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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.MetaTool-module.html">Package MetaTool</a> ::
Module metatool_format
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module metatool_format</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.MetaTool.metatool_format-pysrc.html">source code</a></span></p>
<p>Martel based parser to read MetaTool output files.</p>
<p>This is a huge regular regular expression for MetaTool 3.5 output,
built using the 'regular expressiona on steroids' capabilities of
Martel.</p>
<p>http://www2.bioinf.mdc-berlin.de/metabolic/metatool/</p>
<p>This helps us have endlines be consistent across platforms.</p>
<!-- ==================== VARIABLES ==================== -->
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="blank"></a><span class="summary-name">blank</span> = <code title="' '"><code class="variable-quote">'</code><code class="variable-string"> </code><code class="variable-quote">'</code></code>
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<a name="tab"></a><span class="summary-name">tab</span> = <code title="'\t'"><code class="variable-quote">'</code><code class="variable-string">\t</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a name="blank_space"></a><span class="summary-name">blank_space</span> = <code title="MaxRepeat(Any(blank+ tab), 1, 80)">MaxRepeat(Any(blank+ tab), 1, 80)</code>
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<a name="optional_blank_space"></a><span class="summary-name">optional_blank_space</span> = <code title="Rep(Any(blank+ tab))">Rep(Any(blank+ tab))</code>
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<span class="summary-type"> </span>
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<a name="white_space"></a><span class="summary-name">white_space</span> = <code title="''' \t
\r'''"><code class="variable-quote">'</code><code class="variable-string"> \t\n\r</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a name="blank_line"></a><span class="summary-name">blank_line</span> = <code title="optional_blank_space+ AnyEol()">optional_blank_space+ AnyEol()</code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#lower_case_letter" class="summary-name">lower_case_letter</a> = <code title="Group("lower_case_letter", Any("abcdefghijklmnopqrstuvwxyz"))">Group("lower_case_letter", Any("abcdefghij<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="digits"></a><span class="summary-name">digits</span> = <code title="'0123456789'"><code class="variable-quote">'</code><code class="variable-string">0123456789</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#enzyme" class="summary-name">enzyme</a> = <code title="Group("enzyme", optional_blank_space+ Digits()+ optional_blank_space+ \
Str(':')+ ToEol())">Group("enzyme", optional_blank_space+ Digits()+ optio<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#reaction" class="summary-name">reaction</a> = <code title="Group("reaction", optional_blank_space+ Digits()+ optional_blank_space\
+ Str(":")+ ToEol())">Group("reaction", optional_blank_space+ Digits()+ o<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#not_found_line" class="summary-name">not_found_line</a> = <code title="Group("not_found_line", optional_blank_space+ Str("- not found -")+ To\
Eol())">Group("not_found_line", optional_blank_space+<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#enzymes_header" class="summary-name">enzymes_header</a> = <code title="Group("enzymes_header", optional_blank_space+ Str("enzymes")+ ToEol())">Group("enzymes_header", optional_blank_space+<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#enzymes_list" class="summary-name">enzymes_list</a> = <code title="Group("enzymes_list", Alt(Rep1(enzyme), not_found_line))">Group("enzymes_list", Alt(Rep1(enzyme), not_fou<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#enzymes_block" class="summary-name">enzymes_block</a> = <code title="Group("enzymes_block", enzymes_header+ Rep(blank_line)+ enzymes_list)">Group("enzymes_block", enzymes_header+ Rep(bla<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#reactions_header" class="summary-name">reactions_header</a> = <code title="Group("reactions_header", optional_blank_space+ Str("overall reaction"\
)+ ToEol())">Group("reactions_header", optional_blank_sp<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#reactions_list" class="summary-name">reactions_list</a> = <code title="Group("reactions_list", Alt(Rep1(reaction), not_found_line))">Group("reactions_list", Alt(Rep1(reaction), n<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#reactions_block" class="summary-name">reactions_block</a> = <code title="Group("reactions_block", reactions_header+ Rep(blank_line)+ reactions_\
list)">Group("reactions_block", reactions_header+ R<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="rev"></a><span class="summary-name">rev</span> = <code title="Group("rev", Opt(lower_case_letter))">Group("rev", Opt(lower_case_letter))</code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#version" class="summary-name">version</a> = <code title="Group("version", Digits("version_major")+ Any(".")+ Digits("version_mi\
nor")+ rev)">Group("version", Digits("version_major")+ Any(".")+ <code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="metatool_tag"></a><span class="summary-name">metatool_tag</span> = <code title="Str("METATOOL OUTPUT")">Str("METATOOL OUTPUT")</code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#metatool_line" class="summary-name">metatool_line</a> = <code title="Group("metatool_line", metatool_tag+ blank_space+ Str("Version")+ blan\
k_space+ version+ ToEol())">Group("metatool_line", metatool_tag+ blank_spa<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="input_file_tag"></a><span class="summary-name">input_file_tag</span> = <code title="Str("INPUT FILE:")">Str("INPUT FILE:")</code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#input_file_line" class="summary-name">input_file_line</a> = <code title="Group("input_file_line", input_file_tag+ blank_space+ ToEol("input_fil\
