rebuilt html docs for version 2.10.0-dev0 from branch develop with sphinx at d412c9a

Author: github-actions

2.10.0-dev0/_modules/MDAnalysis/analysis/base.html

@@ -328,6 +328,12 @@ <h1>Source code for MDAnalysis.analysis.base</h1><div class="highlight"><pre>
 <span class="sd">    All results should be stored as attributes of the</span>
 <span class="sd">    :class:`MDAnalysis.analysis.results.Results` container.</span>
 
+<span class="sd">    .. Note::</span>
+<span class="sd">       The instance attributes are created during and on conclusion of</span>
+<span class="sd">       calling the :meth:`AnalysisBase.run` method. Accessing an attribute</span>
+<span class="sd">       before it has been created will raise an :exc:`AttributeError`.</span>
+
+
 <span class="sd">    Parameters</span>
 <span class="sd">    ----------</span>
 <span class="sd">    trajectory : MDAnalysis.coordinates.base.ReaderBase</span>
@@ -338,14 +344,28 @@ <h1>Source code for MDAnalysis.analysis.base</h1><div class="highlight"><pre>
 <span class="sd">    Attributes</span>
 <span class="sd">    ----------</span>
 <span class="sd">    times: numpy.ndarray</span>
-<span class="sd">        array of Timestep times. Only exists after calling</span>
-<span class="sd">        :meth:`AnalysisBase.run`</span>
+<span class="sd">        Array of times of the Timesteps that were analyzed.</span>
+<span class="sd">        Only exists after calling :meth:`AnalysisBase.run`.</span>
 <span class="sd">    frames: numpy.ndarray</span>
-<span class="sd">        array of Timestep frame indices. Only exists after calling</span>
-<span class="sd">        :meth:`AnalysisBase.run`</span>
+<span class="sd">        Array of frame indices that were analyzed.</span>
+<span class="sd">        Only exists after calling :meth:`AnalysisBase.run`.</span>
 <span class="sd">    results: :class:`Results`</span>
-<span class="sd">        results of calculation are stored after call</span>
-<span class="sd">        to :meth:`AnalysisBase.run`</span>
+<span class="sd">        Results of calculation are stored here, after call</span>
+<span class="sd">        to :meth:`AnalysisBase.run`.</span>
+<span class="sd">    n_frames: int</span>
+<span class="sd">        number of *analyzed* frames, i.e., after taking into account</span>
+<span class="sd">        the `start`, `stop`, and `step` values from</span>
+<span class="sd">        :meth:`AnalysisBase.run`.</span>
+<span class="sd">        Only exists after calling :meth:`AnalysisBase.run`.</span>
+<span class="sd">    start: int</span>
+<span class="sd">        Frame index of the first trajectory frame that was analyzed.</span>
+<span class="sd">        Only exists after calling :meth:`AnalysisBase.run`.</span>
+<span class="sd">    stop: int</span>
+<span class="sd">        Frame index of the last trajectory frame that was analyzed.</span>
+<span class="sd">        Only exists after calling :meth:`AnalysisBase.run`.</span>
+<span class="sd">    step: int</span>
+<span class="sd">        Every `step` frame was analyzed, as ``trajectory[start:stop:step]``.</span>
+<span class="sd">        Only exists after calling :meth:`AnalysisBase.run`.</span>
 
 
 <span class="sd">    Example</span>

2.10.0-dev0/documentation_pages/analysis/base.html

@@ -290,6 +290,12 @@ <h2><span class="section-number">4.2.1.3. </span>Classes<a class="headerlink" hr
 <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase._prepare" title="MDAnalysis.analysis.base.AnalysisBase._prepare"><code class="xref py py-meth docutils literal notranslate"><span class="pre">_prepare()</span></code></a> and <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase._conclude" title="MDAnalysis.analysis.base.AnalysisBase._conclude"><code class="xref py py-meth docutils literal notranslate"><span class="pre">_conclude()</span></code></a> for pre- and post-processing.
 All results should be stored as attributes of the
 <a class="reference internal" href="results.html#MDAnalysis.analysis.results.Results" title="MDAnalysis.analysis.results.Results"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.results.Results</span></code></a> container.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>The instance attributes are created during and on conclusion of
+calling the <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a> method. Accessing an attribute
+before it has been created will raise an <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#AttributeError" title="(in Python v3.13)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">AttributeError</span></code></a>.</p>
+</div>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
@@ -301,8 +307,8 @@ <h2><span class="section-number">4.2.1.3. </span>Classes<a class="headerlink" hr
 <dl class="py attribute">
 <dt class="sig sig-object py" id="MDAnalysis.analysis.base.AnalysisBase.times">
 <span class="sig-name descname"><span class="pre">times</span></span><a class="headerlink" href="#MDAnalysis.analysis.base.AnalysisBase.times" title="Link to this definition"></a></dt>
-<dd><p>array of Timestep times. Only exists after calling
-<a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a></p>
+<dd><p>Array of times of the Timesteps that were analyzed.
+Only exists after calling <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
 <dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a></p>
@@ -313,8 +319,8 @@ <h2><span class="section-number">4.2.1.3. </span>Classes<a class="headerlink" hr
 <dl class="py attribute">
 <dt class="sig sig-object py" id="MDAnalysis.analysis.base.AnalysisBase.frames">
 <span class="sig-name descname"><span class="pre">frames</span></span><a class="headerlink" href="#MDAnalysis.analysis.base.AnalysisBase.frames" title="Link to this definition"></a></dt>
-<dd><p>array of Timestep frame indices. Only exists after calling
-<a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a></p>
+<dd><p>Array of frame indices that were analyzed.
+Only exists after calling <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
 <dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a></p>
@@ -325,15 +331,65 @@ <h2><span class="section-number">4.2.1.3. </span>Classes<a class="headerlink" hr
 <dl class="py attribute">
 <dt class="sig sig-object py" id="MDAnalysis.analysis.base.AnalysisBase.results">
 <span class="sig-name descname"><span class="pre">results</span></span><a class="headerlink" href="#MDAnalysis.analysis.base.AnalysisBase.results" title="Link to this definition"></a></dt>
-<dd><p>results of calculation are stored after call
-to <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a></p>
+<dd><p>Results of calculation are stored here, after call
+to <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
 <dd class="field-odd"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">Results</span></code></p>
 </dd>
 </dl>
 </dd></dl>
 
