.py
+++ b/scoring/pymod/__init__.py
@@ -1 +1,17 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from _scoring import *
diff --git a/scoring/pymod/export_all_atom_score.cc b/scoring/pymod/export_all_atom_score.cc
index ddaa3f50594fadf0dad1e71ee833d26e1d970777..a3990a887e39b885b65d9f6f319f216fd0e926bb 100644
--- a/scoring/pymod/export_all_atom_score.cc
+++ b/scoring/pymod/export_all_atom_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/scoring/all_atom_score_base.hh>
diff --git a/scoring/pymod/export_backbone_score.cc b/scoring/pymod/export_backbone_score.cc
index 8bc2b5800aac45118768dc14f9f0a44427bf0b36..78722280ad48d79749bb8a778d3fbd7b839782b5 100644
--- a/scoring/pymod/export_backbone_score.cc
+++ b/scoring/pymod/export_backbone_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/scoring/backbone_score_base.hh>
diff --git a/scoring/pymod/export_constraint_constructor.cc b/scoring/pymod/export_constraint_constructor.cc
index 2de16edbb11164c91ee0604a102ab8e0c9ecc78a..0005e736b693643f62f44b68b5e2abf82aa81241 100644
--- a/scoring/pymod/export_constraint_constructor.cc
+++ b/scoring/pymod/export_constraint_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/scoring/constraint_constructor.hh>
diff --git a/scoring/pymod/export_density_scorer.cc b/scoring/pymod/export_density_scorer.cc
index f022f963aee63b41120ca950a1db90d89b14ffec..b887a2daf1c6ea65c228ca23cbd1bd5c37f152a0 100644
--- a/scoring/pymod/export_density_scorer.cc
+++ b/scoring/pymod/export_density_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/scoring/density_score.hh>
diff --git a/scoring/pymod/export_object_loader.cc b/scoring/pymod/export_object_loader.cc
index 73e8909c4ad1e7912773065470191c24f90e85a7..7c4791327e1fde416bcb15960eb2e5c2c65ca517 100644
--- a/scoring/pymod/export_object_loader.cc
+++ b/scoring/pymod/export_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/scoring/scoring_object_loader.hh>
diff --git a/scoring/pymod/export_pairwise_functions.cc b/scoring/pymod/export_pairwise_functions.cc
index b43f195c41a12ff6c293699127bd54be882de60d..4aa5bfc121d8166367db1da217f5dd0ac7765716 100644
--- a/scoring/pymod/export_pairwise_functions.cc
+++ b/scoring/pymod/export_pairwise_functions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/scoring/pairwise_scoring_function.hh>
#include <promod3/core/export_helper.hh>
diff --git a/scoring/pymod/export_scwrl3_energy_functions.cc b/scoring/pymod/export_scwrl3_energy_functions.cc
index 54c5a8e1e8155b575dc8d0971eeaee102c683a89..58136cc8d88d6483fcd9eeaaf7188c7cfb2fc9b4 100644
--- a/scoring/pymod/export_scwrl3_energy_functions.cc
+++ b/scoring/pymod/export_scwrl3_energy_functions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/scoring/scwrl3_energy_functions.hh>
#include <promod3/core/export_helper.hh>
diff --git a/scoring/pymod/wrap_scoring.cc b/scoring/pymod/wrap_scoring.cc
index 4b717f9cbc40743c1e84fcef141dc8e95bdb874f..a162eec0d2403fe153587642000859552249934e 100644
--- a/scoring/pymod/wrap_scoring.cc
+++ b/scoring/pymod/wrap_scoring.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_BackboneScore();
diff --git a/scoring/src/all_atom_clash_score.cc b/scoring/src/all_atom_clash_score.cc
index eb011421297ff1de8c10f6fbd5a14533c2c2706e..de47faeaf2bbd6c0c3569c73c9699d2789941db9 100644
--- a/scoring/src/all_atom_clash_score.cc
+++ b/scoring/src/all_atom_clash_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_clash_score.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/check_io.hh>
diff --git a/scoring/src/all_atom_clash_score.hh b/scoring/src/all_atom_clash_score.hh
index df69a60646241c8a1c563c8234b7bc30283ee193..39f0ae6bbc80448e9ab25c048bff543933deb27a 100644
--- a/scoring/src/all_atom_clash_score.hh
+++ b/scoring/src/all_atom_clash_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_CLASH_SCORE_HH
#define PM3_SCORING_ALL_ATOM_CLASH_SCORE_HH
diff --git a/scoring/src/all_atom_interaction_env_listener.cc b/scoring/src/all_atom_interaction_env_listener.cc
index 122ab3a28456c0fdacc1d1a5465414ceb98d0e4e..c5cff244cb8cf863e2661a2fe7a0478cbf10673d 100644
--- a/scoring/src/all_atom_interaction_env_listener.cc
+++ b/scoring/src/all_atom_interaction_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_interaction_env_listener.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/scoring/src/all_atom_interaction_env_listener.hh b/scoring/src/all_atom_interaction_env_listener.hh
index f97a9da63f065f0be185e992a423724c1acaca49..bf6f800b0d4a7c9ab18d9db9a35a802b0cc62313 100644
--- a/scoring/src/all_atom_interaction_env_listener.hh
+++ b/scoring/src/all_atom_interaction_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_SCORE_ENV_LISTENER_HH
#define PM3_SCORING_ALL_ATOM_SCORE_ENV_LISTENER_HH
diff --git a/scoring/src/all_atom_interaction_score.cc b/scoring/src/all_atom_interaction_score.cc
index 35c9f4955e2a13070a4b6ff4fa3b93731a90ac4f..2ccc192e07d4b74e807ebd8d6774db4c0dd3fa8c 100644
--- a/scoring/src/all_atom_interaction_score.cc
+++ b/scoring/src/all_atom_interaction_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_interaction_score.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/check_io.hh>
diff --git a/scoring/src/all_atom_interaction_score.hh b/scoring/src/all_atom_interaction_score.hh
index 5aadd05c56ca9b67ac8f86259ef6e06d9350c1fa..0e2166a1c1ed5a020cfbfd3a480dd23fd8c286d4 100644
--- a/scoring/src/all_atom_interaction_score.hh
+++ b/scoring/src/all_atom_interaction_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_INTERACTION_SCORE_HH
#define PM3_SCORING_ALL_ATOM_INTERACTION_SCORE_HH
diff --git a/scoring/src/all_atom_overall_scorer.cc b/scoring/src/all_atom_overall_scorer.cc
index 314f22d7c5e5336bc30fe62b09af20e414561489..891fa9448fa0373eefbcf04feacae82a951cb343 100644
--- a/scoring/src/all_atom_overall_scorer.cc
