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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.ECell-module.html">Package ECell</a> ::
Module ecell_format
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<h1 class="epydoc">Source Code for <a href="Bio.ECell.ecell_format-module.html">Module Bio.ECell.ecell_format</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2001 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Martel based parser to read ECell formatted files.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">This is a huge regular regular expression for ECell, built using</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">the 'regular expressiona on steroids' capabilities of Martel.</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">http://www.bioinformatics.org/ecell2/</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring">Notes:</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring">Just so I remember -- the new end of line syntax is:</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring"> New regexp syntax - \R</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-docstring"> \R means "\n|\r\n?"</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring"> [\R] means "[\n\r]"</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring">This helps us have endlines be consistent across platforms.</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-comment"># standard library</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#http://www.bioinformatics.org/ecell2/</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-comment"># Martel</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-1', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-2', 'RecordReader', 'link-2');">RecordReader</a></tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-3', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Class Martel.Expression.Str=Martel.Expression.Str-class.html,Function Martel.Str()=Martel-module.html#Str"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-4', 'Str', 'link-4');">Str</a></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-5', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Class Martel.Expression.AnyEol=Martel.Expression.AnyEol-class.html"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-6', 'AnyEol', 'link-6');">AnyEol</a></tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-7', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Function Martel.ToEol()=Martel-module.html#ToEol"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-8', 'ToEol', 'link-8');">ToEol</a></tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-9', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Class Martel.Expression.Group=Martel.Expression.Group-class.html,Function Martel.Group()=Martel-module.html#Group"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-10', 'Group', 'link-10');">Group</a></tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-11" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-11', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Function Martel.Alt()=Martel-module.html#Alt,Class Martel.Expression.Alt=Martel.Expression.Alt-class.html"><a title="Martel.Alt
Martel.Expression.Alt" class="py-name" href="#" onclick="return doclink('link-12', 'Alt', 'link-12');">Alt</a></tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-13" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-13', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-14" class="py-name" targets="Package Bio.Pathway.Rep=Bio.Pathway.Rep-module.html,Function Martel.Rep()=Martel-module.html#Rep"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-14', 'Rep', 'link-14');">Rep</a></tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-15" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-15', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-16" class="py-name" targets="Function Martel.Rep1()=Martel-module.html#Rep1"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-16', 'Rep1', 'link-16');">Rep1</a></tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-17" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-17', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-18" class="py-name" targets="Function Martel.Any()=Martel-module.html#Any,Class Martel.Expression.Any=Martel.Expression.Any-class.html"><a title="Martel.Any
