diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
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--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -83,6 +83,7 @@
<ul><li><a href="promod3/loop/_loop.html">promod3.loop._loop</a></li>
</ul><li><a href="promod3/pipeline/run_engine.html">promod3.pipeline.run_engine</a></li>
<li><a href="promod3/rawmodel/_closedels.html">promod3.rawmodel._closedels</a></li>
+<li><a href="promod3/rawmodel/_closegaps.html">promod3.rawmodel._closegaps</a></li>
<li><a href="promod3/rawmodel/_rawmodel.html">promod3.rawmodel._rawmodel</a></li>
<li><a href="promod3/sidechain/_sidechain.html">promod3.sidechain._sidechain</a></li>
<li><a href="promod3/sidechain/reconstruct_sidechains.html">promod3.sidechain.reconstruct_sidechains</a></li>
diff --git a/doc/html/_modules/promod3/rawmodel/_closegaps.html b/doc/html/_modules/promod3/rawmodel/_closegaps.html
new file mode 100644
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+ <h1>Source code for promod3.rawmodel._closegaps</h1><div class="highlight"><pre>
+<span class="sd">'''Single function to be 'injected' into the RawModellingResult class in the</span>
+<span class="sd">__init__.py file.</span>
+<span class="sd">'''</span>
+
+<span class="kn">import</span> <span class="nn">ost</span>
+<span class="c">#pylint: disable=no-name-in-module</span>
+<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">_rawmodel</span> <span class="k">as</span> <span class="n">rawmodel</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+
+<span class="k">def</span> <span class="nf">_CloseSmallDeletions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">scorer</span><span class="p">,</span> <span class="n">extension_steps</span><span class="o">=</span><span class="mi">9</span><span class="p">,</span> <span class="n">clash_thresh</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
+ <span class="n">e_thresh</span><span class="o">=</span><span class="mi">200</span><span class="p">):</span>
+ <span class="sd">'''Close small deletions by relaxing neighbouring residues.</span>
+
+<span class="sd"> Small deletions in the template from the target-template alignment have a</span>
+<span class="sd"> good chance to be bridged just by relaxing neighbours around a tiny gap.</span>
+<span class="sd"> Before diving into the more demanding tasks in modeling, those may be closed</span>
+<span class="sd"> already in the raw-model. After closure some checks are done to see if the</span>
+<span class="sd"> solution is stereochemically sensible.</span>
+
+<span class="sd"> Closed gaps are removed from :attr:`self.gaps`.</span>
+
+<span class="sd"> .. testcode:: closesmalldel</span>
+<span class="sd"> :hide:</span>
+
+<span class="sd"> from promod3 import rawmodel</span>
+<span class="sd"> from promod3 import loop</span>
+
+<span class="sd"> tpl = ost.io.LoadPDB('../tests/rawmodel/data/raw-modeling/gly.pdb')</span>
+<span class="sd"> aln = ost.seq.CreateAlignment(ost.seq.CreateSequence('trg', 'GGG-GGG'),</span>
+<span class="sd"> ost.seq.CreateSequence('tpl', 'GGGAGGG'))</span>
+<span class="sd"> aln.AttachView(1, tpl.CreateFullView())</span>
+<span class="sd"> rmodel = rawmodel.BuildRawModel(aln)</span>
+<span class="sd"> assert len(rmodel.gaps) == 1</span>
+<span class="sd"> scorer = loop.SetupBackboneScorer(rmodel)</span>
+<span class="sd"> rmodel.CloseSmallDeletions(scorer)</span>
+<span class="sd"> assert len(rmodel.gaps) == 0</span>
+
+<span class="sd"> .. doctest:: closesmalldel</span>
+
+<span class="sd"> import ost</span>
+<span class="sd"> from promod3 import rawmodel</span>
+<span class="sd"> from promod3 import loop</span>
+
+<span class="sd"> tpl = ost.io.LoadPDB('gly.pdb')</span>
+<span class="sd"> aln = ost.io.LoadAlignment('seq.fasta')</span>
+<span class="sd"> aln.AttachView(1, tpl.CreateFullView())</span>
+<span class="sd"> rmodel = rawmodel.BuildRawModel(aln)</span>
+<span class="sd"> scorer = loop.SetupBackboneScorer(rmodel)</span>
+<span class="sd"> rmodel.CloseSmallDeletions(scorer)</span>
+
+<span class="sd"> :param scorer: A scorer dedicated to this raw model.</span>
+<span class="sd"> :type scorer: :class:`~promod3.loop.BackboneLoopScorer`</span>
+
+<span class="sd"> :param extension_steps: Iterations allowed for gap extension. This does not</span>
+<span class="sd"> directly mean 'extended size of gap' but no. of</span>
+<span class="sd"> attempts to extend. Extension works like trying to</span>
+<span class="sd"> increase left, then right, then try more on the</span>
+<span class="sd"> left side again...</span>
+<span class="sd"> :type extension_steps: :class:`int`</span>
+
+<span class="sd"> :param clash_thresh: Threshold for the clash score, acceptance means being</span>
+<span class="sd"> lower than this.</span>
+<span class="sd"> :type clash_thresh: :class:`float`</span>
+
+<span class="sd"> :param e_thresh: Potential energy should be lower than this.</span>
+<span class="sd"> :type e_thresh: :class:`float`</span>
+
+<span class="sd"> :return: If gaps are deleted, the scorer needs to be updated and is</span>
+<span class="sd"> returned.</span>
+<span class="sd"> :rtype: :class:`~promod3.loop.BackboneLoopScorer`</span>
+<span class="sd"> '''</span>
+ <span class="n">current_gap_index</span> <span class="o">=</span> <span class="mi">0</span>
+
+ <span class="c"># iterating self.gaps. The number of gaps may change during the process,</span>
+ <span class="c"># hence we run by 'while', breaking out once we've seen all gaps. If a gap</span>
+ <span class="c"># gets closed, it is deleted from self.gaps, otherwise, current_gap_index</span>
+ <span class="c"># as a counter is increased.</span>
+ <span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
+ <span class="c"># check if all gaps were visited</span>
+ <span class="k">if</span> <span class="n">current_gap_index</span> <span class="o">>=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">):</span>
+ <span class="k">break</span>
+
+ <span class="c"># in the end this determines if a gap was closed or not</span>
+ <span class="n">success</span> <span class="o">=</span> <span class="bp">False</span>
+
+ <span class="c"># A deletion is a gap of size 0 in the template, this means that to</span>
+ <span class="c"># transform the template sequence into the target sequence, aa's vanish,</span>