+++ b/scoring/src/all_atom_overall_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_overall_scorer.hh>
namespace promod3 { namespace scoring {
diff --git a/scoring/src/all_atom_overall_scorer.hh b/scoring/src/all_atom_overall_scorer.hh
index ac090a46f7f55b58aba5dd27a09f4a9c0c6c04a1..81770d349d0d94da8b24456b3c92c60221771090 100644
--- a/scoring/src/all_atom_overall_scorer.hh
+++ b/scoring/src/all_atom_overall_scorer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_OVERALL_SCORER_HH
#define PM3_SCORING_ALL_ATOM_OVERALL_SCORER_HH
diff --git a/scoring/src/all_atom_packing_score.cc b/scoring/src/all_atom_packing_score.cc
index aef0d0a0ee488290b48cf5546d863f761c640cdb..786ba8601894329127dc9fd32ee015129efc604e 100644
--- a/scoring/src/all_atom_packing_score.cc
+++ b/scoring/src/all_atom_packing_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_packing_score.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/check_io.hh>
diff --git a/scoring/src/all_atom_packing_score.hh b/scoring/src/all_atom_packing_score.hh
index 71cf70ea1a9359398923571105c41bd6e7a6b71f..899b6b1ccd8ab0e6d1989fbdc7966a6c16230246 100644
--- a/scoring/src/all_atom_packing_score.hh
+++ b/scoring/src/all_atom_packing_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_PACKING_SCORE_HH
#define PM3_SCORING_ALL_ATOM_PACKING_SCORE_HH
diff --git a/scoring/src/all_atom_score_base.hh b/scoring/src/all_atom_score_base.hh
index ba17cb0843b8523633bdcb24d530d3a53f89cfcb..abf7100ee54d1e805402f10bf5a99ca21958122a 100644
--- a/scoring/src/all_atom_score_base.hh
+++ b/scoring/src/all_atom_score_base.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_SCORE_BASE_HH
#define PM3_SCORING_ALL_ATOM_SCORE_BASE_HH
diff --git a/scoring/src/backbone_overall_scorer.cc b/scoring/src/backbone_overall_scorer.cc
index bfa296653be248bcbdca2e27ebe81328abe01840..5af0d12fde653c8dea2a1c4595dd512a7e060152 100644
--- a/scoring/src/backbone_overall_scorer.cc
+++ b/scoring/src/backbone_overall_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/backbone_overall_scorer.hh>
namespace promod3 { namespace scoring {
diff --git a/scoring/src/backbone_overall_scorer.hh b/scoring/src/backbone_overall_scorer.hh
index 94af847f50e8e9bcd99414526e420cdc33da6902..61db071b109699502779aa38506338b692c20f87 100644
--- a/scoring/src/backbone_overall_scorer.hh
+++ b/scoring/src/backbone_overall_scorer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_BACKBONE_OVERALL_SCORER_HH
#define PM3_SCORING_BACKBONE_OVERALL_SCORER_HH
diff --git a/scoring/src/backbone_score_base.cc b/scoring/src/backbone_score_base.cc
index 30888ec88eac26787f32d63406ea5f686404ae07..05ab62387a203e50e5b5607c736c8c356b971f1c 100644
--- a/scoring/src/backbone_score_base.cc
+++ b/scoring/src/backbone_score_base.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/backbone_score_base.hh>
diff --git a/scoring/src/backbone_score_base.hh b/scoring/src/backbone_score_base.hh
index 8631f8a888f3cea59db7c5c4ba5638723c17d2e1..0b8ad73d8cae64341db1b66644d24586aff3335d 100644
--- a/scoring/src/backbone_score_base.hh
+++ b/scoring/src/backbone_score_base.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_BACKBONE_SCORE_HH
#define PM3_SCORING_BACKBONE_SCORE_HH
diff --git a/scoring/src/cb_packing_score.cc b/scoring/src/cb_packing_score.cc
index 0f0b307df7677da899b0d155d7ced9cd72775f56..5d98abc3cda936181be58e2b68741957a5a7a73a 100644
--- a/scoring/src/cb_packing_score.cc
+++ b/scoring/src/cb_packing_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/cb_packing_score.hh>
diff --git a/scoring/src/cb_packing_score.hh b/scoring/src/cb_packing_score.hh
index 0f3e5518e8a17eb2c9eaf7b041a3deafe6c337fb..97772e275154cb1b9f8dd59e48022df843b59b2a 100644
--- a/scoring/src/cb_packing_score.hh
+++ b/scoring/src/cb_packing_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CB_PACKING_SCORE_HH
#define PM3_SCORING_CB_PACKING_SCORE_HH
diff --git a/scoring/src/cbeta_env_listener.cc b/scoring/src/cbeta_env_listener.cc
index 6b8092f5c7ca8d6c93cc9b0cbe1208e48e88b044..9bb3021a9cc222bb69276766ae30aa83412821cb 100644
--- a/scoring/src/cbeta_env_listener.cc
+++ b/scoring/src/cbeta_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/cbeta_env_listener.hh>
diff --git a/scoring/src/cbeta_env_listener.hh b/scoring/src/cbeta_env_listener.hh
index af07e116c9f8386fa9db2313f8ea8b31d5e3ed9c..fd86b4e0a18785332e85eb85677429c82db93d6e 100644
--- a/scoring/src/cbeta_env_listener.hh
+++ b/scoring/src/cbeta_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CBETA_ENV_LISTENER_HH
#define PM3_SCORING_CBETA_ENV_LISTENER_HH
diff --git a/scoring/src/cbeta_score.cc b/scoring/src/cbeta_score.cc
index 1932a20038350aa5d03f1f9c898abd8b62070de3..17eb90f88ce95b67a761477f3b47901d70c71636 100644
--- a/scoring/src/cbeta_score.cc
+++ b/scoring/src/cbeta_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/cbeta_score.hh>
diff --git a/scoring/src/cbeta_score.hh b/scoring/src/cbeta_score.hh
index c2686975efc7e187710954e1d3d32952c35134b2..2a4cb7b629b6c1194d814fcbab80061c1d9108ea 100644
--- a/scoring/src/cbeta_score.hh
+++ b/scoring/src/cbeta_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CBETA_SCORE_HH
#define PM3_SCORING_CBETA_SCORE_HH
diff --git a/scoring/src/clash_env_listener.cc b/scoring/src/clash_env_listener.cc
index 3bf1c656436207a3eb23c2d551d83cb9ed7fe838..f9ff06382e686b1d94a00d2447a244eb05fd732e 100644
--- a/scoring/src/clash_env_listener.cc
+++ b/scoring/src/clash_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/clash_env_listener.hh>
diff --git a/scoring/src/clash_env_listener.hh b/scoring/src/clash_env_listener.hh
index cb4ee362b1d30c99823e6e3517879a7c56103fa7..3d8c121c8f6f7c03fdd2bcf20a0486424fa39075 100644
--- a/scoring/src/clash_env_listener.hh
+++ b/scoring/src/clash_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CLASH_ENV_LISTENER_HH
