From 3ccbaeec8e30deb639eeba04e5ef08f134095f21 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 27 Sep 2017 17:49:29 +0200
Subject: [PATCH] SCHWED-2641: current year is 2017...
---
doc/conf.py.in | 2 +-
doc/html/_modules/index.html | 2 +-
doc/html/_modules/promod3.html | 2 +-
doc/html/_modules/promod3/core/helper.html | 2 +-
doc/html/_modules/promod3/core/pm3argparse.html | 2 +-
doc/html/_modules/promod3/modelling/_closegaps.html | 2 +-
doc/html/_modules/promod3/modelling/_denovo.html | 2 +-
doc/html/_modules/promod3/modelling/_fragger_handle.html | 2 +-
doc/html/_modules/promod3/modelling/_molprobity.html | 2 +-
doc/html/_modules/promod3/modelling/_pipeline.html | 2 +-
.../_modules/promod3/modelling/_reconstruct_sidechains.html | 2 +-
doc/html/_modules/promod3/modelling/_ring_punches.html | 2 +-
doc/html/_modules/test_actions.html | 2 +-
doc/html/actions/index.html | 2 +-
doc/html/actions/index_dev.html | 2 +-
doc/html/buildsystem.html | 2 +-
doc/html/changelog.html | 2 +-
doc/html/cmake/index.html | 2 +-
doc/html/contributing.html | 2 +-
doc/html/core/geometry.html | 2 +-
doc/html/core/helper.html | 2 +-
doc/html/core/index.html | 2 +-
doc/html/core/pm3argparse.html | 2 +-
doc/html/core/runtime_profiling.html | 2 +-
doc/html/core/setcompoundschemlib.html | 2 +-
doc/html/dev_setup.html | 2 +-
doc/html/developers.html | 2 +-
doc/html/genindex.html | 2 +-
doc/html/gettingstarted.html | 2 +-
doc/html/index.html | 2 +-
doc/html/loop/all_atom.html | 2 +-
doc/html/loop/backbone.html | 2 +-
doc/html/loop/index.html | 2 +-
doc/html/loop/load_loop_objects.html | 2 +-
doc/html/loop/mm_system_creation.html | 2 +-
doc/html/loop/structure_db.html | 2 +-
doc/html/loop/torsion_sampler.html | 2 +-
doc/html/modelling/algorithms.html | 2 +-
doc/html/modelling/gap_handling.html | 2 +-
doc/html/modelling/index.html | 2 +-
doc/html/modelling/loop_candidates.html | 2 +-
doc/html/modelling/loop_closing.html | 2 +-
doc/html/modelling/model_checking.html | 2 +-
doc/html/modelling/monte_carlo.html | 2 +-
doc/html/modelling/pipeline.html | 2 +-
doc/html/modelling/sidechain_reconstruction.html | 2 +-
doc/html/portableIO.html | 2 +-
doc/html/py-modindex.html | 2 +-
doc/html/scoring/all_atom_scorers.html | 2 +-
doc/html/scoring/backbone_score_env.html | 2 +-
doc/html/scoring/backbone_scorers.html | 2 +-
doc/html/scoring/index.html | 2 +-
doc/html/search.html | 2 +-
doc/html/searchindex.js | 2 +-
doc/html/sidechain/disulfid.html | 2 +-
doc/html/sidechain/frame.html | 2 +-
doc/html/sidechain/graph.html | 2 +-
doc/html/sidechain/index.html | 2 +-
doc/html/sidechain/loading.html | 2 +-
doc/html/sidechain/rotamer.html | 2 +-
doc/html/sidechain/rotamer_constructor.html | 2 +-
doc/html/sidechain/rotamer_id.html | 2 +-
doc/html/sidechain/rotamer_lib.html | 2 +-
doc/html/sidechain/subrotamer_optimizer.html | 2 +-
doc/html/users.html | 2 +-
65 files changed, 65 insertions(+), 65 deletions(-)
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 915bc9fa..3453b6e9 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'2016, ProMod3 authors'# pylint: disable=redefined-builtin
+copyright = u'2017, 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 8368e225..d3d43313 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -142,7 +142,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3.html b/doc/html/_modules/promod3.html
index 6dc5471a..26f55e3a 100644
--- a/doc/html/_modules/promod3.html
+++ b/doc/html/_modules/promod3.html
@@ -147,7 +147,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index 1aef830b..cf69dc55 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -232,7 +232,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3/core/pm3argparse.html b/doc/html/_modules/promod3/core/pm3argparse.html
index 5c5e3676..a7e1be3f 100644
--- a/doc/html/_modules/promod3/core/pm3argparse.html
+++ b/doc/html/_modules/promod3/core/pm3argparse.html
@@ -726,7 +726,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_closegaps.html b/doc/html/_modules/promod3/modelling/_closegaps.html
index 81fd8a73..fa180db9 100644
--- a/doc/html/_modules/promod3/modelling/_closegaps.html
+++ b/doc/html/_modules/promod3/modelling/_closegaps.html
@@ -1564,7 +1564,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_denovo.html b/doc/html/_modules/promod3/modelling/_denovo.html
index 6135a955..22a37046 100644
--- a/doc/html/_modules/promod3/modelling/_denovo.html
+++ b/doc/html/_modules/promod3/modelling/_denovo.html
@@ -192,7 +192,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_fragger_handle.html b/doc/html/_modules/promod3/modelling/_fragger_handle.html
index 69fb47c7..b364e59e 100644
--- a/doc/html/_modules/promod3/modelling/_fragger_handle.html
+++ b/doc/html/_modules/promod3/modelling/_fragger_handle.html
@@ -424,7 +424,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_molprobity.html b/doc/html/_modules/promod3/modelling/_molprobity.html