e_name"))">Group("input_file_line", input_file_tag+ bla<code class="variable-ellipsis">...</code></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<a name="metabolite_count_tag"></a><span class="summary-name">metabolite_count_tag</span> = <code title="Str("INTERNAL METABOLITES:")">Str("INTERNAL METABOLITES:")</code>
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<span class="summary-type"> </span>
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<a href="Bio.MetaTool.metatool_format-module.html#metabolite_count_line" class="summary-name">metabolite_count_line</a> = <code title="Group("metabolite_count_line", metabolite_count_tag+ blank_space+ Digi\
ts("num_int_metabolites")+ ToEol())">Group("metabolite_count_line", metabol<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reaction_count_tag"></a><span class="summary-name">reaction_count_tag</span> = <code title="Str("REACTIONS:")">Str("REACTIONS:")</code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#reaction_count_line" class="summary-name">reaction_count_line</a> = <code title="Group("reaction_count_line", reaction_count_tag+ blank_space+ Digits("\
num_reactions")+ ToEol())">Group("reaction_count_line", reaction_co<code class="variable-ellipsis">...</code></code>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#type_metabolite" class="summary-name">type_metabolite</a> = <code title="Group("type_metabolite", Alt(Str("int"), Str("external")))">Group("type_metabolite", Alt(Str("int"), Str<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#metabolite_info" class="summary-name">metabolite_info</a> = <code title="Group("metabolite_info", optional_blank_space+ Digits()+ blank_space+ \
type_metabolite+ blank_space+ Rep1(AnyBut(white_space)))">Group("metabolite_info", optional_blank_spac<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#metabolite_line" class="summary-name">metabolite_line</a> = <code title="Group("metabolite_line", metabolite_info+ ToEol())">Group("metabolite_line", metabolite_info+ To<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#metabolites_summary" class="summary-name">metabolites_summary</a> = <code title="Group("metabolites_summary", optional_blank_space+ Digits()+ blank_spa\
ce+ Str("metabolites")+ ToEol())">Group("metabolites_summary", optional_bl<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#metabolites_block" class="summary-name">metabolites_block</a> = <code title="Group("metabolites_block", Rep1(metabolite_line)+ metabolites_summary+\
Rep(blank_line))">Group("metabolites_block", Rep1(metabolite<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#graph_structure_heading" class="summary-name">graph_structure_heading</a> = <code title="Group("graph_structure_heading", optional_blank_space+ Str("edges")+ b\
lank_space+ Str("frequency of nodes")+ ToEol())">Group("graph_structure_heading", opt<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#graph_structure_line" class="summary-name">graph_structure_line</a> = <code title="Group("graph_structure_line", optional_blank_space+ Digits("edge_count\
")+ blank_space+ Digits("num_nodes")+ ToEol())">Group("graph_structure_line", optional_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#graph_structure_block" class="summary-name">graph_structure_block</a> = <code title="Group("graph_structure_block", graph_structure_heading+ Rep(blank_line\
)+ Rep1(graph_structure_line)+ Rep(blank_line))">Group("graph_structure_block", graph_s<code class="variable-ellipsis">...</code></code>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#sum_is_constant_line" class="summary-name">sum_is_constant_line</a> = <code title="Group("sum_is_constant_line", optional_blank_space+ Digits()+ optional\
_blank_space+ Any(":")+ optional_blank_space+ Rep1(AnyBut(white_space)\
)+ Rep(blank_space+ Any("+")+ blank_space+ Rep1(AnyBut(white_space)))+\
optional_blank_space+ Str("=")+ ToEol())">Group("sum_is_constant_line", optional_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#sum_is_constant_block" class="summary-name">sum_is_constant_block</a> = <code title="Group("sum_is_constant_block", Rep(sum_is_constant_line))">Group("sum_is_constant_block", Rep(sum<code class="variable-ellipsis">...</code></code>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#stoichiometric_tag" class="summary-name">stoichiometric_tag</a> = <code title="Group("stoichiometric_tag", Str("STOICHIOMETRIC MATRIX"))">Group("stoichiometric_tag", Str("STOICHIO<code class="variable-ellipsis">...</code></code>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#stoichiometric_line" class="summary-name">stoichiometric_line</a> = <code title="Group("stoichiometric_line", stoichiometric_tag+ ToEol())">Group("stoichiometric_line", stoichiomet<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#not_balanced_tag" class="summary-name">not_balanced_tag</a> = <code title="Group("not_balanced_tag", Str("NOT BALANCED INTERNAL METABOLITES"))">Group("not_balanced_tag", Str("NOT BALANCED<code class="variable-ellipsis">...</code></code>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#not_balanced_line" class="summary-name">not_balanced_line</a> = <code title="Group("not_balanced_line", not_balanced_tag+ ToEol())">Group("not_balanced_line", not_balanced_ta<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="subsets_tag"></a><span class="summary-name">subsets_tag</span> = <code title="Group("subsets_tag", Str("SUBSETS OF REACTIONS"))">Group("subsets_tag", Str("SUBSETS OF REACTIONS"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="subsets_line"></a><span class="summary-name">subsets_line</span> = <code title="Group("subsets_line", subsets_tag+ ToEol())">Group("subsets_line", subsets_tag+ ToEol())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#reduced_system_tag" class="summary-name">reduced_system_tag</a> = <code title="Group("reduced_system_tag", Str("REDUCED SYSTEM"))">Group("reduced_system_tag", Str("REDUCED <code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#reduced_system_line" class="summary-name">reduced_system_line</a> = <code title="Group("reduced_system_line", reduced_system_tag+ Rep1(AnyBut(digits))+\