#define PM3_SCORING_CLASH_ENV_LISTENER_HH
diff --git a/scoring/src/clash_score.cc b/scoring/src/clash_score.cc
index c7c2849124252180da3e5af0f76a4b63dc4f632f..f0589dc74a28a4fc4ba94650b8f6bb220e9e72fc 100644
--- a/scoring/src/clash_score.cc
+++ b/scoring/src/clash_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/clash_score.hh>
#include <promod3/scoring/scwrl3_energy_functions.hh>
diff --git a/scoring/src/clash_score.hh b/scoring/src/clash_score.hh
index 2a06194ca6bb549c887f362bcb18641dc132511c..23251cc607083e34f1e8277e2430efa04c24ff97 100644
--- a/scoring/src/clash_score.hh
+++ b/scoring/src/clash_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CLASH_SCORE_HH
#define PM3_SCORING_CLASH_SCORE_HH
diff --git a/scoring/src/constraint_constructor.cc b/scoring/src/constraint_constructor.cc
index 15e200177219085de069322553b78a6615bd9ba3..127b78aef46598d94336df7d502cf27108f41bea 100644
--- a/scoring/src/constraint_constructor.cc
+++ b/scoring/src/constraint_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/constraint_constructor.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/cluster.hh>
diff --git a/scoring/src/constraint_constructor.hh b/scoring/src/constraint_constructor.hh
index e722bf6c694596bd39d7094dd6058b86ca833bbf..75e2b393032c419cce6a7f63dbe6047fd567e724 100644
--- a/scoring/src/constraint_constructor.hh
+++ b/scoring/src/constraint_constructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CONSTRAINT_CONSTRUCTOR_HH
#define PM3_SCORING_CONSTRAINT_CONSTRUCTOR_HH
diff --git a/scoring/src/density_score.cc b/scoring/src/density_score.cc
index 803a843b68e1dd8396d27b3cd67ef916c5232649..7ad2daac39745dc1d4f3f1efc24d759438c42822 100644
--- a/scoring/src/density_score.cc
+++ b/scoring/src/density_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/density_score.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/density_score.hh b/scoring/src/density_score.hh
index d5e5123c3f733f2976e47c8928d32b6d11dc8f57..fe698cd36eaa5a1b79d52f7357840839be8eb823 100644
--- a/scoring/src/density_score.hh
+++ b/scoring/src/density_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_DENSITY_SCORE_HH
#define PM3_SCORING_DENSITY_SCORE_HH
diff --git a/scoring/src/hbond_env_listener.cc b/scoring/src/hbond_env_listener.cc
index 08a64dce7b0f74939f5d6b7e04580e54038891e2..afe63391a632ba1d1260b7ee6350d73bb95df854 100644
--- a/scoring/src/hbond_env_listener.cc
+++ b/scoring/src/hbond_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/hbond_env_listener.hh>
#include <set>
diff --git a/scoring/src/hbond_env_listener.hh b/scoring/src/hbond_env_listener.hh
index d5e6ea01849d5de7f3d08abfe36652040bccfee5..7b45cdc6eeea1cc8c7aa8a88866928ff0caaff1f 100644
--- a/scoring/src/hbond_env_listener.hh
+++ b/scoring/src/hbond_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_HBOND_ENV_LISTENER_HH
#define PM3_SCORING_HBOND_ENV_LISTENER_HH
diff --git a/scoring/src/hbond_score.cc b/scoring/src/hbond_score.cc
index 19940c002455a7087c7966fbbdcbe7e1bfef8dd8..e7955422b6cf9ee7aaf668040e101a44e0c141b0 100644
--- a/scoring/src/hbond_score.cc
+++ b/scoring/src/hbond_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/hbond_score.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/hbond_score.hh b/scoring/src/hbond_score.hh
index e8211fd43cc83e65585c049b9485c704ed17aa9b..895e93d4f37bfde32cc7221c66fb387f7164284b 100644
--- a/scoring/src/hbond_score.hh
+++ b/scoring/src/hbond_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_HBOND_SCORE_HH
#define PM3_SCORING_HBOND_SCORE_HH
diff --git a/scoring/src/pairwise_score.cc b/scoring/src/pairwise_score.cc
index 1a0ef644e17b316b17ab735e0d34576efa8b2962..fd8f6c421317b2c9961a40393783bf906487ef0e 100644
--- a/scoring/src/pairwise_score.cc
+++ b/scoring/src/pairwise_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/pairwise_score.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/pairwise_score.hh b/scoring/src/pairwise_score.hh
index dcd712e8d3e8ef3564d04252e7a73d2d73435826..60c59f869f3b38974569405c79c5b8502b98f03e 100644
--- a/scoring/src/pairwise_score.hh
+++ b/scoring/src/pairwise_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_PAIRWISE_SCORE_HH
#define PM3_PAIRWISE_SCORE_HH
diff --git a/scoring/src/pairwise_scoring_function.hh b/scoring/src/pairwise_scoring_function.hh
index 5edcf6af1ba5e860429261463b83fe0872963ec0..823f445510f57d7d901616935c3da1801def55bd 100644
--- a/scoring/src/pairwise_scoring_function.hh
+++ b/scoring/src/pairwise_scoring_function.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_PAIRWISE_SCORING_FUNCTION_HH
#define PM3_PAIRWISE_SCORING_FUNCTION_HH
diff --git a/scoring/src/reduced_env_listener.cc b/scoring/src/reduced_env_listener.cc
index 14025821515000582ab9144edf70db3abe4e6f31..1d52b029c1d4d83c7f7ab4154b717cd8e051b27d 100644
--- a/scoring/src/reduced_env_listener.cc
+++ b/scoring/src/reduced_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/reduced_env_listener.hh>
diff --git a/scoring/src/reduced_env_listener.hh b/scoring/src/reduced_env_listener.hh
index 52d405e2ac27c5e427f85e1a5e0b9ea5308bd872..1cfce4d80f5aa91efc64bc6d543d0db68d6fcc56 100644
--- a/scoring/src/reduced_env_listener.hh
+++ b/scoring/src/reduced_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_REDUCED_ENV_LISTENER_HH
#define PM3_SCORING_REDUCED_ENV_LISTENER_HH
diff --git a/scoring/src/reduced_score.cc b/scoring/src/reduced_score.cc
index a8e992ae8a68642a34d5fdf864ca5e6376945d91..c0b9b245ebe2d467274b488daadf3b21f59c5140 100644
--- a/scoring/src/reduced_score.cc
+++ b/scoring/src/reduced_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/reduced_score.hh>
diff --git a/scoring/src/reduced_score.hh b/scoring/src/reduced_score.hh
index e41f784c28bfba0b9e053e11e594eb4105b9f24f..bcfa027202dacc3d58fd0da4455a20c4341bd34c 100644