index b2c6e956..864c296f 100644
--- a/doc/html/_modules/promod3/modelling/_molprobity.html
+++ b/doc/html/_modules/promod3/modelling/_molprobity.html
@@ -190,7 +190,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_pipeline.html b/doc/html/_modules/promod3/modelling/_pipeline.html
index 091f327c..2e1e7144 100644
--- a/doc/html/_modules/promod3/modelling/_pipeline.html
+++ b/doc/html/_modules/promod3/modelling/_pipeline.html
@@ -559,7 +559,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
index 6169c8e1..0f448104 100644
--- a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
+++ b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
@@ -605,7 +605,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_ring_punches.html b/doc/html/_modules/promod3/modelling/_ring_punches.html
index f09b399c..5d01cf28 100644
--- a/doc/html/_modules/promod3/modelling/_ring_punches.html
+++ b/doc/html/_modules/promod3/modelling/_ring_punches.html
@@ -309,7 +309,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/_modules/test_actions.html b/doc/html/_modules/test_actions.html
index 983d0674..e28652fc 100644
--- a/doc/html/_modules/test_actions.html
+++ b/doc/html/_modules/test_actions.html
@@ -198,7 +198,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index 0d940aad..0a4e2803 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -192,7 +192,7 @@ residue in the aligned sequence. Leading/trailing whitespaces of <CHAINID>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 91406c15..5b85e1b1 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -411,7 +411,7 @@ file (also complains if a directory is found instead).</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index fa07a66c..a716f543 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -205,7 +205,7 @@ safely delete the whole source folder.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 47aaee40..0893031c 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -118,7 +118,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index 4f1c4687..4f3556ee 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -373,7 +373,7 @@ target has to be created <strong>before</strong> any action may be attached to i
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index a25d4d65..a603efdf 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -649,7 +649,7 @@ contributions to web pages using ProMod3.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index 0165bf8b..d5c2a5d6 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -347,7 +347,7 @@ angles and one distance and is used in the fragment database for fast lookups.</
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 5a402192..fbc111e1 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -247,7 +247,7 @@ script will terminate if a gzip file is found.</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 09b3e0b7..af6c850e 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">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 4a3ab4f4..6f049e99 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -344,7 +344,7 @@ and with the right constraints.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index 6c91ce1e..c0b3d5d6 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -201,7 +201,7 @@ will fail miserably if timers are currently running.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index 5764d4e4..1d400cd0 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -106,7 +106,7 @@ enabled globally.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index a68295ec..3ff8fe00 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -293,7 +293,7 @@ modules from there, use the binaries from <code class="file docutils literal"><s
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 006b253b..b0e89ed9 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -124,7 +124,7 @@ new features.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 75191f2f..a4b8a6fb 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -3622,7 +3622,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index b2c5b4e5..58aa46d1 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -148,7 +148,7 @@ not set, 1 thread will be used by default.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/index.html b/doc/html/index.html
