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<li class="toctree-l2"><a class="reference internal" href="#compute-partition-function">Compute partition function</a>
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<li class="toctree-l2"><a class="reference internal" href="#compute-structure-free-energy">Compute structure free energy</a>
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<li class="toctree-l2"><a class="reference internal" href="#compute-equilibrium-structure-probability">Compute equilibrium structure probability</a>
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<li class="toctree-l2"><a class="reference internal" href="#compute-boltzmann-sampled-structures">Compute Boltzmann-sampled structures</a>
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<li class="toctree-l2"><a class="reference internal" href="#compute-equilibrium-base-pairing-probabilities">Compute equilibrium base-pairing probabilities</a>
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<li class="toctree-l2"><a class="reference internal" href="#compute-mfe-proxy-structures">Compute MFE proxy structure(s)</a>
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<li class="toctree-l2"><a class="reference internal" href="#compute-suboptimal-proxy-structures">Compute suboptimal proxy structures</a>
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<li class="toctree-l2"><a class="reference internal" href="#compute-complex-ensemble-size">Compute complex ensemble size</a>
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<h1 id="utilities-jobs">Utilities Jobs<a class="headerlink" href="#utilities-jobs" title="Permanent link">¶</a></h1>
<p>Utilities commands analyze or design a single complex ensemble. For each command, the strand ordering of the complex is specified using keyword <code>strands</code> and the <a href="../model/#model-specification">physical model</a> is specified using keyword <code>model</code>.
For commands that require a structure (e.g., calculation of the equilibrium structure probability using <code>prob</code>), the structure is specified using the keyword <code>structure</code>. By default, NUPACK utilities jobs run in <a href="../advanced/#parallelism">parallel</a>.</p>
<p>To initialize a model for the following examples, run the following code:</p>
<div class="highlight"><pre><span></span><code><span class="n">my_model</span> <span class="o">=</span> <span class="n">Model</span><span class="p">(</span><span class="n">material</span><span class="o">=</span><span class="s1">'RNA'</span><span class="p">)</span>
</code></pre></div>
<hr />
<h2 id="compute-partition-function">Compute partition function<a class="headerlink" href="#compute-partition-function" title="Permanent link">¶</a></h2>
<p><code>pfunc</code> calculates the <a href="../definitions/#partition-function">partition function</a> of the complex as well as the free energy of the complex:</p>
<div class="highlight"><pre><span></span><code><span class="n">partition_function</span> <span class="o">=</span> <span class="n">pfunc</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'CCC'</span><span class="p">,</span> <span class="s1">'GGG'</span><span class="p">],</span> <span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">partition_function</span><span class="p">)</span>
<span class="c1"># --> (Decimal('4525.512868'), -5.187871791642832)</span>
</code></pre></div>
<hr />
<h2 id="compute-structure-free-energy">Compute structure free energy<a class="headerlink" href="#compute-structure-free-energy" title="Permanent link">¶</a></h2>
<p><code>structure_energy</code> calculates the <a href="../definitions/#structure-free-energy">structure free energy</a> for the specified secondary structure:</p>
<div class="highlight"><pre><span></span><code><span class="n">dGstruc</span> <span class="o">=</span> <span class="n">structure_energy</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'AAAA'</span><span class="p">,</span> <span class="s1">'UUUU'</span><span class="p">],</span> <span class="n">structure</span><span class="o">=</span><span class="s1">'((((+))))'</span><span class="p">,</span>
<span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">dGstruc</span><span class="p">)</span>
<span class="c1"># --> -0.18135141907945873</span>
</code></pre></div>
<hr />
<h2 id="compute-equilibrium-structure-probability">Compute equilibrium structure probability<a class="headerlink" href="#compute-equilibrium-structure-probability" title="Permanent link">¶</a></h2>
<p><code>structure_probability</code> calculates the <a href="../definitions/#equilibrium-structure-probability">equilibrium structure probability</a> of a specified secondary structure contained in the complex ensemble:</p>