--- a/scoring/src/reduced_score.hh
+++ b/scoring/src/reduced_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_REDUCED_SCORE_HH
#define PM3_SCORING_REDUCED_SCORE_HH
diff --git a/scoring/src/scoring_object_loader.cc b/scoring/src/scoring_object_loader.cc
index fff223a9fb260b0b4eddbad3d6fae500a45a42b5..563e679bd0a6e77c5f443f5246e17d45970d37ea 100644
--- a/scoring/src/scoring_object_loader.cc
+++ b/scoring/src/scoring_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/scoring_object_loader.hh>
#include <promod3/config.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/scoring/src/scoring_object_loader.hh b/scoring/src/scoring_object_loader.hh
index b406f72dd735e51ff470f34326c4cd8095603c07..62ab321c9855c8f63e15b0f3355e95788b9070d4 100644
--- a/scoring/src/scoring_object_loader.hh
+++ b/scoring/src/scoring_object_loader.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SCORING_OBJECT_LOADER_HH
#define PROMOD3_SCORING_OBJECT_LOADER_HH
diff --git a/scoring/src/scwrl3_energy_functions.hh b/scoring/src/scwrl3_energy_functions.hh
index 7db72ebf5611fd7424e940a63f26c1de8b49222d..2829e91b3e085ef30f3c402ef559f4a4f930575a 100644
--- a/scoring/src/scwrl3_energy_functions.hh
+++ b/scoring/src/scwrl3_energy_functions.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCWRL3_ENERGY_FUNCTIONS_HH
#define PM3_SCWRL3_ENERGY_FUNCTIONS_HH
diff --git a/scoring/src/ss_agreement_env_listener.cc b/scoring/src/ss_agreement_env_listener.cc
index e9a090ee09d03511f421b2d052773ae9798cb647..5350a8ba15e64b74a461aacfec6e23b7fd4c4f99 100644
--- a/scoring/src/ss_agreement_env_listener.cc
+++ b/scoring/src/ss_agreement_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/ss_agreement_env_listener.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/ss_agreement_env_listener.hh b/scoring/src/ss_agreement_env_listener.hh
index ad87b4e96753def90f56ff538fa63db1dc30361d..775099fc69e2f704e3ca91a6788d8685a02a168e 100644
--- a/scoring/src/ss_agreement_env_listener.hh
+++ b/scoring/src/ss_agreement_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_SSAGREEMENT_ENV_LISTENER_HH
#define PM3_SCORING_SSAGREEMENT_ENV_LISTENER_HH
diff --git a/scoring/src/ss_agreement_score.cc b/scoring/src/ss_agreement_score.cc
index be4d6640415ed05e6074a9fcdda8e5af5d2677d2..cf92f38ef370e6025d262d929b7417b0d5054d04 100644
--- a/scoring/src/ss_agreement_score.cc
+++ b/scoring/src/ss_agreement_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/ss_agreement_score.hh>
namespace promod3 { namespace scoring {
diff --git a/scoring/src/ss_agreement_score.hh b/scoring/src/ss_agreement_score.hh
index 7e9960cffd65184225e68480da4755be32444282..a34698d840731163620bde3ee985825bd1302ff0 100644
--- a/scoring/src/ss_agreement_score.hh
+++ b/scoring/src/ss_agreement_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_SS_AGREEMENT_SCORE_HH
#define PM3_SCORING_SS_AGREEMENT_SCORE_HH
diff --git a/scoring/src/torsion_score.cc b/scoring/src/torsion_score.cc
index 65cca939dda0a6a59d7ce1bf057a8b9e6329f5bb..22907b1543197ee8f193a07169f2b0dee9296601 100644
--- a/scoring/src/torsion_score.cc
+++ b/scoring/src/torsion_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/torsion_score.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/torsion_score.hh b/scoring/src/torsion_score.hh
index 4cd298c83dab5097d0544b8825e636b540064a3d..d80c42d599a317d0d7b9e64bf56453b07f49bbcb 100644
--- a/scoring/src/torsion_score.hh
+++ b/scoring/src/torsion_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_TORSION_SCORE_HH
#define PM3_SCORING_TORSION_SCORE_HH
diff --git a/scoring/tests/test_all_atom_scorer.cc b/scoring/tests/test_all_atom_scorer.cc
index e1736b216d42e8cd8d70ef564a89e74f45bdcf2c..cf5ac6c945ce52b05d5bd32dde2fef8865c4eb27 100644
--- a/scoring/tests/test_all_atom_scorer.cc
+++ b/scoring/tests/test_all_atom_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/message.hh>
#include <promod3/loop/all_atom_env.hh>
#include <promod3/scoring/scoring_object_loader.hh>
diff --git a/scoring/tests/test_backbone_score_base.cc b/scoring/tests/test_backbone_score_base.cc
index 3706e45ab0cd23c3a05e689ebf2d12a4acfb7a44..b9e5e1d2eb3138e1ff6d4c035270f56a61931867 100644
--- a/scoring/tests/test_backbone_score_base.cc
+++ b/scoring/tests/test_backbone_score_base.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/backbone_score_base.hh>
#define BOOST_TEST_DYN_LINK
diff --git a/scoring/tests/test_backbone_scorer.cc b/scoring/tests/test_backbone_scorer.cc
index 49922b4b65c3292dcf9b519bb4d96c2b0d80ba4c..56e8be5a3afcd8aa6e7807aa0fcd602f4176177d 100644
--- a/scoring/tests/test_backbone_scorer.cc
+++ b/scoring/tests/test_backbone_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/backbone_score_base.hh>
#include <promod3/scoring/backbone_overall_scorer.hh>
diff --git a/scoring/tests/tests.cc b/scoring/tests/tests.cc
index 9ef67f35e664a43f5b72a48108fe82cef9747477..afe7f82308e8672d821fb286ec92f9c02481bc35 100644
--- a/scoring/tests/tests.cc
+++ b/scoring/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_scoring
#define BOOST_AUTO_TEST_MAIN
diff --git a/scripts/pm.in b/scripts/pm.in
index 84618642d6816343ed92a8c0a9ad7d93ad246519..3bafd55c7c8985fdd1c678d90ea82aed4275973f 100755
--- a/scripts/pm.in
+++ b/scripts/pm.in
@@ -1,5 +1,20 @@
#!/bin/bash
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
# Wrapper script that dispatches the actions to the actual Python script. It
# autodetects the most important directories and sets LD_LIBRARY_PATH and
# friends.
diff --git a/sidechain/data/convert_lib.py b/sidechain/data/convert_lib.py
index 56082fa17e686e9df0883933c8e35bc8ccd59f2c..515dc9280f5d3894bdc89f5233633f779cdab8d3 100644
--- a/sidechain/data/convert_lib.py
+++ b/sidechain/data/convert_lib.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Convert files from portable to raw.'''