index c787dae8..99a24e3a 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -125,7 +125,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index f113915a..88e73577 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -1343,7 +1343,7 @@ when residue is N terminal.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index a61a0332..6bad77d4 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -1004,7 +1004,7 @@ backbone list.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index ff61dd91..26fc9a36 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -163,7 +163,7 @@ loops. The following example should give you an idea of what can be done:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index af506ad2..56f91dea 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -211,7 +211,7 @@ Proteins, 62(4):892–908, Mar 2006.</dd>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 10ea8cf1..0c214fb2 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -1593,7 +1593,7 @@ False, False)</em>.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 00fdf43b..3cd58bef 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -1658,7 +1658,7 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index ac5ef5c8..b74d69f2 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -590,7 +590,7 @@ standard amino acid</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 4754a73a..38468c44 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -412,7 +412,7 @@ with the keys of the scores in <strong>scorer</strong></li>
<div class="clearer"></div>
</div>
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diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index ee8bc163..916d24a1 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -653,7 +653,7 @@ 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
index dd80533b..6760e8c8 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -158,7 +158,7 @@ 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 30a91285..411f6291 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -1105,7 +1105,7 @@ 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 9e2e2975..6c740a42 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -648,7 +648,7 @@ 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 a5924d27..ef3d3396 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -283,7 +283,7 @@ 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 c5b4420b..c3239cb8 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -723,7 +723,7 @@ 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
index 5d49519a..fdf455dc 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -1227,7 +1227,7 @@ 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
index bb18cca8..e5940d82 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -440,7 +440,7 @@ 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 7332e3f9..74404d4b 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -478,7 +478,7 @@ 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
index fe540445..71f4bc4d 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -132,7 +132,7 @@
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diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index bbeac53a..8927ea93 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -574,7 +574,7 @@ being assessed.</p>
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diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index 5c1f37ef..68882801 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -493,7 +493,7 @@ 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
index 1a96785f..dec79f57 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -1196,7 +1196,7 @@ combining this to other scores, where it is commonly the other way around.</p>
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diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index 3e0ab52b..eeee0013 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -150,7 +150,7 @@ scorers and finally score some loops:</p>
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diff --git a/doc/html/search.html b/doc/html/search.html
index 9704423e..98d9a3d5 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -84,7 +84,7 @@
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diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index eb3411e4..da50d0e0 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
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Actions","<code class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Contributing","Geometry functions","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","Welcome To ProMod3’s Documentation!","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"docutils literal\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"docutils literal\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Disulfid Bond Evaluation","Frame","Rotamer Graph","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Rotamers","Rotamer Constructor","RotamerID","Rotamer Library","Subrotamer Optimization","Documentation For