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OrderParameter.html
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<title>OrderParameter module — NMRlipids databank 4.9.2023 documentation</title>
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<section id="module-OrderParameter">
<span id="orderparameter-module"></span><h1>OrderParameter module<a class="headerlink" href="#module-OrderParameter" title="Link to this heading"></a></h1>
<blockquote>
<div><p>calculation of order parameters of lipid bilayers
from a MD trajectory</p>
<p>Made by Joe, Last edit 2017/02/02</p>
</div></blockquote>
<blockquote>
<div><p>output: order parameters (2 textfiles)</p>
</div></blockquote>
<hr class="docutils" />
<dl class="py class">
<dt class="sig sig-object py" id="OrderParameter.OrderParameter">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">OrderParameter.</span></span><span class="sig-name descname"><span class="pre">OrderParameter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atom_A_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atom_B_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">M_atom_A_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">M_atom_B_name</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#OrderParameter"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.OrderParameter" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Class for storing&manipulating
order parameter (OP) related metadata (definition, name, …)
and OP trajectories
and methods to evaluate OPs.</p>
<dl class="py method">
<dt class="sig sig-object py" id="OrderParameter.OrderParameter.calc_OP">
<span class="sig-name descname"><span class="pre">calc_OP</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#OrderParameter.calc_OP"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.OrderParameter.calc_OP" title="Link to this definition"></a></dt>
<dd><p>calculates Order Parameter according to equation
S = 1/2 * (3*cos(theta)^2 -1)</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="OrderParameter.OrderParameter.get_avg_std_OP">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_avg_std_OP</span></span><a class="headerlink" href="#OrderParameter.OrderParameter.get_avg_std_OP" title="Link to this definition"></a></dt>
<dd><p>Provides average and stddev of all OPs in self.traj</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="OrderParameter.OrderParameter.get_avg_std_stem_OP">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_avg_std_stem_OP</span></span><a class="headerlink" href="#OrderParameter.OrderParameter.get_avg_std_stem_OP" title="Link to this definition"></a></dt>
<dd><p>Provides average and stddev of all OPs in self.traj</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="OrderParameter.OrderParameter.get_op_res">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_op_res</span></span><a class="headerlink" href="#OrderParameter.OrderParameter.get_op_res" title="Link to this definition"></a></dt>
<dd><p>Provides average and stddev of all OPs in self.traj</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="OrderParameter.calc_angle">
<span class="sig-prename descclassname"><span class="pre">OrderParameter.</span></span><span class="sig-name descname"><span class="pre">calc_angle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">com</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#calc_angle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.calc_angle" title="Link to this definition"></a></dt>
<dd><p>calculates the angle between the vector and z-axis in degrees
no PBC check!
Calculates the center of mass of the selected atoms to invert bottom leaflet vector</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="OrderParameter.calc_z_dim">
<span class="sig-prename descclassname"><span class="pre">OrderParameter.</span></span><span class="sig-name descname"><span class="pre">calc_z_dim</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gro</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#calc_z_dim"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.calc_z_dim" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="OrderParameter.read_trajs_calc_OPs">
<span class="sig-prename descclassname"><span class="pre">OrderParameter.</span></span><span class="sig-name descname"><span class="pre">read_trajs_calc_OPs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ordPars</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trajs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#read_trajs_calc_OPs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.read_trajs_calc_OPs" title="Link to this definition"></a></dt>
<dd><p>procedure that
creates MDAnalysis Universe with top,
reads in trajectories trajs and then
goes through every frame and
evaluates each Order Parameter “S” from the list of OPs ordPars.
ordPars : list of OrderParameter class</p>
<blockquote>
<div><p>each item in this list describes an Order parameter to be calculated in the trajectory</p>
</div></blockquote>
<dl class="simple">
<dt>top<span class="classifier">str</span></dt><dd><p>filename of a top file (e.g. conf.gro)</p>
</dd>
<dt>trajs<span class="classifier">list of strings</span></dt><dd><p>filenames of trajectories</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="OrderParameter.parse_op_input">
<span class="sig-prename descclassname"><span class="pre">OrderParameter.</span></span><span class="sig-name descname"><span class="pre">parse_op_input</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lipid_name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#parse_op_input"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.parse_op_input" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="OrderParameter.find_OP">
<span class="sig-prename descclassname"><span class="pre">OrderParameter.</span></span><span class="sig-name descname"><span class="pre">find_OP</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">inp_fname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top_fname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">traj_fname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lipid_name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#find_OP"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.find_OP" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="OrderParameter.read_trj_PN_angles">
<span class="sig-prename descclassname"><span class="pre">OrderParameter.</span></span><span class="sig-name descname"><span class="pre">read_trj_PN_angles</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top_fname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">traj_fname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gro_fname</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#read_trj_PN_angles"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.read_trj_PN_angles" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="OrderParameter.Dihedrals">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">OrderParameter.</span></span><span class="sig-name descname"><span class="pre">Dihedrals</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atom_1_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atom_2_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atom_3_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atom_4_name</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#Dihedrals"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.Dihedrals" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="OrderParameter.parseDihedralInput">
<span class="sig-prename descclassname"><span class="pre">OrderParameter.</span></span><span class="sig-name descname"><span class="pre">parseDihedralInput</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mapping_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/OrderParameter.html#parseDihedralInput"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#OrderParameter.parseDihedralInput" title="Link to this definition"></a></dt>
<dd></dd></dl>
</section>
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