import sys
import os
diff --git a/sidechain/doc/disulfid.rst b/sidechain/doc/disulfid.rst
index 1cee3075640728b8c205c8bf9d9ff0128d6eeb9d..d078a6c5a65e20f2b4fc682f26a1e5b7853d6a92 100644
--- a/sidechain/doc/disulfid.rst
+++ b/sidechain/doc/disulfid.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Disulfid Bond Evaluation
================================================================================
diff --git a/sidechain/doc/frame.rst b/sidechain/doc/frame.rst
index d5e355915971ca7a0cd140036d366d9812f777e3..d8365f4a5316d2efebaaaafb50a87238b1b3ac2d 100644
--- a/sidechain/doc/frame.rst
+++ b/sidechain/doc/frame.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Frame
================================================================================
diff --git a/sidechain/doc/graph.rst b/sidechain/doc/graph.rst
index 76c50cfccedbe763fe7afd626a771ac9e982c462..44606b2766a57c90bfa7f74d86cfc720ddf4ed71 100644
--- a/sidechain/doc/graph.rst
+++ b/sidechain/doc/graph.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamer Graph
================================================================================
diff --git a/sidechain/doc/index.rst b/sidechain/doc/index.rst
index 3dab62b72a5b6bee06935ae03699d5926a4a6601..aeac7212ce7a9232b81c95d2178cb32d07ff6595 100644
--- a/sidechain/doc/index.rst
+++ b/sidechain/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.sidechain` - Sidechain Modelling
================================================================================
diff --git a/sidechain/doc/loading.rst b/sidechain/doc/loading.rst
index c903f4f67e78634cb4fd8276eaec0658b91fb886..83e9390b16d8b8726c23a58f79dfdbf0eff22790 100644
--- a/sidechain/doc/loading.rst
+++ b/sidechain/doc/loading.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Loading Rotamer Libraries
================================================================================
diff --git a/sidechain/doc/rotamer.rst b/sidechain/doc/rotamer.rst
index d0b7604fb727417f25ddde941e0e026debf88638..30b3c7ca3b06602a1fbade371a3abdbc5a4e9029 100644
--- a/sidechain/doc/rotamer.rst
+++ b/sidechain/doc/rotamer.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamers
================================================================================
diff --git a/sidechain/doc/rotamer_constructor.rst b/sidechain/doc/rotamer_constructor.rst
index 548da6b1dfe74548dd7771b1f4045674ce28362a..82f9626c2afedb57149fc5c55042ee13dcd8fcb8 100644
--- a/sidechain/doc/rotamer_constructor.rst
+++ b/sidechain/doc/rotamer_constructor.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamer Constructor
================================================================================
diff --git a/sidechain/doc/rotamer_id.rst b/sidechain/doc/rotamer_id.rst
index 7eac7b85ca8de53c2ee27619089aa93a1907da66..746a51641352c7295152567a742eda8befedc803 100644
--- a/sidechain/doc/rotamer_id.rst
+++ b/sidechain/doc/rotamer_id.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
RotamerID
================================================================================
diff --git a/sidechain/doc/rotamer_lib.rst b/sidechain/doc/rotamer_lib.rst
index 89d70ac239cb8af4d66e6465ab6838816f042b20..0069c3888b70f7ad37acbf984cd3c95470af9840 100644
--- a/sidechain/doc/rotamer_lib.rst
+++ b/sidechain/doc/rotamer_lib.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamer Library
================================================================================
diff --git a/sidechain/doc/subrotamer_optimizer.rst b/sidechain/doc/subrotamer_optimizer.rst
index e4124466394f2bdc0248aa40056a590f5b556dcb..27315888d85598b7f8830e1241b5139c65af0db5 100644
--- a/sidechain/doc/subrotamer_optimizer.rst
+++ b/sidechain/doc/subrotamer_optimizer.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Subrotamer Optimization
================================================================================
diff --git a/sidechain/pymod/__init__.py b/sidechain/pymod/__init__.py
index a915c37e3d03af93e9e14a35f2d00d40c3deae7b..311426d9e13dc020e82e4f64a0afad86803bc11a 100644
--- a/sidechain/pymod/__init__.py
+++ b/sidechain/pymod/__init__.py
@@ -1,2 +1,18 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from _sidechain import *
diff --git a/sidechain/pymod/export_connector.cc b/sidechain/pymod/export_connector.cc
index b1eaecfef8424924044036ebf0cb24659306f3da..39742c354089d84aab6bd8611ece0d8d4ad80009 100644
--- a/sidechain/pymod/export_connector.cc
+++ b/sidechain/pymod/export_connector.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/sidechain/sidechain_connector.hh>
diff --git a/sidechain/pymod/export_disulfid.cc b/sidechain/pymod/export_disulfid.cc
index b346dc8e834f462a09cdd0a0391775fba05df7d8..86fb589469481cb181736cab155a7455c6101724 100644
--- a/sidechain/pymod/export_disulfid.cc
+++ b/sidechain/pymod/export_disulfid.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
diff --git a/sidechain/pymod/export_frame.cc b/sidechain/pymod/export_frame.cc
index 7d4beedc0938544dbe4abb911002026f5f6eb117..c1aec78b2b9ceeb50b9931fb6ebc2415882dafb5 100644
--- a/sidechain/pymod/export_frame.cc
+++ b/sidechain/pymod/export_frame.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/sidechain/frame.hh>
diff --git a/sidechain/pymod/export_particle.cc b/sidechain/pymod/export_particle.cc
index 7a94286d5652c3adce7a422fb36d15e5500b2d4a..64eb1a0660bcf678d29ebde03afe41d2e3e93377 100644
--- a/sidechain/pymod/export_particle.cc