Digits("branch_points")+ Rep1(AnyBut(digits))+ Digits()+ ToEol())">Group("reduced_system_line", reduced_sys<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="kernel_tag"></a><span class="summary-name">kernel_tag</span> = <code title="Group("kernel_tag", Str("KERNEL"))">Group("kernel_tag", Str("KERNEL"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="kernel_line"></a><span class="summary-name">kernel_line</span> = <code title="Group("kernel_line", kernel_tag+ ToEol())">Group("kernel_line", kernel_tag+ ToEol())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="convex_basis_tag"></a><span class="summary-name">convex_basis_tag</span> = <code title="Group("convex_basis_tag", Str("CONVEX BASIS"))">Group("convex_basis_tag", Str("CONVEX BASIS"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#convex_basis_line" class="summary-name">convex_basis_line</a> = <code title="Group("convex_basis_line", convex_basis_tag+ ToEol())">Group("convex_basis_line", convex_basis_ta<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#conservation_relations_tag" class="summary-name">conservation_relations_tag</a> = <code title="Group("conservation_relations_tag", Str("CONSERVATION RELATIONS"))">Group("conservation_relations_tag<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#conservation_relations_line" class="summary-name">conservation_relations_line</a> = <code title="Group("conservation_relations_line", conservation_relations_tag+ ToEol\
())">Group("conservation_relations_li<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#elementary_modes_tag" class="summary-name">elementary_modes_tag</a> = <code title="Group("elementary_modes_tag", Str("ELEMENTARY MODES"))">Group("elementary_modes_tag", Str("ELEM<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#elementary_modes_line" class="summary-name">elementary_modes_line</a> = <code title="Group("elementary_modes_line", elementary_modes_tag+ ToEol())">Group("elementary_modes_line", element<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="num_rows"></a><span class="summary-name">num_rows</span> = <code title="Group("num_rows", Digits())">Group("num_rows", Digits())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="num_cols"></a><span class="summary-name">num_cols</span> = <code title="Group("num_cols", Digits())">Group("num_cols", Digits())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#matrix_header" class="summary-name">matrix_header</a> = <code title="Group("matrix_header", optional_blank_space+ Str("matrix dimension")+ \
blank_space+ Any("r")+ num_rows+ blank_space+ Any("x")+ blank_space+ A\
ny("c")+ num_cols+ optional_blank_space+ AnyEol())">Group("matrix_header", optional_blank_space+ S<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="matrix_element"></a><span class="summary-name">matrix_element</span> = <code title="Group("matrix_element", Integer())">Group("matrix_element", Integer())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#matrix_row" class="summary-name">matrix_row</a> = <code title="Group("matrix_row", MaxRepeat(optional_blank_space+ matrix_element, "n\
um_cols", "num_cols")+ ToEol())">Group("matrix_row", MaxRepeat(optional_blank_spac<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#matrix" class="summary-name">matrix</a> = <code title="Group("matrix", MaxRepeat(matrix_row, "num_rows", "num_rows"))">Group("matrix", MaxRepeat(matrix_row, "num_rows", "nu<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="matrix_block"></a><span class="summary-name">matrix_block</span> = <code title="Group("matrix_block", matrix_header+ matrix)">Group("matrix_block", matrix_header+ matrix)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#irreversible_vector" class="summary-name">irreversible_vector</a> = <code title="Group("irreversible_vector", MaxRepeat(blank_space+ matrix_element, "n\
um_cols", "num_cols")+ ToEol())">Group("irreversible_vector", MaxRepeat(b<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="little_gap"></a><span class="summary-name">little_gap</span> = <code title="Str(" ")">Str(" ")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="big_gap"></a><span class="summary-name">big_gap</span> = <code title="Alt(Str("\t"), MaxRepeat(Str(" "), 2, 80))">Alt(Str("\t"), MaxRepeat(Str(" "), 2, 80))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#unbalanced_metabolite" class="summary-name">unbalanced_metabolite</a> = <code title="Group("unbalanced_metabolite", Rep1(AnyBut(white_space))+ Opt(little_g\
ap+ Rep1(AnyBut(white_space))))">Group("unbalanced_metabolite", Rep1(An<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#not_balanced_data" class="summary-name">not_balanced_data</a> = <code title="Group("not_balanced_data", optional_blank_space+ unbalanced_metabolite\
+ Rep(big_gap+ unbalanced_metabolite)+ ToEol())">Group("not_balanced_data", optional_blank_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#metabolite_roles_heading" class="summary-name">metabolite_roles_heading</a> = <code title="Group("metabolite_roles_heading", Str("->")+ ToEol())">Group("metabolite_roles_heading", S<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#metabolite_role_cols" class="summary-name">metabolite_role_cols</a> = <code title="Group("metabolite_role_cols", optional_blank_space+ Str("met")+ blank_\
space+ Str("cons")+ blank_space+ Str("built")+ blank_space+ Str("react\
ions")+ ToEol())">Group("metabolite_role_cols", optional_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#branch_metabolite" class="summary-name">branch_metabolite</a> = <code title="Group("branch_metabolite", optional_blank_space+ Rep1(AnyBut(white_spa\
ce))+ blank_space+ RepN(Digits()+ blank_space, 3)+ Rep1(Any("ir"))+ To\
