<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.Pathway.Reaction</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.Pathway-module.html">Package Pathway</a> :: Class Reaction </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.Pathway.Reaction-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Reaction</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Pathway-pysrc.html#Reaction">source code</a></span></p> <pre class="literalblock"> Abstraction for a biochemical transformation. This class represents a (potentially reversible) biochemical transformation of the type: a S1 + b S2 + ... --> c P1 + d P2 + ... where - a, b, c, d ... are positive numeric stochiometric coefficients, - S1, S2, ... are substrates - P1, P2, ... are products A Reaction should be viewed as the net result of one or more individual reaction steps, where each step is potentially facilitated by a different catalyst. Support for 'Reaction algebra' will be added at some point in the future. Attributes: reactants -- map of involved species to their stochiometric coefficients: reactants[S] = stochiometric constant for S catalysts -- list of tuples of catalysts required for this reaction reversible -- true iff reaction is reversible data -- reference to arbitrary additional data Invariants: for all S in reactants.keys(): reactants[S] != 0 for all C in catalysts.keys(): catalysts[C] != 0 </pre> <!-- ==================== INSTANCE METHODS ==================== --> <a name="section-InstanceMethods"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Instance Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-InstanceMethods" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">reactants</span>=<span class="summary-sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>, <span class="summary-sig-arg">catalysts</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>, <span class="summary-sig-arg">reversible</span>=<span class="summary-sig-default">0</span>, <span class="summary-sig-arg">data</span>=<span class="summary-sig-default">None</span>)</span><br /> Initializes a new Reaction object.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Pathway-pysrc.html#Reaction.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="__eq__"></a><span class="summary-sig-name">__eq__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">r</span>)</span><br /> Returns true iff self is equal to r.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Pathway-pysrc.html#Reaction.__eq__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="__ne__"></a><span class="summary-sig-name">__ne__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">r</span>)</span><br /> Returns true iff self is not equal to r.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Pathway-pysrc.html#Reaction.__ne__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="__hash__"></a><span class="summary-sig-name">__hash__</span>(<span class="summary-sig-arg">self</span>)</span><br /> Returns a hashcode for self.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Pathway-pysrc.html#Reaction.__hash__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span><br /> Returns a debugging string representation of self.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Pathway-pysrc.html#Reaction.__repr__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="__str__"></a><span class="summary-sig-name">__str__</span>(<span class="summary-sig-arg">self</span>)</span><br /> Returns a string representation of self.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Pathway-pysrc.html#Reaction.__str__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="reverse"></a><span class="summary-sig-name">reverse</span>(<span class="summary-sig-arg">self</span>)</span><br /> Returns a new Reaction that is the reverse of self.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Pathway-pysrc.html#Reaction.reverse">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="species"></a><span class="summary-sig-name">species</span>(<span class="summary-sig-arg">self</span>)</span><br /> Returns a list of all Species involved in self.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Pathway-pysrc.html#Reaction.species">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:37 2008 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed 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