+++ b/sidechain/pymod/export_particle.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/sidechain/particle.hh>
diff --git a/sidechain/pymod/export_rotamer.cc b/sidechain/pymod/export_rotamer.cc
index 77b138df2e3e5251483d8cca23531fdefe269c82..80468074311b622982c4326c50f579d8293ecf23 100644
--- a/sidechain/pymod/export_rotamer.cc
+++ b/sidechain/pymod/export_rotamer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/sidechain/pymod/export_rotamer_cruncher.cc b/sidechain/pymod/export_rotamer_cruncher.cc
index 0a1458d35f48dfe1d0b4f25727f4cb238182b683..c38ae85bdc4b6df92e2d571b83b8f4fd3470f592 100644
--- a/sidechain/pymod/export_rotamer_cruncher.cc
+++ b/sidechain/pymod/export_rotamer_cruncher.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/sidechain/rotamer_cruncher.hh>
diff --git a/sidechain/pymod/export_rotamer_density.cc b/sidechain/pymod/export_rotamer_density.cc
index 60b9a1eafe6b8178704b4062a7f9dc02f1e10836..942f5f50d3ffe23ee7a40365027f2b9384e92cd2 100644
--- a/sidechain/pymod/export_rotamer_density.cc
+++ b/sidechain/pymod/export_rotamer_density.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/sidechain/pymod/export_rotamer_graph.cc b/sidechain/pymod/export_rotamer_graph.cc
index 782d0e81d070cf83c1ee3220d5483f80e09e6998..001ba6cacb13a0a1284299ebb53b58b155cbf9f9 100644
--- a/sidechain/pymod/export_rotamer_graph.cc
+++ b/sidechain/pymod/export_rotamer_graph.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/graph_minimizer.hh>
diff --git a/sidechain/pymod/export_rotamer_ids.cc b/sidechain/pymod/export_rotamer_ids.cc
index 69988eab1a8b15dc3643bdcca12f0ee64c589d58..28fb24e7569c56611c92cb30f94c736e1b4cea19 100644
--- a/sidechain/pymod/export_rotamer_ids.cc
+++ b/sidechain/pymod/export_rotamer_ids.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/sidechain/rotamer_id.hh>
diff --git a/sidechain/pymod/export_rotamer_lib.cc b/sidechain/pymod/export_rotamer_lib.cc
index 25aa0c09fc4ba4b6803efa9203e196760ee4f8c8..0e5286b7b09698e141e7b729fe015d2a350be95a 100644
--- a/sidechain/pymod/export_rotamer_lib.cc
+++ b/sidechain/pymod/export_rotamer_lib.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
diff --git a/sidechain/pymod/export_scwrl_rotamer_constructor.cc b/sidechain/pymod/export_scwrl_rotamer_constructor.cc
index 539288e3e6363cee544e8815c484c83da32e6971..7b7bd10d64be7304ab9e22cce4f2b5a2f03fa76b 100644
--- a/sidechain/pymod/export_scwrl_rotamer_constructor.cc
+++ b/sidechain/pymod/export_scwrl_rotamer_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/sidechain/pymod/export_sidechain_object_loader.cc b/sidechain/pymod/export_sidechain_object_loader.cc
index 30838988030d7697d55467f8123c0b6dbccc6603..ab7ce781a316d83f16ec05abc9fb20ac4e6e8899 100644
--- a/sidechain/pymod/export_sidechain_object_loader.cc
+++ b/sidechain/pymod/export_sidechain_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/sidechain/sidechain_object_loader.hh>
diff --git a/sidechain/pymod/export_subrotamer_optimizer.cc b/sidechain/pymod/export_subrotamer_optimizer.cc
index 1b168786700daca626ac00b535921e04c6808663..e562637a0cd94415809b7605c425e685c25e1afe 100644
--- a/sidechain/pymod/export_subrotamer_optimizer.cc
+++ b/sidechain/pymod/export_subrotamer_optimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
diff --git a/sidechain/pymod/wrap_sidechain.cc b/sidechain/pymod/wrap_sidechain.cc
index 840b5d3b405eab5f532b7f6cd2de1eccf1a34c4b..f74e4610bb543c1530f8b47e2489675da8f774fe 100644
--- a/sidechain/pymod/wrap_sidechain.cc
+++ b/sidechain/pymod/wrap_sidechain.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_Connector();
diff --git a/sidechain/src/bb_dep_rotamer_lib.cc b/sidechain/src/bb_dep_rotamer_lib.cc
index e2c9b34e8bbd65b7c1800aded07f61962c75fb24..e99ba2e96afdc414b5d66bba06792d767694640b 100644
--- a/sidechain/src/bb_dep_rotamer_lib.cc
+++ b/sidechain/src/bb_dep_rotamer_lib.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/bb_dep_rotamer_lib.hh>
#include <promod3/core/check_io.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/bb_dep_rotamer_lib.hh b/sidechain/src/bb_dep_rotamer_lib.hh
index a01a042f4598998e1d3e48e4b29e98ce941e4df6..c88b19feabe09600944fa453fb675555ab92416a 100644
--- a/sidechain/src/bb_dep_rotamer_lib.hh
+++ b/sidechain/src/bb_dep_rotamer_lib.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_BB_DEP_ROTAMER_LIB_HH
#define PROMOD3_BB_DEP_ROTAMER_LIB_HH
diff --git a/sidechain/src/disulfid.cc b/sidechain/src/disulfid.cc
index 620658f2e17954b972d0b996dd3664a9db293b53..5cdb808cf97ab4b6dcba60b7d88b16419d51f00d 100644
--- a/sidechain/src/disulfid.cc
+++ b/sidechain/src/disulfid.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/disulfid.hh>
#include <promod3/sidechain/rotamer.hh>
#include <promod3/sidechain/particle.hh>
diff --git a/sidechain/src/disulfid.hh b/sidechain/src/disulfid.hh
index ac6aa87e196c4e4f0873c9068e7e932798021aca..6dd98a4ae27b14b2a4c6a624fb3bc57d9ccb7c30 100644
--- a/sidechain/src/disulfid.hh
+++ b/sidechain/src/disulfid.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SIDECHAIN_DISULFID_HH
#define PROMOD3_SIDECHAIN_DISULFID_HH
diff --git a/sidechain/src/frame.cc b/sidechain/src/frame.cc
index 6f79ead37f8ff176f441a7108915b7547b4b0c39..891e2959674a32fe2bfae76ef33fd636e5cddd42 100644
--- a/sidechain/src/frame.cc
+++ b/sidechain/src/frame.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/frame.hh>
#include <promod3/core/runtime_profiling.hh>
#include <ost/mol/xcs_editor.hh>
diff --git a/sidechain/src/frame.hh b/sidechain/src/frame.hh