+<dl class="py attribute">
+<dt class="sig sig-object py" id="MDAnalysis.analysis.base.AnalysisBase.n_frames">
+<span class="sig-name descname"><span class="pre">n_frames</span></span><a class="headerlink" href="#MDAnalysis.analysis.base.AnalysisBase.n_frames" title="Link to this definition"></a></dt>
+<dd><p>number of <em>analyzed</em> frames, i.e., after taking into account
+the <cite>start</cite>, <cite>stop</cite>, and <cite>step</cite> values from
+<a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a>.
+Only exists after calling <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="MDAnalysis.analysis.base.AnalysisBase.start">
+<span class="sig-name descname"><span class="pre">start</span></span><a class="headerlink" href="#MDAnalysis.analysis.base.AnalysisBase.start" title="Link to this definition"></a></dt>
+<dd><p>Frame index of the first trajectory frame that was analyzed.
+Only exists after calling <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="MDAnalysis.analysis.base.AnalysisBase.stop">
+<span class="sig-name descname"><span class="pre">stop</span></span><a class="headerlink" href="#MDAnalysis.analysis.base.AnalysisBase.stop" title="Link to this definition"></a></dt>
+<dd><p>Frame index of the last trajectory frame that was analyzed.
+Only exists after calling <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="MDAnalysis.analysis.base.AnalysisBase.step">
+<span class="sig-name descname"><span class="pre">step</span></span><a class="headerlink" href="#MDAnalysis.analysis.base.AnalysisBase.step" title="Link to this definition"></a></dt>
+<dd><p>Every <cite>step</cite> frame was analyzed, as <code class="docutils literal notranslate"><span class="pre">trajectory[start:stop:step]</span></code>.
+Only exists after calling <a class="reference internal" href="#MDAnalysis.analysis.base.AnalysisBase.run" title="MDAnalysis.analysis.base.AnalysisBase.run"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AnalysisBase.run()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p>
+</dd>
+</dl>
+</dd></dl>
+
 <p class="rubric">Example</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">MDAnalysis.analysis.base</span><span class="w"> </span><span class="kn">import</span> <span class="n">AnalysisBase</span>
 

2.10.0-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">('OE2',</span> <span class="pre">'OW',</span> <span class="pre">'OG',</span> <span class="pre">'OE1',</span> <span class="pre">'OH',</span> <span class="pre">'O',</span> <span class="pre">'OD2',</span> <span class="pre">'ND1',</span> <span class="pre">'OH2',</span> <span class="pre">'OC1',</span> <span class="pre">'OD1',</span> <span class="pre">'SD',</span> <span class="pre">'OC2',</span> <span class="pre">'NE2',</span> <span class="pre">'OG1',</span> <span class="pre">'SG'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OW',</span> <span class="pre">'OS',</span> <span class="pre">'OY',</span> <span class="pre">'N',</span> <span class="pre">'NT',</span> <span class="pre">'OH',</span> <span class="pre">'SM',</span> <span class="pre">'O',</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>
+<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">('OG',</span> <span class="pre">'SD',</span> <span class="pre">'NE2',</span> <span class="pre">'SG',</span> <span class="pre">'OC1',</span> <span class="pre">'OE2',</span> <span class="pre">'OD1',</span> <span class="pre">'OH2',</span> <span class="pre">'OH',</span> <span class="pre">'OC2',</span> <span class="pre">'OE1',</span> <span class="pre">'ND1',</span> <span class="pre">'OG1',</span> <span class="pre">'OW',</span> <span class="pre">'OD2',</span> <span class="pre">'O'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N',</span> <span class="pre">'NT',</span> <span class="pre">'OH',</span> <span class="pre">'O2',</span> <span class="pre">'OS',</span> <span class="pre">'OW',</span> <span class="pre">'OY',</span> <span class="pre">'SM',</span> <span class="pre">'O'),</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">('OW',</span> <span class="pre">'OG',</span> <span class="pre">'ND1',</span> <span class="pre">'NZ',</span> <span class="pre">'ND2',</span> <span class="pre">'NE',</span> <span class="pre">'NH1',</span> <span class="pre">'N',</span> <span class="pre">'NH2',</span> <span class="pre">'OH',</span> <span class="pre">'NE2',</span> <span class="pre">'OG1',</span> <span class="pre">'OH2',</span> <span class="pre">'SG',</span> <span class="pre">'NE1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OW',</span> <span class="pre">'N',</span> <span class="pre">'NT',</span> <span class="pre">'OH',</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>
+<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">('OG',</span> <span class="pre">'N',</span> <span class="pre">'OH2',</span> <span class="pre">'OH',</span> <span class="pre">'ND2',</span> <span class="pre">'NE2',</span> <span class="pre">'ND1',</span> <span class="pre">'OG1',</span> <span class="pre">'NE1',</span> <span class="pre">'NH2',</span> <span class="pre">'OW',</span> <span class="pre">'NZ',</span> <span class="pre">'SG',</span> <span class="pre">'NH1',</span> <span class="pre">'NE'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N3',</span> <span class="pre">'N',</span> <span class="pre">'NT',</span> <span class="pre">'OH',</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>
 <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>