<div class="highlight"><pre><span></span><code><span class="n">probability</span> <span class="o">=</span> <span class="n">structure_probability</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'CCC'</span><span class="p">,</span> <span class="s1">'GGG'</span><span class="p">],</span> <span class="n">structure</span><span class="o">=</span><span class="s1">'(((+)))'</span><span class="p">,</span>
<span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">probability</span><span class="p">)</span>
<span class="c1"># --> 0.7152766753194949</span>
</code></pre></div>
<hr />
<h2 id="compute-boltzmann-sampled-structures">Compute Boltzmann-sampled structures<a class="headerlink" href="#compute-boltzmann-sampled-structures" title="Permanent link">¶</a></h2>
<p><code>sample</code> calculates a set of <a href="../definitions/#boltzmann-sampled-structures">Boltzmann-sampled structures</a> from the complex ensemble. The number of structures is specified using the keyword <code>num_sample</code>:</p>
<div class="highlight"><pre><span></span><code><span class="n">sampled_structures</span> <span class="o">=</span> <span class="n">sample</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'CCC'</span><span class="p">,</span> <span class="s1">'GGG'</span><span class="p">],</span> <span class="n">num_sample</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">sampled_structures</span><span class="p">)</span>
<span class="c1"># --> [Structure('(((+)))'), Structure('(((+)))'), Structure('(((+)))')]</span>
</code></pre></div>
<hr />
<h2 id="compute-equilibrium-base-pairing-probabilities">Compute equilibrium base-pairing probabilities<a class="headerlink" href="#compute-equilibrium-base-pairing-probabilities" title="Permanent link">¶</a></h2>
<p><code>pairs</code> calculates the matrix of <a href="../definitions/#equilibrium-base-pairing-probabilities">equilibrium base-pairing probabilities</a>:</p>
<div class="highlight"><pre><span></span><code><span class="n">probability_matrix</span> <span class="o">=</span> <span class="n">pairs</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'CCC'</span><span class="p">,</span> <span class="s1">'GGG'</span><span class="p">],</span> <span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">probability_matrix</span><span class="p">)</span>
<span class="c1"># --></span>
<span class="c1"># [[0.1002 0.0000 0.0000 0.0007 0.1474 0.7518]</span>
<span class="c1"># [0.0000 0.0037 0.0000 0.1474 0.8307 0.0182]</span>
<span class="c1"># [0.0000 0.0000 0.1904 0.7910 0.0185 0.0001]</span>
<span class="c1"># [0.0007 0.1474 0.7910 0.0609 0.0000 0.0000]</span>
<span class="c1"># [0.1474 0.8307 0.0185 0.0000 0.0035 0.0000]</span>
<span class="c1"># [0.7518 0.0182 0.0001 0.0000 0.0000 0.2299]]</span>
</code></pre></div>
<p>(Convert the result to a numpy array via <code>probability_matrix.to_array()</code>.)</p>
<h2 id="compute-mfe-proxy-structures">Compute MFE proxy structure(s)<a class="headerlink" href="#compute-mfe-proxy-structures" title="Permanent link">¶</a></h2>
<p><code>mfe</code> calculates <a href="../definitions/#mfe-proxy-structure">MFE proxy structure</a>. The algorithm returns the MFE proxy secondary structure, the free energy of the MFE stacking state, and the free energy of the MFE proxy secondary structure:</p>
<div class="highlight"><pre><span></span><code><span class="n">mfe_structures</span> <span class="o">=</span> <span class="n">mfe</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'CCC'</span><span class="p">,</span> <span class="s1">'GGG'</span><span class="p">],</span> <span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Free energy of MFE proxy structure: </span><span class="si">%.2f</span><span class="s1"> kcal/mol'</span> <span class="o">%</span> <span class="n">mfe_structures</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">energy</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'MFE proxy structure in dot-parens-plus notation: </span><span class="si">%s</span><span class="s1">'</span> <span class="o">%</span> <span class="n">mfe_structures</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">structure</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'MFE proxy structure as structure matrix:</span><span class="se">\n</span><span class="si">%s</span><span class="s1">'</span> <span class="o">%</span> <span class="n">mfe_structures</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">matrix</span><span class="p">())</span>
</code></pre></div>
<p>Output:</p>
<div class="highlight"><pre><span></span><code>Free energy of MFE proxy structure: -4.98 kcal/mol
MFE proxy structure in dot-parens-plus notation: (((+)))
MFE proxy structure as structure matrix:
[[0 0 0 0 0 1]
[0 0 0 0 1 0]
[0 0 0 1 0 0]
[0 0 1 0 0 0]
[0 1 0 0 0 0]
[1 0 0 0 0 0]]
</code></pre></div>