Users"],titleterms:{"class":[16,17,21,22,24,26,31,33,34,35],"default":30,"function":[4,6,7,8,24,31,34],acid:[16,20,22],action:[0,1,4,5],actiontestcas:1,algorithm:23,all:[16,27,33],allatomclashscor:33,allatomenv:16,allatomenvposit:16,allatominteractionscor:33,allatomoverallscor:33,allatompackingscor:33,allatomposit:16,allatomscor:33,amino:[16,20,22],angl:22,api:1,argument:9,atom:[16,27,33],backbon:[27,34,35,45],backbonelist:17,backboneoverallscor:35,backbonescor:35,backbonescoreenv:34,base:[21,33,35],binari:32,block:[23,42],bond:37,branch:12,build:[0,2,30,42],can:44,candid:26,cbetascor:35,cbpackingscor:35,ccd:27,chain:21,changelog:3,check:28,clashscor:35,closer:29,cmake:[1,2,4,12],code:32,command:9,construct:[34,43],constructor:43,contribut:5,conveni:34,cooler:29,core:8,creat:[1,20],data:[21,32],databas:21,defin:[21,22],definit:4,densityscor:35,depend:[2,45],detect:28,develop:13,dihedr:22,directori:12,distinguish:16,disulfid:37,document:[4,5,13,15,47],entri:45,enumerador:[],environ:34,evalu:37,everyth:7,exampl:[26,32],execut:1,exisit:32,extend:24,featur:[5,21],file:[7,32],find:21,fit:27,forcefield:20,fragment:21,frame:[38,43],gap:[24,27],gener:[20,29],geometr:21,geometri:6,get:[14,44],git:12,graph:39,group:42,handl:[16,18,24,26,30],have:1,hbondscor:35,header:32,helper:7,hook:12,how:[5,44],indic:15,instal:2,integr:1,introduct:[4,7,9],issu:5,keep:26,kic:27,librari:[41,45],licens:5,line:9,load:[19,41],lookup:20,loop:[17,18,20,26,27,29,36],loopcandid:26,mainten:4,make:[1,2],messag:7,model:[0,14,23,25,26,28,30,40],modul:[4,5],mol:20,molprob:28,must:1,non:45,novo:[23,29],object:[19,29,38],optim:46,ost:20,output:1,own:5,pairwis:34,pairwisescor:35,pars:9,parser:9,parti:5,particl:42,pipelin:[14,30],pm3argpars:9,portabl:32,posit:16,precomput:19,profil:10,promod3:[0,2,4,5,8,12,14,15,32],protein:25,psipredpredict:21,punch:28,quick:5,raw:30,reconstruct:31,reducedscor:35,relax:27,releas:3,repres:17,residu:43,rigid:23,ring:28,rotam:[39,41,42,43,45],rotamerid:44,run:[1,2,14],runtim:10,sampl:22,sampler:[22,29],score:[26,34,36],scorer:[5,29,33,35],script:1,sequenc:21,setcompoundschemlib:11,setup:12,share:[4,7],sidechain:[31,40],sidechainreconstructiondata:31,sidechainreconstructor:31,smallest:42,ssagreementscor:35,stage:12,start:[5,14],step:30,structur:[12,21],subclass:1,subrotam:46,system:20,tabl:15,test:[1,4,5,7],test_act:1,third:5,torsion:22,torsionscor:35,track:26,triplet:22,type:45,unit:[1,4,5],user:47,welcom:15,write:5,your:5}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 8b7eea9a..2c3f97b6 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -208,7 +208,7 @@ describe the optimal rotamers in the according rotamer groups.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index 3d35363e..776c8e4f 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -169,7 +169,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index 493363fc..2a2e6c16 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -503,7 +503,7 @@ with: e = pairwise_energies[i][j]</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index e6df0fc0..496c0b28 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -216,7 +216,7 @@ pipelines available in the modelling module.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
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Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index f8bbf36f..449c456a 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -168,7 +168,7 @@ incomplete if the last problem gets triggered.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 8a523385..1ae73b51 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -1223,7 +1223,7 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
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Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 915022bf..f277f834 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -382,7 +382,7 @@ to be assigned</td>
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</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
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Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/sidechain/rotamer_id.html b/doc/html/sidechain/rotamer_id.html
index 54b108a5..bda09870 100644
--- a/doc/html/sidechain/rotamer_id.html
+++ b/doc/html/sidechain/rotamer_id.html
@@ -184,7 +184,7 @@ defined in <a class="reference external" href="http://www.openstructure.org/docs
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 8d3e548b..84f762d5 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -650,7 +650,7 @@ considered similar</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
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Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 351ff031..11532099 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -126,7 +126,7 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
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Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
diff --git a/doc/html/users.html b/doc/html/users.html
index 69b609dc..2a206b56 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -150,7 +150,7 @@ scripts using the functionality of this library.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2016, ProMod3 authors.
+ ©2017, ProMod3 authors.
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