diff --git a/doc/conf.py.in b/doc/conf.py.in
index fddcc7ef702e11e7aa7d2f83910172e02a61f536..1219c73e05d9a4047ac23d72dcc449f8581265eb 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'2017, ProMod3 authors'# pylint: disable=redefined-builtin
+copyright = u'2018, ProMod3 authors'# 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/html/_modules/index.html b/doc/html/_modules/index.html
index 14ae5c46c28bdd1237ebef92280d2f3a56c1da83..6964cf96734a79a1c9de4932da5588a9924935da 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -146,7 +146,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3.html b/doc/html/_modules/promod3.html
index 56ad569c5a015eba844c0845422f1cb0b1216859..140c70b9d3e7b6edc1001cd57344d3a21c5babd7 100644
--- a/doc/html/_modules/promod3.html
+++ b/doc/html/_modules/promod3.html
@@ -146,7 +146,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index 8307571516583bdd8aa501989cbe682ec047b0ed..2266f1a35bc7f1a3cb8be03cbadf869949896d0b 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -231,7 +231,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/core/pm3argparse.html b/doc/html/_modules/promod3/core/pm3argparse.html
index c1d0b98a4fbe6006fddcc641a57dd76f0c1256f9..e10fff03f913d8b7779021287b59d397b5f58634 100644
--- a/doc/html/_modules/promod3/core/pm3argparse.html
+++ b/doc/html/_modules/promod3/core/pm3argparse.html
@@ -725,7 +725,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_closegaps.html b/doc/html/_modules/promod3/modelling/_closegaps.html
index 274675b56c5696d99e24d980f82da9afb4a611fd..85c8c033bdc62ac51dc8c0529b0e2ca2ad5f1f0f 100644
--- a/doc/html/_modules/promod3/modelling/_closegaps.html
+++ b/doc/html/_modules/promod3/modelling/_closegaps.html
@@ -1627,7 +1627,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_denovo.html b/doc/html/_modules/promod3/modelling/_denovo.html
index f50cd4b99d40498b61ea82a2c03c5d7a1c4c4bf1..b2100964e66fb6ebbc6d9f4a3a710767ffecfc50 100644
--- a/doc/html/_modules/promod3/modelling/_denovo.html
+++ b/doc/html/_modules/promod3/modelling/_denovo.html
@@ -200,7 +200,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_fragger_handle.html b/doc/html/_modules/promod3/modelling/_fragger_handle.html
index 531c603fc37fa40fa0b34bc9931b32ad1dab6c19..0ef683b33454d388f4ec6354c16ddeef42fc101d 100644
--- a/doc/html/_modules/promod3/modelling/_fragger_handle.html
+++ b/doc/html/_modules/promod3/modelling/_fragger_handle.html
@@ -423,7 +423,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_molprobity.html b/doc/html/_modules/promod3/modelling/_molprobity.html
index 5af12776a9189ac243531d219e89b194a8bf091d..b9441021b1cca2bd98ef90666bf96c15f20509f6 100644
--- a/doc/html/_modules/promod3/modelling/_molprobity.html
+++ b/doc/html/_modules/promod3/modelling/_molprobity.html
@@ -189,7 +189,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_pipeline.html b/doc/html/_modules/promod3/modelling/_pipeline.html
index c1d5adaffcd1f890ae61ad2840f19f3a1b480a06..3ea48e01d1e4a82180c71d72adbae5297ad85c69 100644
--- a/doc/html/_modules/promod3/modelling/_pipeline.html
+++ b/doc/html/_modules/promod3/modelling/_pipeline.html
@@ -560,7 +560,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
index d7c7bff455f34534db648e909c33f71fac8d4e60..a8840922170b8f1448c05531aba3a51c444ff34e 100644
--- a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
+++ b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
@@ -594,7 +594,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_ring_punches.html b/doc/html/_modules/promod3/modelling/_ring_punches.html
index 4b771e840db23370bf8db5fe918d73265fbcbcfb..a443928984846cc8360ea5a3b7339d0c45757d85 100644
--- a/doc/html/_modules/promod3/modelling/_ring_punches.html
+++ b/doc/html/_modules/promod3/modelling/_ring_punches.html
@@ -308,7 +308,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/test_actions.html b/doc/html/_modules/test_actions.html
index 3e38acd2755e242982dc4cbd339696947ca9543e..f9739b382679bc7bfe2aafe0e47bace71563dd75 100644
--- a/doc/html/_modules/test_actions.html
+++ b/doc/html/_modules/test_actions.html
@@ -197,7 +197,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index 296203fb4df2cd69e74608d63abeb52226269b35..f83632f45740b0b6ed02b2d4176abe058c068625 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -191,7 +191,7 @@ residue in the aligned sequence. Leading/trailing whitespaces of &lt;CHAINID&gt;