index 1ba20cec8f4eae40a4b9cb03908ce52db20bbf8a..b073bb0989e60eb581a17f33d299de0bdc201368 100644
--- a/sidechain/src/frame.hh
+++ b/sidechain/src/frame.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_FRAME_HH
#define PROMOD3_FRAME_HH
diff --git a/sidechain/src/particle.cc b/sidechain/src/particle.cc
index 91fa11d16ce2d64ad14f47746da934174d4ee3e6..e4c79f01a01b4216a97b30cc3c53b0dedb2dc785 100644
--- a/sidechain/src/particle.cc
+++ b/sidechain/src/particle.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/particle.hh>
diff --git a/sidechain/src/particle.hh b/sidechain/src/particle.hh
index 663a37f676fa8a89c1567d807ee6927bf68afec9..9675e0ccf95afc8bd9682641c0e8673e0bcae711 100644
--- a/sidechain/src/particle.hh
+++ b/sidechain/src/particle.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_PARTICLE_HH
#define PROMOD3_PARTICLE_HH
diff --git a/sidechain/src/rotamer.cc b/sidechain/src/rotamer.cc
index 71443cb8feb51f25abc7805f41a5973777f51e99..41d1f9e2b4678ce83c72ff8b4368b43f4f5ab4d4 100644
--- a/sidechain/src/rotamer.cc
+++ b/sidechain/src/rotamer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/rotamer.hh b/sidechain/src/rotamer.hh
index 45ce313939a798828f47988b1158678907f7c0d2..068f3578fe5f0da278425c593d33a4db226c5d3b 100644
--- a/sidechain/src/rotamer.hh
+++ b/sidechain/src/rotamer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_HH
#define PROMOD3_ROTAMER_HH
diff --git a/sidechain/src/rotamer_cruncher.cc b/sidechain/src/rotamer_cruncher.cc
index f6769858fe96e0124513e3b61b0586ed2a975aab..dfe7c57ca9ca1092b69f81600f1b97b2e1b13242 100644
--- a/sidechain/src/rotamer_cruncher.cc
+++ b/sidechain/src/rotamer_cruncher.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_cruncher.hh>
diff --git a/sidechain/src/rotamer_cruncher.hh b/sidechain/src/rotamer_cruncher.hh
index fecff6096bf14f93d02e737f9ba3b943374a4793..bd4e6e95981342d5184252325309d8d46d5e25bd 100644
--- a/sidechain/src/rotamer_cruncher.hh
+++ b/sidechain/src/rotamer_cruncher.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_CRUNCHER_HH
#define PROMOD3_ROTAMER_CRUNCHER_HH
diff --git a/sidechain/src/rotamer_density.cc b/sidechain/src/rotamer_density.cc
index 92c1fd1fa056baf3e85342d6020cb0150537d504..c3502ef25841181adbc9641c5ea972b400b3570d 100644
--- a/sidechain/src/rotamer_density.cc
+++ b/sidechain/src/rotamer_density.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_density.hh>
namespace promod3{ namespace sidechain{
diff --git a/sidechain/src/rotamer_density.hh b/sidechain/src/rotamer_density.hh
index 3f9d4236cb69a6a15241d9d8294c6c1cca0763b1..acf38b55dda8d3b61a742db27256c19a6b4981bf 100644
--- a/sidechain/src/rotamer_density.hh
+++ b/sidechain/src/rotamer_density.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_DENSITY_HH
#define PROMOD3_ROTAMER_DENSITY_HH
diff --git a/sidechain/src/rotamer_graph.hh b/sidechain/src/rotamer_graph.hh
index 4e447b684191e0b33b7ab4ef4c8aae860ba3aebd..7ff2c37769467ebf5bc94625b410d91be2c9586e 100644
--- a/sidechain/src/rotamer_graph.hh
+++ b/sidechain/src/rotamer_graph.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_GRAPH_COMPONENTS_HH
#define PROMOD3_ROTAMER_GRAPH_COMPONENTS_HH
diff --git a/sidechain/src/rotamer_group.cc b/sidechain/src/rotamer_group.cc
index dd20d27cb85307258a8b00c7693430a018bf49ce..ed6fde6c96b03d07a152f5211bf6f9102ca55e05 100644
--- a/sidechain/src/rotamer_group.cc
+++ b/sidechain/src/rotamer_group.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_group.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/rotamer_group.hh b/sidechain/src/rotamer_group.hh
index 0ed5555e040b2a5f87c45dcdad5568b23ae90a08..b2556becc273619a187b085275e7fde33395dc08 100644
--- a/sidechain/src/rotamer_group.hh
+++ b/sidechain/src/rotamer_group.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_GROUP_HH
#define PROMOD3_ROTAMER_GROUP_HH
diff --git a/sidechain/src/rotamer_id.cc b/sidechain/src/rotamer_id.cc
index e5427def61b2a9256650f0c62060d9118c83ea5b..76a11c985ca94b97b74d59959017142ce96df195 100644
--- a/sidechain/src/rotamer_id.cc
+++ b/sidechain/src/rotamer_id.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_id.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/rotamer_id.hh b/sidechain/src/rotamer_id.hh
index 2ba2cb2e02701b758b1fd493140bb0dd97fe8a0b..407924d50f0170192ec3233d4040395d196b4a4b 100644
--- a/sidechain/src/rotamer_id.hh
+++ b/sidechain/src/rotamer_id.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_ID_HH
#define PROMOD3_ROTAMER_ID_HH
diff --git a/sidechain/src/rotamer_lib.cc b/sidechain/src/rotamer_lib.cc
index 10ae3e6438f212aaac69a6e9b7b893e604d0ddde..5c5fa4db1d322226dccd453f46e0798a8aefd0b3 100644
--- a/sidechain/src/rotamer_lib.cc
+++ b/sidechain/src/rotamer_lib.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_lib.hh>
#include <promod3/core/check_io.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/rotamer_lib.hh b/sidechain/src/rotamer_lib.hh
index f6fdbe02df6c48158ad1eda3e12e7114f8a07dd5..49e8fb7bce78fb5e0df9a95409240c865ac76b64 100644
--- a/sidechain/src/rotamer_lib.hh
+++ b/sidechain/src/rotamer_lib.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_LIB_HH
#define PROMOD3_ROTAMER_LIB_HH
diff --git a/sidechain/src/rotamer_lib_entry.cc b/sidechain/src/rotamer_lib_entry.cc
index 50f00da938bff4f09cfb473bebc11eb983fdc345..5379598395a65a9484c410714b45d3b3c5f39b27 100644
--- a/sidechain/src/rotamer_lib_entry.cc
