Deploying to gh-pages from @ 3d814c8 🚀

Author: rmtfleming

stable/modules/analysis/thermo/experimentalData/index.html

@@ -335,7 +335,8 @@ <h1>The COBRA Toolbox</h1>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>metBoundsFile</strong> – name of tab delimited file with metabolite bounds
 format: ‘%s %f %f’
-i.e. abbreviation lowerBound upperBound</p></li>
+i.e. abbreviation lowerBound upperBound
+Concentration units in Molar</p></li>
 <li><p><strong>rxnBoundsFile</strong> – name of tab delimited file with reaction bounds
 format: ‘%s %f %f’
 i.e. abbreviation lowerBound upperBound</p></li>

stable/modules/analysis/thermo/utilities/index.html

@@ -279,12 +279,13 @@ <h1>The COBRA Toolbox</h1>
 <span id="id1"></span><h1>Utilities<a class="headerlink" href="#utilities" title="Permalink to this heading">¶</a></h1>
 <span class="target" id="module-src.analysis.thermo.utilities"></span><dl class="mat function">
 <dt class="sig sig-object mat" id="src.analysis.thermo.utilities.logmod">
-<span class="sig-name descname"><span class="pre">logmod</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">x</span></em>, <em class="sig-param"><span class="pre">base</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/thermo/utilities/logmod.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.thermo.utilities.logmod" title="Permalink to this definition">¶</a></dt>
-<dd><p>log modulus function</p>
+<span class="sig-name descname"><span class="pre">logmod</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">x</span></em>, <em class="sig-param"><span class="pre">base</span></em>, <em class="sig-param"><span class="pre">signed</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/thermo/utilities/logmod.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.thermo.utilities.logmod" title="Permalink to this definition">¶</a></dt>
+<dd><p>log modulus function, signed by default</p>
 <p>INPUT
 x     n x 1 real vector</p>
 <p>OPTIONAL INPUT
-base  exp(1),2,10</p>
+logarithm base  exp(1),2,10
+signed = 1 returns a signed y (the default)</p>
 </dd></dl>
 
 <dl class="mat function">

stable/modules/analysis/thermo/vonBertalanffy/index.html

@@ -384,7 +384,7 @@ <h1>The COBRA Toolbox</h1>
 <li><p>.DfG0 - <cite>m x 1</cite> array of standard Gibbs energies of formation.</p></li>
 <li><p>.pKa - <cite>m x 1</cite> structure array with metabolite pKa values.</p></li>
 <li><p>.DfG0_Uncertainty - <cite>m x 1</cite> array of uncertainty in estimated standard
-Gibbs energies of formation. uf will be large for
+Gibbs energies of formation. Will be large for
 metabolites that are not covered by component contributions.</p></li>
 </ul>
 </dd>
@@ -590,6 +590,9 @@ <h1>The COBRA Toolbox</h1>
 transformed reaction Gibbs energies.</p></li>
 <li><p>.DrGtMax - <cite>n x 1</cite> array of estimated upper bounds on
 transformed reaction Gibbs energies.</p></li>
+<li><p>.DfG0_Uncertainty - <cite>m x 1</cite> array of uncertainty in estimated standard
+Gibbs energies of formation. Will be large for
+metabolites that are not covered by component contributions.</p></li>
 </ul>
 </dd>
 </dl>