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 6ccb9257a0cccddf2f00c2951bde20792f651ac3..7a72c1a6616b45888b696930be029d8e2cb467f2 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -410,7 +410,7 @@ file (also complains if a directory is found instead).</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 35f13e27f897ffd19b473c8b25914860f5296b0c..05f730f28a2e8349dffce5b4b7a0fcbfb68a61a0 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -204,7 +204,7 @@ safely delete the whole source folder.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index eb7599505c23f99c322703313c255a3e1b2221d5..776b517f5d8af27418df83b927924c2b327d2a65 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -147,7 +147,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index 1fc84c2ff3361ed264a8c77a5004745a711fd9a0..f80cc16828502e7b936f090bbb38cd803d3b88ee 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -372,7 +372,7 @@ target has to be created <strong>before</strong> any action may be attached to i
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index bac4dc1ddde827f6df550f11ea81f3c188323372..069ec304aa26f141410c4fe3bfd06b0b7624cbce 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -648,7 +648,7 @@ contributions to web pages using ProMod3.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index 900922c9480a79a05d8d4d0393301ca893b7ba61..3cdcb509f583cc24facb60b9bcd5c19e7db01f34 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -346,7 +346,7 @@ angles and one distance and is used in the fragment database for fast lookups.</
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index b77f621ee96716e2529ad7cbd601bfa656199ce3..b99d92a070ce4ed9faef1242be310ea4eb2a9fe7 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -384,7 +384,7 @@ The second element is the according energy value.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index b15aa835e6882643e637d7eb5a35c4ab2dfed05b..2ef049d9bc9fdc579ad7b7dffa6e9227371c6429 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -246,7 +246,7 @@ script will terminate if a gzip file is found.</li>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 5181a7ec3f9ebc0f20af734e7e212686766b04df..774d53ed424cd8915182a7f8216297a4fe85bde9 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -104,7 +104,7 @@ modeling per se but cover standard programming issues.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index d62653ffea18b35be5d89bfbb6bc57a49f822885..c92c89603a57ec80a32e2435a5661d076d14f31a 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -343,7 +343,7 @@ and with the right constraints.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index 9a316a58d06f5c3532b8285059c6330bbd0d804b..2466ad9d3f6e6d8de264e1874c43332677a3a97a 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -200,7 +200,7 @@ will fail miserably if timers are currently running.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index f508395a188297ba61d37c1f24607c48a129d7ee..e0e9cb4d4256b35a60b91b487c28cbea9efd04cf 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -105,7 +105,7 @@ enabled globally.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index e9d4c0d3b23421906c54b4db0b65a092ee138e38..f58b1ee6ad20de2cf87c9fc6bf8c81d1ba15d6b5 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -292,7 +292,7 @@ modules from there, use the binaries from <code class="file docutils literal"><s
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index b4788adaa2c9a212f38ce7a82ff156f543384003..89882a9474b79f60d2d36dbbc47bec5394e3ccc3 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -123,7 +123,7 @@ new features.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 9c340199ed41ec9655e600be1df72fc7e51dbcdd..4e5da3b46b5ba10cbb6458cf8b9eee2e6aeedac4 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -3715,7 +3715,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index 59d380cc535caf6eeeef9579265227872a159245..f984958d7fd43ff0e604a8031e37bb8b44e74eec 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -147,7 +147,7 @@ not set, 1 thread will be used by default.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/index.html b/doc/html/index.html
index 8366b1a0370f0e05e9ef08a432a26c596cc7599a..9a9a20281972b758a64c9e1976765ce31fd410cc 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -124,7 +124,7 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index f55f5ccc9606e4d4f586b92a251c0db72815ab2f..df65f9c542ab9108208ba0e8740ebb02e80413e0 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -1342,7 +1342,7 @@ when residue is N terminal.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index 66ce38d5af9496f7bbe2f19aba706759a7b4b519..096e988e0855d432d670e2d868e5e9d6da9309ab 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -1003,7 +1003,7 @@ backbone list.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index a5305baf5a718d55881b2c2c0a09a37b90b63495..4ceff047a047b214b7ec544b3426b6026963b818 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -162,7 +162,7 @@ loops. The following example should give you an idea of what can be done:</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index f4448c847bc47421cb1cea2cac00a984da67ef97..8425953c8165937468f1c690d1e44d38250cfe99 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -210,7 +210,7 @@ Proteins, 62(4):892–908, Mar 2006.</dd>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2017, ProMod3 authors.