Martel.Expression.Any" class="py-name" href="#" onclick="return doclink('link-18', 'Any', 'link-18');">Any</a></tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-19" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-19', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-20" class="py-name" targets="Function Martel.AnyBut()=Martel-module.html#AnyBut"><a title="Martel.AnyBut" class="py-name" href="#" onclick="return doclink('link-20', 'AnyBut', 'link-20');">AnyBut</a></tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-21" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-21', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-22" class="py-name" targets="Class Bio.EUtils.Datatypes.Expression=Bio.EUtils.Datatypes.Expression-class.html,Module Martel.Expression=Martel.Expression-module.html,Class Martel.Expression.Expression=Martel.Expression.Expression-class.html"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-22', 'Expression', 'link-22');">Expression</a></tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-comment"># --- first set up some helper constants and functions</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Copyright 2001 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt id="link-23" class="py-name" targets="Variable Bio.ECell.ecell_format.excluded_chars=Bio.ECell.ecell_format-module.html#excluded_chars,Variable Bio.NBRF.nbrf_format.excluded_chars=Bio.NBRF.nbrf_format-module.html#excluded_chars"><a title="Bio.ECell.ecell_format.excluded_chars
Bio.NBRF.nbrf_format.excluded_chars" class="py-name" href="#" onclick="return doclink('link-23', 'excluded_chars', 'link-23');">excluded_chars</a></tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt> <tt class="py-op">+</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt> <tt class="py-number">0x09</tt> <tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt> <tt class="py-number">10</tt> <tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt> <tt class="py-number">13</tt> <tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt id="link-24" class="py-name" targets="Variable Bio.ECell.ecell_format.block_type=Bio.ECell.ecell_format-module.html#block_type"><a title="Bio.ECell.ecell_format.block_type" class="py-name" href="#" onclick="return doclink('link-24', 'block_type', 'link-24');">block_type</a></tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-25', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"block_type"</tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-26', 'Expression', 'link-22');">Expression</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Function Martel.Expression.NoCase()=Martel.Expression-module.html#NoCase"><a title="Martel.Expression.NoCase" class="py-name" href="#" onclick="return doclink('link-27', 'NoCase', 'link-27');">NoCase</a></tt><tt class="py-op">(</tt> <tt id="link-28" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-28', 'Str', 'link-4');">Str</a></tt><tt class="py-op">(</tt> <tt class="py-string">"Type"</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt id="link-29" class="py-name" targets="Method Bio.ECell._RecordConsumer.header_line()=Bio.ECell._RecordConsumer-class.html#header_line,Variable Bio.ECell.ecell_format.header_line=Bio.ECell.ecell_format-module.html#header_line"><a title="Bio.ECell._RecordConsumer.header_line
Bio.ECell.ecell_format.header_line" class="py-name" href="#" onclick="return doclink('link-29', 'header_line', 'link-29');">header_line</a></tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-30', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"header_line"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="Bio.ECell.ecell_format.block_type" class="py-name" href="#" onclick="return doclink('link-31', 'block_type', 'link-24');">block_type</a></tt> <tt class="py-op">+</tt> <tt id="link-32" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-32', 'ToEol', 'link-8');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"><tt id="link-33" class="py-name" targets="Variable Bio.ECell.ecell_format.tab=Bio.ECell.ecell_format-module.html#tab,Variable Bio.MetaTool.metatool_format.tab=Bio.MetaTool.metatool_format-module.html#tab"><a title="Bio.ECell.ecell_format.tab
Bio.MetaTool.metatool_format.tab" class="py-name" href="#" onclick="return doclink('link-33', 'tab', 'link-33');">tab</a></tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-34', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"tab"</tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-35', 'Str', 'link-4');">Str</a></tt><tt class="py-op">(</tt> <tt class="py-string">'\t'</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"><tt id="link-36" class="py-name" targets="Variable Bio.ECell.ecell_format.system_tag=Bio.ECell.ecell_format-module.html#system_tag"><a title="Bio.ECell.ecell_format.system_tag" class="py-name" href="#" onclick="return doclink('link-36', 'system_tag', 'link-36');">system_tag</a></tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-37', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"system_tag"</tt><tt class="py-op">,</tt> <tt id="link-38" class="py-name"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-38', 'Expression', 'link-22');">Expression</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Martel.Expression.NoCase" class="py-name" href="#" onclick="return doclink('link-39', 'NoCase', 'link-27');">NoCase</a></tt><tt class="py-op">(</tt> <tt id="link-40" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-40', 'Str', 'link-4');">Str</a></tt><tt class="py-op">(</tt> <tt class="py-string">"system"</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"><tt