<p>If there is more than one MFE stacking state, the algorithm returns a list of the corresponding MFE proxy secondary structures, each with the free energy of the MFE proxy secondary structure and the (same) free energy of the MFE stacking state.</p>
<hr />
<h2 id="compute-suboptimal-proxy-structures">Compute suboptimal proxy structures<a class="headerlink" href="#compute-suboptimal-proxy-structures" title="Permanent link">¶</a></h2>
<p><code>subopt</code> calculates the set of <a href="../definitions/#suboptimal-proxy-structures">suboptimal proxy structures</a> with a stacking state within a specified free energy gap of the MFE stacking state. The (non-negative) free energy gap is specified with keyword <code>energy_gap</code> in kcal/mol. The algorithm returns a list of suboptimal proxy secondary strutures, each with the free energy of the suboptimal proxy secondary structure and with the free energy of its lowest-energy stacking state that falls within the energy gap:</p>
<div class="highlight"><pre><span></span><code><span class="n">subopt_structures</span> <span class="o">=</span> <span class="n">subopt</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'CCC'</span><span class="p">,</span> <span class="s1">'GGG'</span><span class="p">],</span> <span class="n">energy_gap</span><span class="o">=</span><span class="mf">1.5</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">subopt_structures</span><span class="p">)</span>
<span class="c1"># --> [StructureEnergy(Structure('(((+)))'), energy=-4.981351375579834, stack_energy=-4.981351375579834),</span>
<span class="c1"># StructureEnergy(Structure('((.+)).'), energy=-4.000725746154785, stack_energy=-3.781351089477539)]</span>
</code></pre></div>
<hr />
<h2 id="compute-complex-ensemble-size">Compute complex ensemble size<a class="headerlink" href="#compute-complex-ensemble-size" title="Permanent link">¶</a></h2>
<p><code>ensemble_size</code> calculates the <a href="../definitions/#complex-ensemble-size">complex ensemble size</a> in terms of either number of secondary structures or number of stacking states. Specify a <a href="../model/#model-specification">physical model</a> with <code>nostacking</code> to obtain the number of secondary structures:</p>
<div class="highlight"><pre><span></span><code><span class="n">num_struc</span> <span class="o">=</span> <span class="n">ensemble_size</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'CCC'</span><span class="p">,</span> <span class="s1">'GGG'</span><span class="p">],</span>
<span class="n">model</span><span class="o">=</span><span class="n">Model</span><span class="p">(</span><span class="n">material</span><span class="o">=</span><span class="s1">'RNA'</span><span class="p">,</span> <span class="n">ensemble</span><span class="o">=</span><span class="s1">'nostacking'</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">num_struc</span><span class="p">)</span>
<span class="c1"># --> 18</span>
</code></pre></div>
<p>Specify a physical model with <code>stacking</code> to obtain the number of stacking states:</p>
<div class="highlight"><pre><span></span><code><span class="n">num_stack</span> <span class="o">=</span> <span class="n">ensemble_size</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'CCC'</span><span class="p">,</span> <span class="s1">'GGG'</span><span class="p">],</span>
<span class="n">model</span><span class="o">=</span><span class="n">Model</span><span class="p">(</span><span class="n">material</span><span class="o">=</span><span class="s1">'RNA'</span><span class="p">,</span> <span class="n">ensemble</span><span class="o">=</span><span class="s1">'stacking'</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">num_stack</span><span class="p">)</span>
<span class="c1"># --> 90</span>
</code></pre></div>
<hr />
<h2 id="design-a-sequence">Design a sequence<a class="headerlink" href="#design-a-sequence" title="Permanent link">¶</a></h2>
<p><code>des</code> performs complex design to generate a sequence intended to adopt a target secondary structure at equilibrium within the ensemble of the complex. The strand ordering of the complex can be specified using IUPAC <a href="../definitions/#IUPAC-degenerate-nucleotide-codes">degenerate nucleotide codes</a> to incorporate any sequence constraints (the strand ordering can be omitted if there are no sequence constraints). The target structure is specified using keyword <code>structure</code>:</p>
<div class="highlight"><pre><span></span><code><span class="c1"># design a sequence without sequence constraints</span>
<span class="n">designed_sequence1</span> <span class="o">=</span> <span class="n">des</span><span class="p">(</span><span class="n">structure</span><span class="o">=</span><span class="s1">'(((+)))'</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">designed_sequence1</span><span class="p">)</span>