+      &copy;2018, ProMod3 authors.
       
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diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 7a13b5a81bab534b6c2f5ab1556b940c28955f58..38cdf31e4748d13ed4624067799504894827ea98 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -1592,7 +1592,7 @@ False, False)</em>.</p>
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diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
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--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -1779,7 +1779,7 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
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diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
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--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -589,7 +589,7 @@ standard amino acid</td>
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diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index b1460016b5cbcfe61e31e8ed6d1046b06db0591c..0cd8be8702bde9b8f390725a811a36e6c272ea21 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -411,7 +411,7 @@ with the keys of the scores in <strong>scorer</strong></li>
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diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 8e83430f89eac925f45cf57d400164e1a46dfd4b..032f3350c35708976935479acb04659939e587f6 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -652,7 +652,7 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
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diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
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--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -157,7 +157,7 @@ a model fully automatically as follows:</p>
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diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index d150dfe33b6c2843f8a4e7add8ce97a950b1c2fa..b1803ae6baaba3a96330a07192ae2987307a9f9b 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -1139,7 +1139,7 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
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diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index 855a9c19766f437ec7e4b9163396c9abfdfab5f0..d6e5827539347b83e178f2de00f6fbfc0a8fd73c 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -655,7 +655,7 @@ the one given in the constructor.</td>
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diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 09e289a764b2ca1f29fb91b4b6340b7a7d009a0e..914620c01d9b7ab91692936ea61927682e9a7a87 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -282,7 +282,7 @@ executable is not found.</p>
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diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 699ce4a0b55d40d6f04e0ac58e79ee5df88f86fb..6732e2a0fa011a0b43ada5c9968d35caabf3e393 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -735,7 +735,7 @@ the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
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diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
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--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -1240,7 +1240,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
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diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
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--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -439,7 +439,7 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
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diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index b91204173e557b1e87324a27ef1dca714af4745b..ce9c3bed25946e90ca661dc414a86805a914c840 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -477,7 +477,7 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
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diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
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--- a/doc/html/py-modindex.html
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@@ -131,7 +131,7 @@
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diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 13c1d1c279dfbd5ac7e6fde246648a6a043be515..983fd1a43688c709ba13f6608a27e1cbd61780b1 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -671,7 +671,7 @@ of residues in the input loop. True by default.</td>
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diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
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--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -510,7 +510,7 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
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diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
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--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -1387,7 +1387,7 @@ of residues to be scored. True by default.</td>
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diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
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--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -147,7 +147,7 @@ scorers to it and finally score some loops:</p>
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diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
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--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -164,7 +164,7 @@ construction algorithm <a class="reference internal" href="#canutescu2003b" id="
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diff --git a/doc/html/search.html b/doc/html/search.html
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--- a/doc/html/search.html
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@@ -86,7 +86,7 @@
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diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
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--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -179,7 +179,7 @@ describe the optimal rotamers in the according rotamer groups.</p>
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diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
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--- a/doc/html/sidechain/frame.html
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@@ -168,7 +168,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
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diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
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+++ b/doc/html/sidechain/graph.html
@@ -119,7 +119,7 @@ conformations for every amino acid position.</td>
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diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
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--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -215,7 +215,7 @@ pipelines available in the modelling module.</p>
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diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
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+++ b/doc/html/sidechain/loading.html
@@ -167,7 +167,7 @@ incomplete if the last problem gets triggered.</td>
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diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
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--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -1224,7 +1224,7 @@ rotamers with <em>self_energy</em> &gt; <em>l_e</em> + <em>thresh</em></p>
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diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
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@@ -368,7 +368,7 @@ to be assigned</td>
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diff --git a/doc/html/sidechain/rotamer_id.html b/doc/html/sidechain/rotamer_id.html
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diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
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diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
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@@ -125,7 +125,7 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
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@@ -151,7 +151,7 @@ scripts using the functionality of this library.</p>
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