+++ b/sidechain/src/rotamer_lib_entry.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_lib_entry.hh>
namespace{
diff --git a/sidechain/src/rotamer_lib_entry.hh b/sidechain/src/rotamer_lib_entry.hh
index 5da7ecda6493e9ce341bcdc3baef7add59588178..45dc6bb826d419deee441d144c196ec9a19a3d10 100644
--- a/sidechain/src/rotamer_lib_entry.hh
+++ b/sidechain/src/rotamer_lib_entry.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_LIB_ENTRY_HH
#define PROMOD3_ROTAMER_LIB_ENTRY_HH
diff --git a/sidechain/src/rotamer_lib_reader.cc b/sidechain/src/rotamer_lib_reader.cc
index 4025bd4d502641685d443eff4dc66705a5c4d811..3f381fb2c335a9971c08fd00986da23a6bf75f8e 100644
--- a/sidechain/src/rotamer_lib_reader.cc
+++ b/sidechain/src/rotamer_lib_reader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_lib_reader.hh>
namespace promod3{ namespace sidechain{
diff --git a/sidechain/src/rotamer_lib_reader.hh b/sidechain/src/rotamer_lib_reader.hh
index 606a4c37787b436dde260e867758f034eac48880..1abcdd30fa16954877e4fd64aa8eaa8761fe5e9a 100644
--- a/sidechain/src/rotamer_lib_reader.hh
+++ b/sidechain/src/rotamer_lib_reader.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_LIB_READER_HH
#define PROMOD3_ROTAMER_LIB_READER_HH
diff --git a/sidechain/src/scwrl_rotamer_constructor.cc b/sidechain/src/scwrl_rotamer_constructor.cc
index 39a6e987ac6f87d6a175f192f5a0b491504f4b6a..0fd13660cc5de6a6d69693446f80e8440d04a87f 100644
--- a/sidechain/src/scwrl_rotamer_constructor.cc
+++ b/sidechain/src/scwrl_rotamer_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/scwrl_rotamer_constructor.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/message.hh>
diff --git a/sidechain/src/scwrl_rotamer_constructor.hh b/sidechain/src/scwrl_rotamer_constructor.hh
index 8beea0819bacefa5d12de50ce1500740b23c20ed..28915f2fa59bf841721061eaf45f76e7f87dc360 100644
--- a/sidechain/src/scwrl_rotamer_constructor.hh
+++ b/sidechain/src/scwrl_rotamer_constructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SCWRL_ROTAMER_CONSTRUCTOR_HH
#define PROMOD3_SCWRL_ROTAMER_CONSTRUCTOR_HH
diff --git a/sidechain/src/sidechain_connector.cc b/sidechain/src/sidechain_connector.cc
index c8e5c21966e75605c268289514016fbbc1beafae..ca9250bc5478bb77445205062345abc031075023 100644
--- a/sidechain/src/sidechain_connector.cc
+++ b/sidechain/src/sidechain_connector.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/sidechain_connector.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/sidechain_connector.hh b/sidechain/src/sidechain_connector.hh
index 4a74884544e0ea68cc52d148159d0b85e5e1e482..55617577d7708b5233afb38f94b8ef2d7ceb048e 100644
--- a/sidechain/src/sidechain_connector.hh
+++ b/sidechain/src/sidechain_connector.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SIDECHAIN_CONNECTOR_HH
#define PROMOD3_SIDECHAIN_CONNECTOR_HH
diff --git a/sidechain/src/sidechain_object_loader.cc b/sidechain/src/sidechain_object_loader.cc
index e814cd05af89b7e21357e8881167b4546179ab61..62850f20a5f5142c475594a896efb41599e858e9 100644
--- a/sidechain/src/sidechain_object_loader.cc
+++ b/sidechain/src/sidechain_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/sidechain_object_loader.hh>
#include <promod3/config.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/sidechain_object_loader.hh b/sidechain/src/sidechain_object_loader.hh
index 85273a4c9e6eb14fcdbac7db1eb93f9347762ae1..3a15201b437f8c40602bdbbd2e7e52456cd2fd70 100644
--- a/sidechain/src/sidechain_object_loader.hh
+++ b/sidechain/src/sidechain_object_loader.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SIDECHAIN_OBJECT_LOADER_HH
#define PROMOD3_SIDECHAIN_OBJECT_LOADER_HH
diff --git a/sidechain/src/subrotamer_optimizer.cc b/sidechain/src/subrotamer_optimizer.cc
index 3594a5bcbe07e39b76c0e1098ac7eb440c031e15..3444eb3c5d4e3ced83bef7ad954f7f8374ff157c 100644
--- a/sidechain/src/subrotamer_optimizer.cc
+++ b/sidechain/src/subrotamer_optimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/subrotamer_optimizer.hh>
namespace promod3{ namespace sidechain{
diff --git a/sidechain/src/subrotamer_optimizer.hh b/sidechain/src/subrotamer_optimizer.hh
index df415f00cadbaebca42f393dce66c7bb8e620d80..371c5e7763a50f86bce7526abbbfb9caa5737206 100644
--- a/sidechain/src/subrotamer_optimizer.hh
+++ b/sidechain/src/subrotamer_optimizer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SUBROTAMER_OPTIMIZER_HH
#define PROMOD3_SUBROTAMER_OPTIMIZER_HH
diff --git a/sidechain/tests/test_frame_construction.cc b/sidechain/tests/test_frame_construction.cc
index 5c6801168270bd96ee3ae08bde1c0486fa8ce8b0..0817985b9a9d2708693957562ac4f196fb4efeac 100644
--- a/sidechain/tests/test_frame_construction.cc
+++ b/sidechain/tests/test_frame_construction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/scwrl_rotamer_constructor.hh>
#include <promod3/core/message.hh>
diff --git a/sidechain/tests/test_rotamers.cc b/sidechain/tests/test_rotamers.cc
index cd1151bbd2e4edbac1d6873eb4f1ffc7b301a6c9..11143888c2c85c246ee6c46c170560e5cfd045a0 100644
--- a/sidechain/tests/test_rotamers.cc
+++ b/sidechain/tests/test_rotamers.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/scwrl_rotamer_constructor.hh>
#include <promod3/core/message.hh>
diff --git a/sidechain/tests/tests.cc b/sidechain/tests/tests.cc
index 70ebea3f331ef95dbb6c42b2a9a95646f9fb1259..bfcbfd198384cb41889ca820c948fa813c243dc6 100644
--- a/sidechain/tests/tests.cc
+++ b/sidechain/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_sidechain
#define BOOST_AUTO_TEST_MAIN