<span class="c1"># --> ['GGC', 'GCC']</span>
<span class="c1"># alternative specification to design a sequence without sequence constraints</span>
<span class="n">designed_sequence1</span> <span class="o">=</span> <span class="n">des</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'NNN'</span><span class="p">,</span><span class="s1">'NNN'</span><span class="p">],</span> <span class="n">structure</span><span class="o">=</span><span class="s1">'(((+)))'</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">designed_sequence1</span><span class="p">)</span>
<span class="c1"># --> ['GGC', 'GCC']</span>
<span class="c1"># design a sequence with sequence constraints</span>
<span class="n">designed_sequence2</span> <span class="o">=</span> <span class="n">des</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'HHH'</span><span class="p">,</span><span class="s1">'BBW'</span><span class="p">],</span> <span class="n">structure</span><span class="o">=</span><span class="s1">'(((+)))'</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">designed_sequence2</span><span class="p">)</span>
<span class="c1"># --> ['ACC', 'GGU']</span>
</code></pre></div>
<hr />
<h2 id="compute-complex-ensemble-defect">Compute complex ensemble defect<a class="headerlink" href="#compute-complex-ensemble-defect" title="Permanent link">¶</a></h2>
<p><code>defect</code> evaluates the normalized <a href="../definitions/#complex-ensemble-defect">complex ensemble defect</a> with respect to the structure specified using keyword <code>structure</code>:</p>
<div class="highlight"><pre><span></span><code><span class="n">ensemble_defect</span> <span class="o">=</span> <span class="n">defect</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'CCC'</span><span class="p">,</span> <span class="s1">'GGG'</span><span class="p">],</span> <span class="n">structure</span><span class="o">=</span><span class="s1">'(((+)))'</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">ensemble_defect</span><span class="p">)</span>
<span class="c1"># --> 0.20883411169052118</span>
</code></pre></div>
<hr />
<h2 id="represent-a-structure">Represent a structure<a class="headerlink" href="#represent-a-structure" title="Permanent link">¶</a></h2>
<p>A <a href="../definitions/#secondary-structure">secondary structure</a> can be defined using any of three notations (keyword <code>Structure</code>):</p>
<div class="highlight"><pre><span></span><code><span class="n">s1</span> <span class="o">=</span> <span class="n">Structure</span><span class="p">(</span><span class="s1">'((((((((((((+..........))))))))))))'</span><span class="p">)</span> <span class="c1"># dot-parens-plus notation</span>
<span class="n">s2</span> <span class="o">=</span> <span class="n">Structure</span><span class="p">(</span><span class="s1">'(12+.10)12'</span><span class="p">)</span> <span class="c1"># run-length-encoded dot-parens-plus notation</span>
<span class="n">s3</span> <span class="o">=</span> <span class="n">Structure</span><span class="p">(</span><span class="s1">'D12 (+ U10)'</span><span class="p">)</span> <span class="c1"># DU+ notation</span>
</code></pre></div>
<p>Any object or command that accepts a structure as an argument (e.g, <code>TargetComplex</code> in Design or <code>structure_probability</code> in Utilities) will accept either a structure defined in one of the above three notations, or a previously defined <code>Structure</code> object:</p>
<div class="highlight"><pre><span></span><code><span class="n">dGstruc</span> <span class="o">=</span> <span class="n">structure_energy</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'AAAA'</span><span class="p">,</span> <span class="s1">'TTTT'</span><span class="p">],</span> <span class="n">structure</span><span class="o">=</span><span class="s1">'((((+))))'</span><span class="p">,</span>
<span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
<span class="n">my_struc</span> <span class="o">=</span> <span class="n">Structure</span><span class="p">(</span><span class="s1">'((((+))))'</span><span class="p">)</span>
<span class="n">dGstruc</span> <span class="o">=</span> <span class="n">structure_energy</span><span class="p">(</span><span class="n">strands</span><span class="o">=</span><span class="p">[</span><span class="s1">'AAAA'</span><span class="p">,</span> <span class="s1">'TTTT'</span><span class="p">],</span> <span class="n">structure</span><span class="o">=</span><span class="n">my_struc</span><span class="p">,</span>
<span class="n">model</span><span class="o">=</span><span class="n">my_model</span><span class="p">)</span>
</code></pre></div>
<p><code>Structure</code> supports the following methods to assist with structure representation:</p>
<ul>
