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<div class="title">kekulize.cpp File Reference</div> </div>
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<div class="textblock"><code>#include <openbabel/babelconfig.h></code><br/>
<code>#include <<a class="el" href="mol_8h_source.shtml">openbabel/mol.h</a>></code><br/>
<code>#include <<a class="el" href="ring_8h_source.shtml">openbabel/ring.h</a>></code><br/>
<code>#include <<a class="el" href="obiter_8h_source.shtml">openbabel/obiter.h</a>></code><br/>
<code>#include <<a class="el" href="graphsym_8h_source.shtml">openbabel/graphsym.h</a>></code><br/>
<code>#include <sstream></code><br/>
</div><table class="memberdecls">
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Namespaces</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">namespace  </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml">OpenBabel</a></td></tr>
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Defines</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#ad72dbcf6d0153db1b8d8a58001feed83">DEBUG</a>   0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#a5320d4457a472d8888ec1905bc0e0a1c">MAX_TIME</a>   15</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#a5db49eeef5c9bb774f02996f684df238">MAX_DEPTH</a>   30</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#a7f2a734b84f750bb35708fd8f3d0121e">UNASSIGNED</a>   0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#aae597f206a8cf88b5a0593f39044b937">SINGLE</a>   1</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#a8747af38b86aa2bbcda2f1b1aa0888c2">DOUBLE</a>   2</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#a4e255ac95eebc3646108368c9b37546c">NOT_IN_RINGS</a>   -1</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#a774312b4b8c69831cdf734226146616d">DOUBLE_ASSIGNED</a>   0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#a56355ba5602b88bd129ca59e54bc28fa">DOUBLE_ALLOWED</a>   1</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="kekulize_8cpp.shtml#a5fb1e2d33a402297814dcd0905e27d46">DOUBLE_PROHIBITED</a>   2</td></tr>
<tr><td colspan="2"><h2><a name="func-members"></a>
Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#a31ce8b089ca36508940585406a2f93f1">expand_cycle</a> (OBMol *mol, OBAtom *atom, OBBitVec &avisit, OBBitVec &cvisit, const OBBitVec &potAromBonds, int rootIdx, Timeout &timeout, int prevAtomIdx, int depth)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#a62de79552e98ffdb88a9b8509a705158">expandKekulize</a> (OBMol *mol, int bond_idx, std::vector< int > &atomState, std::vector< int > &bondState, Timeout &timeout)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#a9645071cedc98dac304402a63e32d700">expand_kekulize_lssr</a> (OBMol *mol, std::vector< int > &atomState, std::vector< int > &bondState, std::vector< OBRing * > &lssr, std::vector< bool > &lssrAssigned, std::vector< OBBond * > &bondsThisRing)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#a8a423a9a023698abe77ee30550619f54">count_assigned_bonds</a> (std::vector< OBBond * > &bondsThisRing, std::vector< int > &bondState)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#a7b44d43b56950aff23fbca88664ad996">isPotentialAromaticAtom</a> (OBAtom *atom)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#a7e62ffcac6073c5fb792d2f5bc62c522">potentialAromaticBonds</a> (OBMol *mol, OBBitVec &bonds)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#adbf96b6f2307d00a5f525ecc3a4c5bca">get_bonds_of_ring</a> (OBMol *mol, OBRing *ring, std::vector< OBBond * > &ring_bonds)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#a67f559671aa9d68ce3888baab8f7fc1a">has_leftover_electrons</a> (OBMol *mol, std::vector< int > &atomState)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#a07faa5acbed4a3cbbfd0d711321c0439">has_leftover_electrons</a> (OBMol *mol, std::vector< int > &atomState, std::vector< int > &bondState)</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Alternate algorithm to kekulize a molecule (OBMol::NewPerceiveKekuleBonds()). </p>
</div><hr/><h2>Define Documentation</h2>
<a class="anchor" id="ad72dbcf6d0153db1b8d8a58001feed83"></a><!-- doxytag: member="kekulize.cpp::DEBUG" ref="ad72dbcf6d0153db1b8d8a58001feed83" args="" -->
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<td class="memname">#define DEBUG   0</td>
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<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a31ce8b089ca36508940585406a2f93f1">OpenBabel::expand_cycle()</a>, <a class="el" href="namespaceOpenBabel.shtml#a9645071cedc98dac304402a63e32d700">OpenBabel::expand_kekulize_lssr()</a>, <a class="el" href="namespaceOpenBabel.shtml#a62de79552e98ffdb88a9b8509a705158">OpenBabel::expandKekulize()</a>, <a class="el" href="namespaceOpenBabel.shtml#a67f559671aa9d68ce3888baab8f7fc1a">OpenBabel::has_leftover_electrons()</a>, <a class="el" href="classOpenBabel_1_1OBMol.shtml#ab74a82552a9576514b189e2a265d5f5a">OBMol::NewPerceiveKekuleBonds()</a>, and <a class="el" href="classOpenBabel_1_1OBMol.shtml#a6d03ef3f811fa2c085694ccbf76051d4">OBMol::start_kekulize()</a>.</p>
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<a class="anchor" id="a5320d4457a472d8888ec1905bc0e0a1c"></a><!-- doxytag: member="kekulize.cpp::MAX_TIME" ref="a5320d4457a472d8888ec1905bc0e0a1c" args="" -->
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<td class="memname">#define MAX_TIME   15</td>
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<div class="memdoc">