Eol())">Group("branch_metabolite", optional_blank_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#non_branch_metabolite" class="summary-name">non_branch_metabolite</a> = <code title="Group("non_branch_metabolite", optional_blank_space+ Rep1(AnyBut(white\
_space))+ blank_space+ RepN(Digits()+ blank_space, 3)+ Rep1(Any("ir"))\
+ ToEol())">Group("non_branch_metabolite", optiona<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#branch_metabolite_block" class="summary-name">branch_metabolite_block</a> = <code title="Group("branch_metabolite_block", metabolite_roles_heading+ metabolite_\
role_cols+ Rep(branch_metabolite))">Group("branch_metabolite_block", met<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#non_branch_metabolite_block" class="summary-name">non_branch_metabolite_block</a> = <code title="Group("non_branch_metabolite_block", metabolite_roles_heading+ metabol\
ite_role_cols+ Rep(non_branch_metabolite))">Group("non_branch_metabolite_blo<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#end_stoichiometric" class="summary-name">end_stoichiometric</a> = <code title="Group("end_stochiometric", Rep(Expression.Assert(not_balanced_tag, 1)+\
Expression.Assert(kernel_tag, 1)+ ToEol()))">Group("end_stochiometric", Rep(Expression<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#end_not_balanced" class="summary-name">end_not_balanced</a> = <code title="Group("end_not_balanced", Rep(Expression.Assert(kernel_tag, 1)+ ToEol(\
)))">Group("end_not_balanced", Rep(Expression.As<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#end_kernel" class="summary-name">end_kernel</a> = <code title="Group("end_kernel", Rep(Expression.Assert(subsets_tag, 1)+ ToEol()))">Group("end_kernel", Rep(Expression.Assert(subsets<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#end_subsets" class="summary-name">end_subsets</a> = <code title="Group("end_subsets", Rep(Expression.Assert(reduced_system_tag, 1)+ ToE\
ol()))">Group("end_subsets", Rep(Expression.Assert(reduc<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#end_reduced_system" class="summary-name">end_reduced_system</a> = <code title="Group("end_reduced_system", Rep(Expression.Assert(convex_basis_tag, 1)\
+ ToEol()))">Group("end_reduced_system", Rep(Expressio<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#end_convex_basis" class="summary-name">end_convex_basis</a> = <code title="Group("end_convex_basis", Rep(Expression.Assert(conservation_relations\
_tag, 1)+ ToEol()))">Group("end_convex_basis", Rep(Expression.As<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#end_conservation_relations" class="summary-name">end_conservation_relations</a> = <code title="Group("end_conservation_relations", Rep(Expression.Assert(elementary_m\
odes_tag, 1)+ ToEol()))">Group("end_conservation_relations<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#end_elementary_modes" class="summary-name">end_elementary_modes</a> = <code title="Group("end_elementary_modes", Rep(ToEol()))">Group("end_elementary_modes", Rep(ToEol<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#input_file_block" class="summary-name">input_file_block</a> = <code title="Group("input_file_block", input_file_line+ Rep(blank_line))">Group("input_file_block", input_file_line+ <code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#metatool_block" class="summary-name">metatool_block</a> = <code title="Group("metatool_block", metatool_line+ Rep1(blank_line))">Group("metatool_block", metatool_line+ Rep1(b<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#metabolite_count_block" class="summary-name">metabolite_count_block</a> = <code title="Group("metabolite_count_block", metabolite_count_line+ Rep(blank_line)\
)">Group("metabolite_count_block", metab<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#reaction_count_block" class="summary-name">reaction_count_block</a> = <code title="Group("reaction_count_block", reaction_count_line+ Rep(blank_line)+ me\
tabolites_block+ Rep(blank_line)+ graph_structure_block+ Rep(blank_lin\
e))">Group("reaction_count_block", reaction_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#stoichiometric_block" class="summary-name">stoichiometric_block</a> = <code title="Group("stoichiometric_block", stoichiometric_line+ Rep(blank_line)+ ma\
trix_block+ ToEol()+ irreversible_vector+ end_stoichiometric)">Group("stoichiometric_block", stoichiom<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#not_balanced_block" class="summary-name">not_balanced_block</a> = <code title="Group("not_balanced_block", not_balanced_line+ Rep(blank_line)+ not_ba\
lanced_data+ Rep(blank_line))">Group("not_balanced_block", not_balanced_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#kernel_block" class="summary-name">kernel_block</a> = <code title="Group("kernel_block", kernel_line+ Rep(blank_line)+ matrix_block+ ToEo\
l()+ Rep(blank_line)+ enzymes_block+ Rep(blank_line)+ reactions_block+\
end_kernel)">Group("kernel_block", kernel_line+ Rep(blank_li<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#subsets_block" class="summary-name">subsets_block</a> = <code title="Group("subsets_block", subsets_line+ Rep(blank_line)+ matrix_block+ To\
Eol()+ Rep(blank_line)+ enzymes_block+ Rep(blank_line)+ reactions_bloc\
k+ end_subsets)">Group("subsets_block", subsets_line+ Rep(blank<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#reduced_system_block" class="summary-name">reduced_system_block</a> = <code title="Group("reduced_system_block", reduced_system_line+ Rep(blank_line)+ ma\
trix_block+ ToEol()+ irreversible_vector+ Rep(blank_line)+ branch_meta\
bolite_block+ Rep(blank_line)+ non_branch_metabolite_block+ end_reduce\
d_system)">Group("reduced_system_block", reduced_s<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#convex_basis_block" class="summary-name">convex_basis_block</a> = <code title="Group("convex_basis_block", convex_basis_line+ Rep(blank_line)+ matrix\
_block+ Opt(ToEol())+ Rep(blank_line)+ enzymes_block+ Rep(blank_line)+\
