rebuilt html docs for version 2.11.0-dev0 from branch develop with sphinx at 8ff4d09

Author: github-actions

2.11.0-dev0/_modules/MDAnalysis/analysis/dssp/dssp.html

@@ -354,7 +354,7 @@ <h1>Source code for MDAnalysis.analysis.dssp.dssp</h1><div class="highlight"><pr
 <span class="sd">    Parameters</span>
 <span class="sd">    ----------</span>
 <span class="sd">    atoms : Union[Universe, AtomGroup]</span>
-<span class="sd">        input Universe or AtomGroup. In both cases, only protein residues will</span>
+<span class="sd">        input Universe or AtomGroup with at least 6 protein residues. In both cases, only protein residues will</span>
 <span class="sd">        be chosen prior to the analysis via `select_atoms(&#39;protein&#39;)`.</span>
 <span class="sd">        Heavy atoms of the protein are then selected by name</span>
 <span class="sd">        `heavyatom_names`, and hydrogens are selected by name</span>
@@ -384,6 +384,8 @@ <h1>Source code for MDAnalysis.analysis.dssp.dssp</h1><div class="highlight"><pr
 <span class="sd">    Raises</span>
 <span class="sd">    ------</span>
 <span class="sd">    ValueError</span>
+<span class="sd">        If fewer than 6 residues are provided in the selection.</span>
+<span class="sd">    ValueError</span>
 <span class="sd">        if ``guess_hydrogens`` is True but some non-PRO hydrogens are missing.</span>
 
 <span class="sd">    Examples</span>
@@ -504,6 +506,12 @@ <h1>Source code for MDAnalysis.analysis.dssp.dssp</h1><div class="highlight"><pr
                 <span class="p">)</span>
             <span class="p">)</span>
 
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ag</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">6</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="s2">&quot;DSSP requires at least 6 residues for secondary structure analysis, &quot;</span>
+                <span class="sa">f</span><span class="s2">&quot;but only </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">ag</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span><span class="si">}</span><span class="s2"> residue(s) were provided in the selection.&quot;</span>
+            <span class="p">)</span>
+
     <span class="k">def</span><span class="w"> </span><span class="nf">_prepare</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">results</span><span class="o">.</span><span class="n">dssp_ndarray</span> <span class="o">=</span> <span class="p">[]</span>
 

2.11.0-dev0/documentation_pages/analysis/dssp.html

@@ -307,7 +307,7 @@ <h2><span class="section-number">4.8.1.4.2. </span>Analysis classes<a class="hea
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>atoms</strong> (<em>Union</em><em>[</em><a class="reference internal" href="../core/universe.html#MDAnalysis.core.universe.Universe" title="MDAnalysis.core.universe.Universe"><em>Universe</em></a><em>, </em><a class="reference internal" href="../core/groups.html#MDAnalysis.core.groups.AtomGroup" title="MDAnalysis.core.groups.AtomGroup"><em>AtomGroup</em></a><em>]</em>) – input Universe or AtomGroup. In both cases, only protein residues will
+<li><p><strong>atoms</strong> (<em>Union</em><em>[</em><a class="reference internal" href="../core/universe.html#MDAnalysis.core.universe.Universe" title="MDAnalysis.core.universe.Universe"><em>Universe</em></a><em>, </em><a class="reference internal" href="../core/groups.html#MDAnalysis.core.groups.AtomGroup" title="MDAnalysis.core.groups.AtomGroup"><em>AtomGroup</em></a><em>]</em>) – input Universe or AtomGroup with at least 6 protein residues. In both cases, only protein residues will
 be chosen prior to the analysis via <cite>select_atoms(‘protein’)</cite>.
 Heavy atoms of the protein are then selected by name
 <cite>heavyatom_names</cite>, and hydrogens are selected by name
@@ -334,7 +334,10 @@ <h2><span class="section-number">4.8.1.4.2. </span>Analysis classes<a class="hea
 </ul>
 </dd>
 <dt class="field-even">Raises<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.14)"><strong>ValueError</strong></a> – if <code class="docutils literal notranslate"><span class="pre">guess_hydrogens</span></code> is True but some non-PRO hydrogens are missing.</p>
+<dd class="field-even"><ul class="simple">
+<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.14)"><strong>ValueError</strong></a> – If fewer than 6 residues are provided in the selection.</p></li>
+<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.14)"><strong>ValueError</strong></a> – if <code class="docutils literal notranslate"><span class="pre">guess_hydrogens</span></code> is True but some non-PRO hydrogens are missing.</p></li>
+</ul>
 </dd>
 </dl>
 <p class="rubric">Examples</p>