id="link-41" class="py-name" targets="Variable Bio.ECell.ecell_format.reactor_tag=Bio.ECell.ecell_format-module.html#reactor_tag"><a title="Bio.ECell.ecell_format.reactor_tag" class="py-name" href="#" onclick="return doclink('link-41', 'reactor_tag', 'link-41');">reactor_tag</a></tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-42', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"reactor_tag"</tt><tt class="py-op">,</tt> <tt id="link-43" class="py-name"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-43', 'Expression', 'link-22');">Expression</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Martel.Expression.NoCase" class="py-name" href="#" onclick="return doclink('link-44', 'NoCase', 'link-27');">NoCase</a></tt><tt class="py-op">(</tt> <tt id="link-45" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-45', 'Str', 'link-4');">Str</a></tt><tt class="py-op">(</tt> <tt class="py-string">"Reactor"</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"><tt id="link-46" class="py-name" targets="Variable Bio.ECell.ecell_format.substance_tag=Bio.ECell.ecell_format-module.html#substance_tag"><a title="Bio.ECell.ecell_format.substance_tag" class="py-name" href="#" onclick="return doclink('link-46', 'substance_tag', 'link-46');">substance_tag</a></tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-47', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"substance_tag"</tt><tt class="py-op">,</tt> <tt id="link-48" class="py-name"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-48', 'Expression', 'link-22');">Expression</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Martel.Expression.NoCase" class="py-name" href="#" onclick="return doclink('link-49', 'NoCase', 'link-27');">NoCase</a></tt><tt class="py-op">(</tt> <tt id="link-50" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-50', 'Str', 'link-4');">Str</a></tt><tt class="py-op">(</tt> <tt class="py-string">"Substance"</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"><tt id="link-51" class="py-name" targets="Method Bio.ECell._RecordConsumer.system_line()=Bio.ECell._RecordConsumer-class.html#system_line,Variable Bio.ECell.ecell_format.system_line=Bio.ECell.ecell_format-module.html#system_line"><a title="Bio.ECell._RecordConsumer.system_line
Bio.ECell.ecell_format.system_line" class="py-name" href="#" onclick="return doclink('link-51', 'system_line', 'link-51');">system_line</a></tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-52', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"system_line"</tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.ECell.ecell_format.system_tag" class="py-name" href="#" onclick="return doclink('link-53', 'system_tag', 'link-36');">system_tag</a></tt> <tt class="py-op">+</tt> <tt id="link-54" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-54', 'ToEol', 'link-8');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"><tt id="link-55" class="py-name" targets="Variable Bio.ECell.ecell_format.reactor_line=Bio.ECell.ecell_format-module.html#reactor_line"><a title="Bio.ECell.ecell_format.reactor_line" class="py-name" href="#" onclick="return doclink('link-55', 'reactor_line', 'link-55');">reactor_line</a></tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-56', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"reactor_line"</tt><tt class="py-op">,</tt> <tt id="link-57" class="py-name"><a title="Bio.ECell.ecell_format.reactor_tag" class="py-name" href="#" onclick="return doclink('link-57', 'reactor_tag', 'link-41');">reactor_tag</a></tt> <tt class="py-op">+</tt> <tt id="link-58" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-58', 'ToEol', 'link-8');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt id="link-59" class="py-name" targets="Variable Bio.ECell.ecell_format.substance_line=Bio.ECell.ecell_format-module.html#substance_line"><a title="Bio.ECell.ecell_format.substance_line" class="py-name" href="#" onclick="return doclink('link-59', 'substance_line', 'link-59');">substance_line</a></tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-60', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"substance_line"</tt><tt class="py-op">,</tt> <tt id="link-61" class="py-name"><a title="Bio.ECell.ecell_format.substance_tag" class="py-name" href="#" onclick="return doclink('link-61', 'substance_tag', 'link-46');">substance_tag</a></tt> <tt class="py-op">+</tt> <tt id="link-62" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-62', 'ToEol', 'link-8');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"><tt id="link-63" class="py-name" targets="Variable Bio.ECell.ecell_format.continuation_line=Bio.ECell.ecell_format-module.html#continuation_line"><a title="Bio.ECell.ecell_format.continuation_line" class="py-name" href="#" onclick="return doclink('link-63', 'continuation_line', 'link-63');">continuation_line</a></tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-64', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"continuation_line"</tt><tt class="py-op">,</tt> <tt id="link-65" class="py-name"><a title="Bio.ECell.ecell_format.tab