reactions_block+ end_convex_basis)">Group("convex_basis_block", convex_basis_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#conservation_relations_block" class="summary-name">conservation_relations_block</a> = <code title="Group("conservation_relations_block", conservation_relations_line+ Rep\
(blank_line)+ matrix_block+ Rep(blank_line)+ sum_is_constant_block+ en\
d_conservation_relations)">Group("conservation_relations_b<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#elementary_modes_block" class="summary-name">elementary_modes_block</a> = <code title="Group("elementary_modes_block", elementary_modes_line+ Rep(blank_line)\
+ matrix_block+ Opt(ToEol())+ Rep(blank_line)+ enzymes_block+ Rep(blan\
k_line)+ reactions_block+ end_elementary_modes)">Group("elementary_modes_block", eleme<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MetaTool.metatool_format-module.html#metatool_record" class="summary-name">metatool_record</a> = <code title="Group("metatool_record", metatool_block+ input_file_block+ metabolite_\
count_block+ reaction_count_block+ stoichiometric_block+ Opt(not_balan\
ced_block)+ kernel_block+ subsets_block+ reduced_system_block+ convex_\
basis_block+ conservation_relations_block+ elementary_modes_block)">Group("metatool_record", metatool_block+ inp<code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
<table class="details" 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">Variables Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="lower_case_letter"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">lower_case_letter</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("lower_case_letter", Any("abcdefghijklmnopqrstuvwxyz"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="enzyme"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">enzyme</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("enzyme", optional_blank_space+ Digits()+ optional_blank_space+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Str(':')+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reaction"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reaction</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reaction", optional_blank_space+ Digits()+ optional_blank_space<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ Str(":")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="not_found_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">not_found_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("not_found_line", optional_blank_space+ Str("- not found -")+ To<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Eol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="enzymes_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">enzymes_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("enzymes_header", optional_blank_space+ Str("enzymes")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="enzymes_list"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">enzymes_list</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("enzymes_list", Alt(Rep1(enzyme), not_found_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="enzymes_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">enzymes_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("enzymes_block", enzymes_header+ Rep(blank_line)+ enzymes_list)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reactions_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reactions_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reactions_header", optional_blank_space+ Str("overall reaction"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reactions_list"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reactions_list</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reactions_list", Alt(Rep1(reaction), not_found_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reactions_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reactions_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reactions_block", reactions_header+ Rep(blank_line)+ reactions_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
list)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="version"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">version</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("version", Digits("version_major")+ Any(".")+ Digits("version_mi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
nor")+ rev)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metatool_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metatool_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metatool_line", metatool_tag+ blank_space+ Str("Version")+ blan<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
k_space+ version+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="input_file_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">input_file_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("input_file_line", input_file_tag+ blank_space+ ToEol("input_fil<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
e_name"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metabolite_count_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metabolite_count_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metabolite_count_line", metabolite_count_tag+ blank_space+ Digi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ts("num_int_metabolites")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reaction_count_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reaction_count_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reaction_count_line", reaction_count_tag+ blank_space+ Digits("<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
num_reactions")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="type_metabolite"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">type_metabolite</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("type_metabolite", Alt(Str("int"), Str("external")))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metabolite_info"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metabolite_info</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metabolite_info", optional_blank_space+ Digits()+ blank_space+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