+ <span class="c"># so the target sequence has gap caracters, the template not.</span>
+ <span class="c"># If we are not looking at a deletion, do nothing.</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">]</span><span class="o">.</span><span class="n">seq</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c"># work on a copy of the gap, if not closed in the end, no harm done</span>
+ <span class="n">current_gap</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+ <span class="n">current_chain</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span>
+ <span class="n">current_chain_index</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
+
+ <span class="c"># Try to close gap by relaxation: by checking how far we may extend</span>
+ <span class="c"># the gap, we get the backbone to be stretched. If no more extension</span>
+ <span class="c"># is possible, break out. On first successful relaxation for an</span>
+ <span class="c"># extension, we successfully stop.</span>
+ <span class="n">extender</span> <span class="o">=</span> <span class="n">rawmodel</span><span class="o">.</span><span class="n">GapExtender</span><span class="p">(</span><span class="n">current_gap</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">extension_steps</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">extender</span><span class="o">.</span><span class="n">Extend</span><span class="p">():</span>
+ <span class="k">break</span>
+ <span class="c"># gather residues for backbone relaxation, check that we get a</span>
+ <span class="c"># bunch of actual residues, otherwise jump to next extension</span>
+ <span class="n">res_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+ <span class="n">current_resnum</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
+ <span class="n">after_resnum</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
+ <span class="n">found_residues</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">current_resnum</span> <span class="o">></span> <span class="n">after_resnum</span><span class="p">:</span>
+ <span class="k">break</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="n">current_chain</span><span class="o">.</span><span class="n">FindResidue</span><span class="p">(</span><span class="n">current_resnum</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">res</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
+ <span class="n">found_residues</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="k">break</span>
+ <span class="n">res_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res</span><span class="p">)</span>
+ <span class="n">current_resnum</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">found_residues</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="c"># backbone relaxation, for now we allow 300 steps or stop at</span>
+ <span class="c"># max. force of 0.1</span>
+ <span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">current_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span> <span class="n">res_list</span><span class="p">)</span>
+ <span class="n">bb_relaxer</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneRelaxer</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span>
+ <span class="n">potential_e</span> <span class="o">=</span> <span class="n">bb_relaxer</span><span class="o">.</span><span class="n">Run</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="mi">300</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
+ <span class="c"># check for clashes</span>
+ <span class="n">score</span> <span class="o">=</span> <span class="n">scorer</span><span class="o">.</span><span class="n">CalculateClashScore</span><span class="p">(</span>\
+ <span class="n">bb_list</span><span class="p">,</span>
+ <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="n">current_chain_index</span><span class="p">)</span>
+ <span class="c"># if there is no clash and potential energy is low enough we</span>
+ <span class="c"># just solved a gap, delete it and update the scorer for the</span>
+ <span class="c"># changed model</span>
+ <span class="k">if</span> <span class="n">score</span> <span class="o"><</span> <span class="n">clash_thresh</span> <span class="ow">and</span> \
+ <span class="n">potential_e</span> <span class="o"><</span> <span class="n">e_thresh</span> <span class="ow">and</span> \
+ <span class="n">scorer</span><span class="o">.</span><span class="n">TransOmegaTorsions</span><span class="p">(</span><span class="n">bb_list</span><span class="p">):</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Closed: </span><span class="si">%s</span><span class="s"> by relaxing </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> \
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">],</span> <span class="n">current_gap</span><span class="p">))</span>
+ <span class="n">chain</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span>
+ <span class="n">bb_list</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="n">chain</span><span class="p">,</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">(),</span>
+ <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">())</span>
+ <span class="n">scorer</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span>\
+ <span class="n">bb_list</span><span class="p">,</span>
+ <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ClearGaps</span><span class="p">(</span><span class="n">current_gap</span><span class="p">)</span>
+ <span class="n">success</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">break</span>
+ <span class="c"># On closed gap, it is removed so the no. of gaps goes down by itself.</span>
+ <span class="c"># In case of no success, counter needs to be increased to jump to the</span>
+ <span class="c"># next gap.</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">success</span><span class="p">:</span>
+ <span class="n">current_gap_index</span> <span class="o">+=</span> <span class="mi">1</span>
+
+ <span class="k">return</span> <span class="n">scorer</span>
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s">'_CloseSmallDeletions'</span><span class="p">]</span>
+
+<span class="c"># LocalWords: modeling stereochemically param</span>
+</pre></div>
+
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