Bio.MetaTool.metatool_format.tab" class="py-name" href="#" onclick="return doclink('link-65', 'tab', 'link-33');">tab</a></tt> <tt class="py-op">+</tt> <tt id="link-66" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-66', 'ToEol', 'link-8');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"><tt id="link-67" class="py-name" targets="Method Bio.ECell._RecordConsumer.include_line()=Bio.ECell._RecordConsumer-class.html#include_line,Variable Bio.ECell.ecell_format.include_line=Bio.ECell.ecell_format-module.html#include_line"><a title="Bio.ECell._RecordConsumer.include_line
Bio.ECell.ecell_format.include_line" class="py-name" href="#" onclick="return doclink('link-67', 'include_line', 'link-67');">include_line</a></tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-68', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"include_line"</tt><tt class="py-op">,</tt> <tt id="link-69" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-69', 'Str', 'link-4');">Str</a></tt><tt class="py-op">(</tt> <tt class="py-string">'include'</tt> <tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-70" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-70', 'ToEol', 'link-8');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"><tt id="link-71" class="py-name" targets="Method Bio.ECell._RecordConsumer.substance_multiline()=Bio.ECell._RecordConsumer-class.html#substance_multiline,Variable Bio.ECell.ecell_format.substance_multiline=Bio.ECell.ecell_format-module.html#substance_multiline"><a title="Bio.ECell._RecordConsumer.substance_multiline
Bio.ECell.ecell_format.substance_multiline" class="py-name" href="#" onclick="return doclink('link-71', 'substance_multiline', 'link-71');">substance_multiline</a></tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-72', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"substance_multiline"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt id="link-73" class="py-name"><a title="Bio.ECell.ecell_format.substance_line" class="py-name" href="#" onclick="return doclink('link-73', 'substance_line', 'link-59');">substance_line</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt id="link-74" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-74', 'Rep', 'link-14');">Rep</a></tt><tt class="py-op">(</tt> <tt id="link-75" class="py-name"><a title="Bio.ECell.ecell_format.continuation_line" class="py-name" href="#" onclick="return doclink('link-75', 'continuation_line', 'link-63');">continuation_line</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"><tt id="link-76" class="py-name" targets="Method Bio.ECell._RecordConsumer.reactor_multiline()=Bio.ECell._RecordConsumer-class.html#reactor_multiline,Variable Bio.ECell.ecell_format.reactor_multiline=Bio.ECell.ecell_format-module.html#reactor_multiline"><a title="Bio.ECell._RecordConsumer.reactor_multiline
Bio.ECell.ecell_format.reactor_multiline" class="py-name" href="#" onclick="return doclink('link-76', 'reactor_multiline', 'link-76');">reactor_multiline</a></tt> <tt class="py-op">=</tt> <tt id="link-77" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-77', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"reactor_multiline"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt id="link-78" class="py-name"><a title="Bio.ECell.ecell_format.reactor_line" class="py-name" href="#" onclick="return doclink('link-78', 'reactor_line', 'link-55');">reactor_line</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt id="link-79" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-79', 'Rep', 'link-14');">Rep</a></tt><tt class="py-op">(</tt> <tt id="link-80" class="py-name"><a title="Bio.ECell.ecell_format.continuation_line" class="py-name" href="#" onclick="return doclink('link-80', 'continuation_line', 'link-63');">continuation_line</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"><tt id="link-81" class="py-name" targets="Variable Bio.ECell.ecell_format.system_block=Bio.ECell.ecell_format-module.html#system_block"><a title="Bio.ECell.ecell_format.system_block" class="py-name" href="#" onclick="return doclink('link-81', 'system_block', 'link-81');">system_block</a></tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-82', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"system_block"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt id="link-83" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-83', 'Rep1', 'link-16');">Rep1</a></tt><tt class="py-op">(</tt> <tt id="link-84" class="py-name"><a title="Bio.ECell._RecordConsumer.system_line