stable/modules/analysis/topology/extremeRays/lrs/index.html

@@ -339,26 +339,31 @@ <h1>The COBRA Toolbox</h1>
 
 <dl class="mat function">
 <dt class="sig sig-object mat" id="src.analysis.topology.extremeRays.lrs.extremePools">
-<span class="sig-name descname"><span class="pre">extremePools</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">model</span></em>, <em class="sig-param"><span class="pre">positivity</span></em>, <em class="sig-param"><span class="pre">inequality</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/topology/extremeRays/lrs/extremePools.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.topology.extremeRays.lrs.extremePools" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculates the extreme pools of a stoichiometric model using the vertex / facet enumeration package</p>
+<span class="sig-name descname"><span class="pre">extremePools</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">model</span></em>, <em class="sig-param"><span class="pre">param</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/topology/extremeRays/lrs/extremePools.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.topology.extremeRays.lrs.extremePools" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates the extreme pools of a stoichiometric model using the vertex / facet enumeration package
+such that</p>
 <dl class="field-list simple">
 <dt class="field-odd">INPUT</dt>
-<dd class="field-odd"><p><strong>model</strong> – structure with:</p>
-<ul class="simple">
-<li><p>.S - <cite>m x n</cite> Stoichiometric matrix with integer coefficients. If no
-other inputs are specified it is assumed that all reactions are
-reversible and <cite>S.v = 0</cite></p></li>
-<li><p>.SIntRxnBool - <cite>n x 1</cite> boolean vector with 1 for internal reactions</p></li>
-<li><p>.description - description</p></li>
-</ul>
+<dd class="field-odd"><p><strong>model.S  - `m x</strong> (<em>n + k</em>)</p>
 </dd>
-<dt class="field-even">OPTIONAL INPUT</dt>
+<dt class="field-even">OPTIONAL INPUTS</dt>
 <dd class="field-even"><ul class="simple">
+<li><p><strong>model.SConsistentRxnBool</strong> – n x 1  boolean indicating  stoichiometrically consistent metabolites</p></li>
+<li><p><strong>model.SIntRxnBool - Boolean of reactions heuristically though to be mass balanced.</strong></p></li>
+<li><p><strong>model.SIntMetBool - Boolean of metabolites heuristically though to be involved in mass balanced reactions.</strong></p></li>
 <li><p><strong>positivity</strong> – {0, (1)} if <cite>positivity == 1</cite>, then positive orthant base</p></li>
 <li><p><strong>inequality</strong> – {(0), 1} if <cite>inequality == 1</cite>, then use two inequalities rather than a single equaltiy</p></li>
 </ul>
 </dd>
+<dt class="field-odd">OUTPUT</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>P</strong> – p x m matrix of non-negative entries such that P*N = 0.</p></li>
+<li><p><strong>vertexBool         n x 1 Boolean vector indicating which columns of P are vertices</strong></p></li>
+<li><p><strong>N</strong> – m x n stoichiometric matrix used such that P*N.</p></li>
+</ul>
+</dd>
 </dl>
+<p>Author(s) Ronan Fleming</p>
 </dd></dl>
 
 </section>

stable/modules/analysis/topology/extremeRays/lrs/lrsInterface/index.html

@@ -341,6 +341,17 @@ <h1>The COBRA Toolbox</h1>
 <blockquote>
 <div><p>It is assumed the file is pwd/<a href="#id12"><span class="problematic" id="id13">*</span></a>.ine, otherwise provide the full path.</p>
 </div></blockquote>
+<dl class="field-list simple">
+<dt class="field-odd">OPTIONAL INPUT</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>param</strong> – parameter structure with the following fields:</p></li>
+<li><p><strong>*.positivity</strong> – if equals to 1, then positive orthant base</p></li>
+<li><p><strong>*.inequality</strong> – if equals to 1, then represent as two inequalities rather than a single equality</p></li>
+<li><p><strong>*.shellScript</strong> – if equals to 1, then lrs is run through a bash script</p></li>
+<li><p><strong>*.redund         if equals to 0, then remove redundant linear equalities</strong></p></li>
+</ul>
+</dd>
+</dl>
 <p>OUTPUT:
 Q             m x n integer matrix where each row is a variable and each column is a vertex or ray
 vertexBool         n x 1 Boolean vector indicating which columns of Q are vertices</p>
@@ -386,28 +397,20 @@ <h1>The COBRA Toolbox</h1>
 <span class="sig-name descname"><span class="pre">lrsWriteHalfspace</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">A</span></em>, <em class="sig-param"><span class="pre">b</span></em>, <em class="sig-param"><span class="pre">csense</span></em>, <em class="sig-param"><span class="pre">modelName</span></em>, <em class="sig-param"><span class="pre">param</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/topology/extremeRays/lrs/lrsInterface/lrsWriteHalfspace.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.topology.extremeRays.lrs.lrsInterface.lrsWriteHalfspace" title="Permalink to this definition">¶</a></dt>
 <dd><p>Outputs a file for lrs to convert an H-representation (half-space) of a
 polyhedron to a V-representation (vertex / ray) via vertex enumeration</p>
-<dl class="field-list">
+<dl class="field-list simple">
 <dt class="field-odd">USAGE</dt>
-<dd class="field-odd"><p><strong>lrsInputHalfspace</strong> (<em>A, D, filename, positivity, inequality, a, d, f, sh</em>)</p>
+<dd class="field-odd"><p><strong>lrsWriteHalfspace</strong> (<em>A, b, csense, modelName, param</em>)</p>
 </dd>
 <dt class="field-even">INPUTS</dt>
-<dd class="field-even"><ul class="simple">
-<li><p><strong>A</strong> – matrix of linear equalities <span class="math notranslate nohighlight">\(A x =(a)\)</span></p></li>
-<li><p><strong>D</strong> – matrix of linear inequalities <span class="math notranslate nohighlight">\(D x \geq (d)\)</span></p></li>
-<li><p><strong>filename</strong> – base name of output file</p></li>
-</ul>
+<dd class="field-even"><p><strong>A</strong> – m x n matrix of linear constraints <span class="math notranslate nohighlight">\(A x (csense) b\)</span></p>
 </dd>
 <dt class="field-odd">OPTIONAL INPUTS</dt>
-<dd class="field-odd"><ul>
-<li><p><strong>positivity</strong> – {0, (1)} if positivity == 1, then positive orthant base</p></li>
-<li><p><strong>inequality</strong> – {0, (1)} if inequality == 1, then use two inequalities rather than a single equaltiy</p></li>
-<li><p><strong>a</strong> – boundary values for matrix of linear equalities <span class="math notranslate nohighlight">\(A x = a\)</span></p></li>
-<li><p><strong>d</strong> – boundary values for matrix of linear inequalities <span class="math notranslate nohighlight">\(D x \geq d\)</span></p></li>
-<li><p><strong>f</strong> – linear objective for a linear optimization problem in rational arithmetic</p>
-<p>minimise <span class="math notranslate nohighlight">\(f^T x\)</span>,
-subject to <span class="math notranslate nohighlight">\(A x = (a)\)</span>, <span class="math notranslate nohighlight">\(D x \geq (d)\)</span></p>
-</li>
-<li><p><strong>sh</strong> – {(0), 1} if <cite>sh == 1</cite>, output a shell script for submitting qsub job</p></li>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>b</strong> – m x 1 rhs of linear constraints</p></li>
+<li><p><strong>csense</strong> – m x 1 char with (‘E’),’G’ or ‘L’</p></li>
+<li><p><strong>modelName</strong> – name of the model to be used when generating filenames, ‘model’ by default</p></li>
+<li><p><strong>param.positivity</strong> – {0, (1)} if positivity == 1, then positive orthant base</p></li>
+<li><p><strong>param.inequality</strong> – {0, (1)} if inequality == 1, then use two inequalities rather than a single equaltiy</p></li>
 </ul>
 </dd>
 </dl>