<li><code>pairlist()</code>: A pair list contains a list <span class="arithmatex"><span class="MathJax_Preview">S</span><script type="math/tex">S</script></span> of zero-based indices such that <span class="arithmatex"><span class="MathJax_Preview">S_i = j</span><script type="math/tex">S_i = j</script></span> if bases <span class="arithmatex"><span class="MathJax_Preview">i</span><script type="math/tex">i</script></span> and <span class="arithmatex"><span class="MathJax_Preview">j</span><script type="math/tex">j</script></span> are paired, and <span class="arithmatex"><span class="MathJax_Preview">S_i = i</span><script type="math/tex">S_i = i</script></span> if base <span class="arithmatex"><span class="MathJax_Preview">i</span><script type="math/tex">i</script></span> is unpaired.</li>
<li><code>matrix()</code>: A <a href="../definitions/#secondary-structure">structure matrix</a> of the structure.</li>
<li><code>nicks()</code>: A list of zero-based indices of each base 3<span class="arithmatex"><span class="MathJax_Preview">'</span><script type="math/tex">'</script></span> of a nick between strands (one entry per strand)</li>
<li><code>dotparensplus()</code>: Representation of the structure in dot-parens-plus notation.</li>
<li><code>rle_dotparensplus()</code>: Representation of the structure in run-length-encoded dot-parens-plus notation.</li>
</ul>
<p>For example:</p>
<div class="highlight"><pre><span></span><code><span class="n">s4</span> <span class="o">=</span> <span class="n">Structure</span><span class="p">(</span><span class="s1">'(((+))).'</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s4</span><span class="o">.</span><span class="n">pairlist</span><span class="p">())</span> <span class="c1"># --> [5 4 3 2 1 0 6]</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s4</span><span class="o">.</span><span class="n">matrix</span><span class="p">())</span> <span class="c1"># --> [[0 0 0 0 0 1 0]</span>
<span class="c1"># [0 0 0 0 1 0 0]</span>
<span class="c1"># [0 0 0 1 0 0 0]</span>
<span class="c1"># [0 0 1 0 0 0 0]</span>
<span class="c1"># [0 1 0 0 0 0 0]</span>
<span class="c1"># [1 0 0 0 0 0 0]</span>
<span class="c1"># [0 0 0 0 0 0 1]]</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s4</span><span class="o">.</span><span class="n">nicks</span><span class="p">())</span> <span class="c1"># --> [3 7]</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s4</span><span class="o">.</span><span class="n">dotparensplus</span><span class="p">())</span> <span class="c1"># --> (((+))).</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s4</span><span class="o">.</span><span class="n">rle_dotparensplus</span><span class="p">())</span> <span class="c1"># --> (3+)3.</span>
</code></pre></div>
<h2 id="compute-sequence-distance">Compute sequence distance<a class="headerlink" href="#compute-sequence-distance" title="Permanent link">¶</a></h2>
<p><code>seq_distance</code> calculates the <a href="../definitions/#secondary-structure">sequence distance</a> for two sequences that have the same number of nucleotides:</p>
<div class="highlight"><pre><span></span><code><span class="n">seq_distance</span><span class="p">(</span><span class="s1">'ACGUUUU+ACCC'</span><span class="p">,</span><span class="s1">'ACGUUUU+AGGG'</span><span class="p">)</span> <span class="c1"># --> 3</span>
<span class="n">seq_distance</span><span class="p">(</span><span class="s1">'G5'</span><span class="p">,</span> <span class="s1">'G3C2'</span><span class="p">)</span> <span class="c1"># --> 2</span>
</code></pre></div>
<h2 id="compute-structure-distance">Compute structure distance<a class="headerlink" href="#compute-structure-distance" title="Permanent link">¶</a></h2>
<p><code>struc_distance</code> calculates the <a href="../definitions/#secondary-structure">structure distance</a> for two structures that have the same number of nucleotides:</p>
<div class="highlight"><pre><span></span><code><span class="n">struc_distance</span><span class="p">(</span><span class="s1">'((((((((+..........))))))))'</span><span class="p">,</span> <span class="s1">'(((((((.+...........)))))))'</span><span class="p">)</span> <span class="c1"># --> 2</span>
<span class="n">struc_distance</span><span class="p">(</span><span class="s1">'.15'</span><span class="p">,</span> <span class="s1">'(5.5)5'</span><span class="p">)</span> <span class="c1"># --> 10</span>
</code></pre></div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Note that <a href="../definitions/#sequence">sequence distance</a> and <a href="../definitions/#secondary-structure">structure distance</a> are defined independent of whether the nick locations match between two sequences or two structures. However, <code>seq_distance</code> and <code>struc_distance</code> will return a warning if the nick locations do not match.</p>
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