type_metabolite+ blank_space+ Rep1(AnyBut(white_space)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metabolite_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metabolite_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metabolite_line", metabolite_info+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metabolites_summary"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metabolites_summary</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metabolites_summary", optional_blank_space+ Digits()+ blank_spa<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ce+ Str("metabolites")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metabolites_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metabolites_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metabolites_block", Rep1(metabolite_line)+ metabolites_summary+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Rep(blank_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="graph_structure_heading"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">graph_structure_heading</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("graph_structure_heading", optional_blank_space+ Str("edges")+ b<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
lank_space+ Str("frequency of nodes")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="graph_structure_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">graph_structure_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("graph_structure_line", optional_blank_space+ Digits("edge_count<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
")+ blank_space+ Digits("num_nodes")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="graph_structure_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">graph_structure_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("graph_structure_block", graph_structure_heading+ Rep(blank_line<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Rep1(graph_structure_line)+ Rep(blank_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="sum_is_constant_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">sum_is_constant_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("sum_is_constant_line", optional_blank_space+ Digits()+ optional<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_blank_space+ Any(":")+ optional_blank_space+ Rep1(AnyBut(white_space)<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Rep(blank_space+ Any("+")+ blank_space+ Rep1(AnyBut(white_space)))+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
optional_blank_space+ Str("=")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="sum_is_constant_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">sum_is_constant_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("sum_is_constant_block", Rep(sum_is_constant_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="stoichiometric_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">stoichiometric_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("stoichiometric_tag", Str("STOICHIOMETRIC MATRIX"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="stoichiometric_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">stoichiometric_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("stoichiometric_line", stoichiometric_tag+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="not_balanced_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">not_balanced_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("not_balanced_tag", Str("NOT BALANCED INTERNAL METABOLITES"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="not_balanced_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">not_balanced_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("not_balanced_line", not_balanced_tag+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reduced_system_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reduced_system_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reduced_system_tag", Str("REDUCED SYSTEM"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reduced_system_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reduced_system_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reduced_system_line", reduced_system_tag+ Rep1(AnyBut(digits))+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Digits("branch_points")+ Rep1(AnyBut(digits))+ Digits()+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="convex_basis_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">convex_basis_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("convex_basis_line", convex_basis_tag+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="conservation_relations_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">conservation_relations_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("conservation_relations_tag", Str("CONSERVATION RELATIONS"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="conservation_relations_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">conservation_relations_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("conservation_relations_line", conservation_relations_tag+ ToEol<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="elementary_modes_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">elementary_modes_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("elementary_modes_tag", Str("ELEMENTARY MODES"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="elementary_modes_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">elementary_modes_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("elementary_modes_line", elementary_modes_tag+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="matrix_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">matrix_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("matrix_header", optional_blank_space+ Str("matrix dimension")+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