Bio.ECell.ecell_format.system_line" class="py-name" href="#" onclick="return doclink('link-84', 'system_line', 'link-51');">system_line</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"><tt id="link-85" class="py-name" targets="Variable Bio.ECell.ecell_format.reactor_block=Bio.ECell.ecell_format-module.html#reactor_block"><a title="Bio.ECell.ecell_format.reactor_block" class="py-name" href="#" onclick="return doclink('link-85', 'reactor_block', 'link-85');">reactor_block</a></tt> <tt class="py-op">=</tt> <tt id="link-86" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-86', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"reactor_block"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> <tt id="link-87" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-87', 'Rep1', 'link-16');">Rep1</a></tt><tt class="py-op">(</tt> <tt id="link-88" class="py-name"><a title="Bio.ECell._RecordConsumer.reactor_multiline
Bio.ECell.ecell_format.reactor_multiline" class="py-name" href="#" onclick="return doclink('link-88', 'reactor_multiline', 'link-76');">reactor_multiline</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"><tt id="link-89" class="py-name" targets="Variable Bio.ECell.ecell_format.substance_block=Bio.ECell.ecell_format-module.html#substance_block"><a title="Bio.ECell.ecell_format.substance_block" class="py-name" href="#" onclick="return doclink('link-89', 'substance_block', 'link-89');">substance_block</a></tt> <tt class="py-op">=</tt> <tt id="link-90" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-90', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"substance_block"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> <tt id="link-91" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-91', 'Rep1', 'link-16');">Rep1</a></tt><tt class="py-op">(</tt> <tt id="link-92" class="py-name"><a title="Bio.ECell._RecordConsumer.substance_multiline
Bio.ECell.ecell_format.substance_multiline" class="py-name" href="#" onclick="return doclink('link-92', 'substance_multiline', 'link-71');">substance_multiline</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"><tt id="link-93" class="py-name" targets="Variable Bio.ECell.ecell_format.valid_block=Bio.ECell.ecell_format-module.html#valid_block"><a title="Bio.ECell.ecell_format.valid_block" class="py-name" href="#" onclick="return doclink('link-93', 'valid_block', 'link-93');">valid_block</a></tt> <tt class="py-op">=</tt> <tt id="link-94" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-94', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"valid_block"</tt><tt class="py-op">,</tt> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> <tt id="link-95" class="py-name"><a title="Bio.ECell._RecordConsumer.header_line
Bio.ECell.ecell_format.header_line" class="py-name" href="#" onclick="return doclink('link-95', 'header_line', 'link-29');">header_line</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"> <tt id="link-96" class="py-name"><a title="Martel.Alt
Martel.Expression.Alt" class="py-name" href="#" onclick="return doclink('link-96', 'Alt', 'link-12');">Alt</a></tt><tt class="py-op">(</tt> <tt id="link-97" class="py-name"><a title="Bio.ECell.ecell_format.system_block" class="py-name" href="#" onclick="return doclink('link-97', 'system_block', 'link-81');">system_block</a></tt><tt class="py-op">,</tt> <tt id="link-98" class="py-name"><a title="Bio.ECell.ecell_format.reactor_block" class="py-name" href="#" onclick="return doclink('link-98', 'reactor_block', 'link-85');">reactor_block</a></tt><tt class="py-op">,</tt> <tt id="link-99" class="py-name"><a title="Bio.ECell.ecell_format.substance_block" class="py-name" href="#" onclick="return doclink('link-99', 'substance_block', 'link-89');">substance_block</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"><tt id="link-100" class="py-name" targets="Variable Bio.ECell.ecell_format.valid_contents=Bio.ECell.ecell_format-module.html#valid_contents"><a title="Bio.ECell.ecell_format.valid_contents" class="py-name" href="#" onclick="return doclink('link-100', 'valid_contents', 'link-100');">valid_contents</a></tt> <tt class="py-op">=</tt> <tt id="link-101" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-101', 'Group', 'link-10');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"valid_contents"</tt><tt class="py-op">,</tt> <tt id="link-102" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-102', 'Rep1', 'link-16');">Rep1</a></tt><tt class="py-op">(</tt> <tt id="link-103" class="py-name"><a title="Bio.ECell.ecell_format.valid_block" class="py-name" href="#" onclick="return doclink('link-103', 'valid_block', 'link-93');">valid_block</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno">83</tt> <tt class="py-line"><tt id="link-104" class="py-name" targets="Variable Bio.ECell.ecell_format.ecell_record=Bio.ECell.ecell_format-module.html#ecell_record"><a title="Bio.ECell.ecell_format.ecell_record" class="py-name" href="#" onclick="return doclink('link-104', 'ecell_record', 'link-104');">ecell_record</a></tt> <tt class="py-op">=</tt> <tt id="link-105" class="py-name"><a title="Bio.ECell.ecell_format.valid_contents" class="py-name" href="#" onclick="return doclink('link-105', 'valid_contents', 'link-100');">valid_contents</a></tt> </tt>
<a name="L84"></a><tt class="py-lineno">84</tt> <tt class="py-line"> </tt><script type="text/javascript">
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