2.11.0-dev0/documentation_pages/analysis/wbridge_analysis.html

@@ -1048,15 +1048,15 @@ <h2><span class="section-number">4.4.3.8. </span>Classes<a class="headerlink" hr
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS">
-<span class="sig-name descname"><span class="pre">DEFAULT_ACCEPTORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('O',</span> <span class="pre">'OC2',</span> <span class="pre">'OE1',</span> <span class="pre">'OW',</span> <span class="pre">'ND1',</span> <span class="pre">'OG',</span> <span class="pre">'OE2',</span> <span class="pre">'SG',</span> <span class="pre">'OC1',</span> <span class="pre">'OH',</span> <span class="pre">'SD',</span> <span class="pre">'NE2',</span> <span class="pre">'OG1',</span> <span class="pre">'OH2',</span> <span class="pre">'OD1',</span> <span class="pre">'OD2'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('O',</span> <span class="pre">'OH',</span> <span class="pre">'O2',</span> <span class="pre">'NT',</span> <span class="pre">'SM',</span> <span class="pre">'OW',</span> <span class="pre">'N',</span> <span class="pre">'OS',</span> <span class="pre">'OY'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">DEFAULT_ACCEPTORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('OC2',</span> <span class="pre">'OE2',</span> <span class="pre">'O',</span> <span class="pre">'NE2',</span> <span class="pre">'OG1',</span> <span class="pre">'OD1',</span> <span class="pre">'OC1',</span> <span class="pre">'OW',</span> <span class="pre">'OD2',</span> <span class="pre">'OG',</span> <span class="pre">'OH',</span> <span class="pre">'OH2',</span> <span class="pre">'SD',</span> <span class="pre">'OE1',</span> <span class="pre">'ND1',</span> <span class="pre">'SG'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'OS',</span> <span class="pre">'OW',</span> <span class="pre">'O',</span> <span class="pre">'OH',</span> <span class="pre">'N',</span> <span class="pre">'OY',</span> <span class="pre">'SM',</span> <span class="pre">'O2'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Link to this definition"></a></dt>
 <dd><p>default atom names that are treated as hydrogen <em>acceptors</em>
 (see <a class="reference internal" href="#default-atom-names-for-water-bridge-analysis"><span class="std std-ref">Default heavy atom names for CHARMM27 force field.</span></a>);
 use the keyword <cite>acceptors</cite> to add a list of additional acceptor names.</p>
 </dd></dl>
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS">
-<span class="sig-name descname"><span class="pre">DEFAULT_DONORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('OH',</span> <span class="pre">'NE',</span> <span class="pre">'NE1',</span> <span class="pre">'NH1',</span> <span class="pre">'OW',</span> <span class="pre">'NE2',</span> <span class="pre">'N',</span> <span class="pre">'ND1',</span> <span class="pre">'ND2',</span> <span class="pre">'OG',</span> <span class="pre">'OG1',</span> <span class="pre">'NZ',</span> <span class="pre">'SG',</span> <span class="pre">'OH2',</span> <span class="pre">'NH2'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'N',</span> <span class="pre">'N3',</span> <span class="pre">'NT',</span> <span class="pre">'OW'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">DEFAULT_DONORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('OW',</span> <span class="pre">'ND2',</span> <span class="pre">'NH2',</span> <span class="pre">'NZ',</span> <span class="pre">'NE1',</span> <span class="pre">'OG',</span> <span class="pre">'OH',</span> <span class="pre">'N',</span> <span class="pre">'OH2',</span> <span class="pre">'NE2',</span> <span class="pre">'OG1',</span> <span class="pre">'NE',</span> <span class="pre">'ND1',</span> <span class="pre">'SG',</span> <span class="pre">'NH1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'OH',</span> <span class="pre">'OW',</span> <span class="pre">'N',</span> <span class="pre">'N3'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS" title="Link to this definition"></a></dt>
 <dd><p>default heavy atom names whose hydrogens are treated as <em>donors</em>
 (see <a class="reference internal" href="#default-atom-names-for-water-bridge-analysis"><span class="std std-ref">Default heavy atom names for CHARMM27 force field.</span></a>);
 use the keyword <cite>donors</cite> to add a list of additional donor names.</p>