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBMol.shtml#a6be250d574bdbcae500c9207cb0f2400">OBMol::expand_kekulize()</a>, <a class="el" href="classOpenBabel_1_1OBMol.shtml#ab74a82552a9576514b189e2a265d5f5a">OBMol::NewPerceiveKekuleBonds()</a>, and <a class="el" href="classOpenBabel_1_1OBMol.shtml#a6d03ef3f811fa2c085694ccbf76051d4">OBMol::start_kekulize()</a>.</p>
</div>
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<a class="anchor" id="a5db49eeef5c9bb774f02996f684df238"></a><!-- doxytag: member="kekulize.cpp::MAX_DEPTH" ref="a5db49eeef5c9bb774f02996f684df238" args="" -->
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<td class="memname">#define MAX_DEPTH   30</td>
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<a class="anchor" id="a7f2a734b84f750bb35708fd8f3d0121e"></a><!-- doxytag: member="kekulize.cpp::UNASSIGNED" ref="a7f2a734b84f750bb35708fd8f3d0121e" args="" -->
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<td class="memname">#define UNASSIGNED   0</td>
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<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a8a423a9a023698abe77ee30550619f54">OpenBabel::count_assigned_bonds()</a>, <a class="el" href="namespaceOpenBabel.shtml#a9645071cedc98dac304402a63e32d700">OpenBabel::expand_kekulize_lssr()</a>, and <a class="el" href="namespaceOpenBabel.shtml#a07faa5acbed4a3cbbfd0d711321c0439">OpenBabel::has_leftover_electrons()</a>.</p>
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</div>
<a class="anchor" id="aae597f206a8cf88b5a0593f39044b937"></a><!-- doxytag: member="kekulize.cpp::SINGLE" ref="aae597f206a8cf88b5a0593f39044b937" args="" -->
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<td class="memname">#define SINGLE   1</td>
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<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a9645071cedc98dac304402a63e32d700">OpenBabel::expand_kekulize_lssr()</a>, and <a class="el" href="classOpenBabel_1_1OBMol.shtml#a6d03ef3f811fa2c085694ccbf76051d4">OBMol::start_kekulize()</a>.</p>
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<a class="anchor" id="a8747af38b86aa2bbcda2f1b1aa0888c2"></a><!-- doxytag: member="kekulize.cpp::DOUBLE" ref="a8747af38b86aa2bbcda2f1b1aa0888c2" args="" -->
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<td class="memname">#define DOUBLE   2</td>
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<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a9645071cedc98dac304402a63e32d700">OpenBabel::expand_kekulize_lssr()</a>, <a class="el" href="namespaceOpenBabel.shtml#a62de79552e98ffdb88a9b8509a705158">OpenBabel::expandKekulize()</a>, and <a class="el" href="classOpenBabel_1_1OBMol.shtml#a6d03ef3f811fa2c085694ccbf76051d4">OBMol::start_kekulize()</a>.</p>
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<a class="anchor" id="a4e255ac95eebc3646108368c9b37546c"></a><!-- doxytag: member="kekulize.cpp::NOT_IN_RINGS" ref="a4e255ac95eebc3646108368c9b37546c" args="" -->
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<td class="memname">#define NOT_IN_RINGS   -1</td>
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<div class="memdoc">
<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a62de79552e98ffdb88a9b8509a705158">OpenBabel::expandKekulize()</a>, <a class="el" href="namespaceOpenBabel.shtml#a07faa5acbed4a3cbbfd0d711321c0439">OpenBabel::has_leftover_electrons()</a>, and <a class="el" href="classOpenBabel_1_1OBMol.shtml#a6d03ef3f811fa2c085694ccbf76051d4">OBMol::start_kekulize()</a>.</p>
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<a class="anchor" id="a774312b4b8c69831cdf734226146616d"></a><!-- doxytag: member="kekulize.cpp::DOUBLE_ASSIGNED" ref="a774312b4b8c69831cdf734226146616d" args="" -->
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<td class="memname">#define DOUBLE_ASSIGNED   0</td>
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<div class="memdoc">
<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a9645071cedc98dac304402a63e32d700">OpenBabel::expand_kekulize_lssr()</a>, and <a class="el" href="namespaceOpenBabel.shtml#a62de79552e98ffdb88a9b8509a705158">OpenBabel::expandKekulize()</a>.</p>
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<a class="anchor" id="a56355ba5602b88bd129ca59e54bc28fa"></a><!-- doxytag: member="kekulize.cpp::DOUBLE_ALLOWED" ref="a56355ba5602b88bd129ca59e54bc28fa" args="" -->
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<td class="memname">#define DOUBLE_ALLOWED   1</td>
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<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a9645071cedc98dac304402a63e32d700">OpenBabel::expand_kekulize_lssr()</a>, <a class="el" href="namespaceOpenBabel.shtml#a62de79552e98ffdb88a9b8509a705158">OpenBabel::expandKekulize()</a>, <a class="el" href="namespaceOpenBabel.shtml#a67f559671aa9d68ce3888baab8f7fc1a">OpenBabel::has_leftover_electrons()</a>, and <a class="el" href="classOpenBabel_1_1OBMol.shtml#a6d03ef3f811fa2c085694ccbf76051d4">OBMol::start_kekulize()</a>.</p>
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<a class="anchor" id="a5fb1e2d33a402297814dcd0905e27d46"></a><!-- doxytag: member="kekulize.cpp::DOUBLE_PROHIBITED" ref="a5fb1e2d33a402297814dcd0905e27d46" args="" -->
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<td class="memname">#define DOUBLE_PROHIBITED   2</td>
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<p>Referenced by <a class="el" href="classOpenBabel_1_1OBMol.shtml#a6d03ef3f811fa2c085694ccbf76051d4">OBMol::start_kekulize()</a>.</p>
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Generated on Thu Oct 13 2011 16:08:08 by <a href="http://www.doxygen.org/"><img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.7.5.1.
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