stable/modules/analysis/topology/index.html

@@ -467,21 +467,18 @@ <h1>The COBRA Toolbox</h1>
 
 <dl class="mat function">
 <dt class="sig sig-object mat" id="src.analysis.topology.integerizeS">
-<span class="sig-name descname"><span class="pre">integerizeS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">S</span></em>, <em class="sig-param"><span class="pre">SIntRxnBool</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/topology/integerizeS.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.topology.integerizeS" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">integerizeS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">model</span></em>, <em class="sig-param"><span class="pre">printLevel</span></em>, <em class="sig-param"><span class="pre">internalRxnsOnly</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/topology/integerizeS.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.topology.integerizeS" title="Permalink to this definition">¶</a></dt>
 <dd><p>convert an S matrix with some non integer coefficients into an S matrix
 with all integer coefficients
 assumes that there are a maximum of six significant digits in the biomass
 reaction</p>
 <dl class="simple">
 <dt>INPUT</dt><dd><p>S         stoichiometric matrix</p>
 </dd>
-<dt>OPTIONAL INPUT</dt><dd><dl class="simple">
-<dt>SIntRxnBool         Boolean of internal (mass balanced) reactions.</dt><dd><p>If provided, only these reactions are integerised</p>
+<dt>OPTIONAL INPUT</dt><dd><p>internalRxnsOnly (1),0. 1 = integerise internal reactions only</p>
 </dd>
-</dl>
-</dd>
-<dt>OUTPUT</dt><dd><p>SInteger  stoichiometric matrix of integers
-G         scaling matrix, SInteger=S*G;</p>
+<dt>OUTPUT</dt><dd><p>S         stoichiometric matrix with internal reactions integers, unless internalRxnsOnly =0, whence all reactions will be integerised
+g         scaling vector such that modelIn.S*diag(g)=modelOut.S;</p>
 </dd>
 </dl>
 </dd></dl>

stable/modules/analysis/wholeBody/PSCMToolbox/io/index.html

@@ -323,7 +323,7 @@ <h1>The COBRA Toolbox</h1>
 % Giving the exact name of the .mat file loads the exact
 specified mode:
 female = loadPSCMfile(‘Harvetta_1_03d’);
-% Specifiying the search directory loads the .mat file
+% Also specifiying the search directory loads the .mat file
 within that directory:
 male = loadPSCMfile(‘Harvetta’,’MYDIRECTORY’)</p>
 <p class="rubric">AUTHORS</p>