2.11.0-dev0/searchindex.js

@@ -354,7 +354,7 @@ <h1>Source code for MDAnalysis.analysis.dssp.dssp</h1><div class="highlight"><pr
 <span class="sd">    Parameters</span>
 <span class="sd">    ----------</span>
 <span class="sd">    atoms : Union[Universe, AtomGroup]</span>
-<span class="sd">        input Universe or AtomGroup. In both cases, only protein residues will</span>
+<span class="sd">        input Universe or AtomGroup with at least 6 protein residues. In both cases, only protein residues will</span>
 <span class="sd">        be chosen prior to the analysis via `select_atoms(&#39;protein&#39;)`.</span>
 <span class="sd">        Heavy atoms of the protein are then selected by name</span>
 <span class="sd">        `heavyatom_names`, and hydrogens are selected by name</span>
@@ -384,6 +384,8 @@ <h1>Source code for MDAnalysis.analysis.dssp.dssp</h1><div class="highlight"><pr
 <span class="sd">    Raises</span>
 <span class="sd">    ------</span>
 <span class="sd">    ValueError</span>
+<span class="sd">        If fewer than 6 residues are provided in the selection.</span>
+<span class="sd">    ValueError</span>
 <span class="sd">        if ``guess_hydrogens`` is True but some non-PRO hydrogens are missing.</span>
 
 <span class="sd">    Examples</span>
@@ -504,6 +506,12 @@ <h1>Source code for MDAnalysis.analysis.dssp.dssp</h1><div class="highlight"><pr
                 <span class="p">)</span>
             <span class="p">)</span>
 
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ag</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">6</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="s2">&quot;DSSP requires at least 6 residues for secondary structure analysis, &quot;</span>
+                <span class="sa">f</span><span class="s2">&quot;but only </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">ag</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span><span class="si">}</span><span class="s2"> residue(s) were provided in the selection.&quot;</span>
+            <span class="p">)</span>
+
     <span class="k">def</span><span class="w"> </span><span class="nf">_prepare</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">results</span><span class="o">.</span><span class="n">dssp_ndarray</span> <span class="o">=</span> <span class="p">[]</span>
 

dev/_modules/MDAnalysis/analysis/dssp/dssp.html

@@ -307,7 +307,7 @@ <h2><span class="section-number">4.8.1.4.2. </span>Analysis classes<a class="hea
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>atoms</strong> (<em>Union</em><em>[</em><a class="reference internal" href="../core/universe.html#MDAnalysis.core.universe.Universe" title="MDAnalysis.core.universe.Universe"><em>Universe</em></a><em>, </em><a class="reference internal" href="../core/groups.html#MDAnalysis.core.groups.AtomGroup" title="MDAnalysis.core.groups.AtomGroup"><em>AtomGroup</em></a><em>]</em>) – input Universe or AtomGroup. In both cases, only protein residues will
+<li><p><strong>atoms</strong> (<em>Union</em><em>[</em><a class="reference internal" href="../core/universe.html#MDAnalysis.core.universe.Universe" title="MDAnalysis.core.universe.Universe"><em>Universe</em></a><em>, </em><a class="reference internal" href="../core/groups.html#MDAnalysis.core.groups.AtomGroup" title="MDAnalysis.core.groups.AtomGroup"><em>AtomGroup</em></a><em>]</em>) – input Universe or AtomGroup with at least 6 protein residues. In both cases, only protein residues will
 be chosen prior to the analysis via <cite>select_atoms(‘protein’)</cite>.
 Heavy atoms of the protein are then selected by name
 <cite>heavyatom_names</cite>, and hydrogens are selected by name
@@ -334,7 +334,10 @@ <h2><span class="section-number">4.8.1.4.2. </span>Analysis classes<a class="hea
 </ul>
 </dd>
 <dt class="field-even">Raises<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.14)"><strong>ValueError</strong></a> – if <code class="docutils literal notranslate"><span class="pre">guess_hydrogens</span></code> is True but some non-PRO hydrogens are missing.</p>
+<dd class="field-even"><ul class="simple">
+<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.14)"><strong>ValueError</strong></a> – If fewer than 6 residues are provided in the selection.</p></li>
+<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.14)"><strong>ValueError</strong></a> – if <code class="docutils literal notranslate"><span class="pre">guess_hydrogens</span></code> is True but some non-PRO hydrogens are missing.</p></li>
+</ul>
 </dd>
 </dl>
 <p class="rubric">Examples</p>