blank_space+ Any("r")+ num_rows+ blank_space+ Any("x")+ blank_space+ A<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ny("c")+ num_cols+ optional_blank_space+ AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="matrix_row"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">matrix_row</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("matrix_row", MaxRepeat(optional_blank_space+ matrix_element, "n<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
um_cols", "num_cols")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="matrix"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">matrix</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("matrix", MaxRepeat(matrix_row, "num_rows", "num_rows"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="irreversible_vector"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">irreversible_vector</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("irreversible_vector", MaxRepeat(blank_space+ matrix_element, "n<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
um_cols", "num_cols")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="unbalanced_metabolite"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">unbalanced_metabolite</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("unbalanced_metabolite", Rep1(AnyBut(white_space))+ Opt(little_g<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ap+ Rep1(AnyBut(white_space))))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="not_balanced_data"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">not_balanced_data</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("not_balanced_data", optional_blank_space+ unbalanced_metabolite<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ Rep(big_gap+ unbalanced_metabolite)+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metabolite_roles_heading"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metabolite_roles_heading</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metabolite_roles_heading", Str("->")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metabolite_role_cols"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metabolite_role_cols</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metabolite_role_cols", optional_blank_space+ Str("met")+ blank_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
space+ Str("cons")+ blank_space+ Str("built")+ blank_space+ Str("react<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ions")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="branch_metabolite"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">branch_metabolite</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("branch_metabolite", optional_blank_space+ Rep1(AnyBut(white_spa<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ce))+ blank_space+ RepN(Digits()+ blank_space, 3)+ Rep1(Any("ir"))+ To<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Eol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="non_branch_metabolite"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">non_branch_metabolite</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("non_branch_metabolite", optional_blank_space+ Rep1(AnyBut(white<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_space))+ blank_space+ RepN(Digits()+ blank_space, 3)+ Rep1(Any("ir"))<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="branch_metabolite_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">branch_metabolite_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("branch_metabolite_block", metabolite_roles_heading+ metabolite_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
role_cols+ Rep(branch_metabolite))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="non_branch_metabolite_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">non_branch_metabolite_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("non_branch_metabolite_block", metabolite_roles_heading+ metabol<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ite_role_cols+ Rep(non_branch_metabolite))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="end_stoichiometric"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">end_stoichiometric</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("end_stochiometric", Rep(Expression.Assert(not_balanced_tag, 1)+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Expression.Assert(kernel_tag, 1)+ ToEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="end_not_balanced"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">end_not_balanced</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("end_not_balanced", Rep(Expression.Assert(kernel_tag, 1)+ ToEol(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="end_kernel"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">end_kernel</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("end_kernel", Rep(Expression.Assert(subsets_tag, 1)+ ToEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="end_subsets"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">end_subsets</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("end_subsets", Rep(Expression.Assert(reduced_system_tag, 1)+ ToE<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="end_reduced_system"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">end_reduced_system</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("end_reduced_system", Rep(Expression.Assert(convex_basis_tag, 1)<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ ToEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="end_convex_basis"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">end_convex_basis</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("end_convex_basis", Rep(Expression.Assert(conservation_relations<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_tag, 1)+ ToEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="end_conservation_relations"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">end_conservation_relations</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("end_conservation_relations", Rep(Expression.Assert(elementary_m<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
odes_tag, 1)+ ToEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="end_elementary_modes"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">end_elementary_modes</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("end_elementary_modes", Rep(ToEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="input_file_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">input_file_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("input_file_block", input_file_line+ Rep(blank_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metatool_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metatool_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metatool_block", metatool_line+ Rep1(blank_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metabolite_count_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metabolite_count_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metabolite_count_block", metabolite_count_line+ Rep(blank_line)<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reaction_count_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reaction_count_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reaction_count_block", reaction_count_line+ Rep(blank_line)+ me<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tabolites_block+ Rep(blank_line)+ graph_structure_block+ Rep(blank_lin<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
e))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="stoichiometric_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">stoichiometric_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("stoichiometric_block", stoichiometric_line+ Rep(blank_line)+ ma<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
trix_block+ ToEol()+ irreversible_vector+ end_stoichiometric)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="not_balanced_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">not_balanced_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("not_balanced_block", not_balanced_line+ Rep(blank_line)+ not_ba<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
lanced_data+ Rep(blank_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="kernel_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">kernel_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("kernel_block", kernel_line+ Rep(blank_line)+ matrix_block+ ToEo<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
l()+ Rep(blank_line)+ enzymes_block+ Rep(blank_line)+ reactions_block+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
end_kernel)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="subsets_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">subsets_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("subsets_block", subsets_line+ Rep(blank_line)+ matrix_block+ To<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Eol()+ Rep(blank_line)+ enzymes_block+ Rep(blank_line)+ reactions_bloc<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
k+ end_subsets)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reduced_system_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reduced_system_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reduced_system_block", reduced_system_line+ Rep(blank_line)+ ma<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
trix_block+ ToEol()+ irreversible_vector+ Rep(blank_line)+ branch_meta<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
bolite_block+ Rep(blank_line)+ non_branch_metabolite_block+ end_reduce<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
d_system)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="convex_basis_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">convex_basis_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("convex_basis_block", convex_basis_line+ Rep(blank_line)+ matrix<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_block+ Opt(ToEol())+ Rep(blank_line)+ enzymes_block+ Rep(blank_line)+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
reactions_block+ end_convex_basis)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="conservation_relations_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">conservation_relations_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("conservation_relations_block", conservation_relations_line+ Rep<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
(blank_line)+ matrix_block+ Rep(blank_line)+ sum_is_constant_block+ en<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
d_conservation_relations)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="elementary_modes_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">elementary_modes_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("elementary_modes_block", elementary_modes_line+ Rep(blank_line)<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ matrix_block+ Opt(ToEol())+ Rep(blank_line)+ enzymes_block+ Rep(blan<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
k_line)+ reactions_block+ end_elementary_modes)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="metatool_record"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">metatool_record</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("metatool_record", metatool_block+ input_file_block+ metabolite_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
count_block+ reaction_count_block+ stoichiometric_block+ Opt(not_balan<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ced_block)+ kernel_block+ subsets_block+ reduced_system_block+ convex_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
basis_block+ conservation_relations_block+ elementary_modes_block)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
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