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<div id="projectname">The Gnome Chemistry Utils
 <span id="projectnumber">0.14.2</span>
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<li class="navelem"><a class="el" href="namespacegcu.html">gcu</a></li><li class="navelem"><a class="el" href="classgcu_1_1Residue.html">Residue</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<p><code>#include <<a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>></code></p>
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Inheritance diagram for gcu::Residue:</div>
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<img src="classgcu_1_1Residue.png" usemap="#gcu::Residue_map" alt=""/>
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<area href="classgcp_1_1Residue.html" title="a GChemPaint specific Residue class." alt="gcp::Residue" shape="rect" coords="0,56,84,80"/>
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<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a72f5130fa5fd589db8a28aca5f90524e"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a72f5130fa5fd589db8a28aca5f90524e">Residue</a> ()</td></tr>
<tr class="memitem:a6e602355c4a19c56d4fadfec20423554"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a6e602355c4a19c56d4fadfec20423554">Residue</a> (char const *name, <a class="el" href="classgcu_1_1Document.html">Document</a> *doc=NULL)</td></tr>
<tr class="memitem:a62b6b69527e5db5bbb70b9fefa64cba8"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a62b6b69527e5db5bbb70b9fefa64cba8">~Residue</a> ()</td></tr>
<tr class="memitem:a1a861fa8e57112b8025fc640b6f885ae"><td class="memItemLeft" align="right" valign="top">std::map< int, int > const & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a1a861fa8e57112b8025fc640b6f885ae">GetRawFormula</a> () const </td></tr>
<tr class="memitem:ad4d8a7d85d659bf901c597fea3793683"><td class="memItemLeft" align="right" valign="top">std::map< std::string, bool ><br class="typebreak"/>
const & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#ad4d8a7d85d659bf901c597fea3793683">GetSymbols</a> () const </td></tr>
<tr class="memitem:a1871b94a8f5bcec18e4ffa38c6f36c1f"><td class="memItemLeft" align="right" valign="top">std::map< std::string, <br class="typebreak"/>
std::string > const & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a1871b94a8f5bcec18e4ffa38c6f36c1f">GetNames</a> () const </td></tr>
<tr class="memitem:ae088f4d7d8c67d2cddfb91b4b6a7ce25"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#ae088f4d7d8c67d2cddfb91b4b6a7ce25">SetName</a> (char const *name)</td></tr>
<tr class="memitem:aec88c7c40f56373bff9a87934d43476b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#aec88c7c40f56373bff9a87934d43476b">AddSymbol</a> (char const *symbol)</td></tr>
<tr class="memitem:a22551d87f7bd3429ab7f9e9b81f91319"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a22551d87f7bd3429ab7f9e9b81f91319">RemoveSymbol</a> (char const *symbol)</td></tr>
<tr class="memitem:a92052b6044adf168b01ae8031e3ba3b9"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a92052b6044adf168b01ae8031e3ba3b9">Load</a> (xmlNodePtr node, <a class="el" href="classgcu_1_1Application.html">Application</a> *app)</td></tr>
<tr class="memitem:ade70b99416f4e0f23ffd84f093f2dd92"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#ade70b99416f4e0f23ffd84f093f2dd92">operator==</a> (G_GNUC_UNUSED <a class="el" href="classgcu_1_1Molecule.html">Molecule</a> const &mol) const </td></tr>
<tr class="memitem:a05cbc14c6089d25d809d39a9d591fdbd"><td class="memItemLeft" align="right" valign="top">char const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a05cbc14c6089d25d809d39a9d591fdbd">GetName</a> (void) const </td></tr>
<tr class="memitem:a3a75e74ef6c8f6816a6d2dd22961c965"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a3a75e74ef6c8f6816a6d2dd22961c965">SetGeneric</a> (bool val)</td></tr>
<tr class="memitem:a6701d1149ed0a02f72ad16c2a33a03fd"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a6701d1149ed0a02f72ad16c2a33a03fd">GetGeneric</a> (void) const </td></tr>
<tr class="memitem:a20f525e567cbdb896447680b7b292c89"><td class="memItemLeft" align="right" valign="top">bool & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a20f525e567cbdb896447680b7b292c89">GetRefGeneric</a> (void)</td></tr>
<tr class="memitem:acc4b9089357090d0cc1c484e5874f775"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Document.html">Document</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#acc4b9089357090d0cc1c484e5874f775">GetDocument</a> (void)</td></tr>
<tr class="memitem:adfd41c037e534060849b2332464a2fdb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Molecule.html">Molecule</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#adfd41c037e534060849b2332464a2fdb">GetMolecule</a> (void)</td></tr>
<tr class="memitem:ad8674695234f709328305da3855b12ae"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Document.html">Document</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#ad8674695234f709328305da3855b12ae">GetOwner</a> (void) const </td></tr>
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<tr class="heading"><td colspan="2"><h2><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:a4591a80941c42c5ce8ca479397b7743c"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classgcu_1_1Residue.html">Residue</a> const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a4591a80941c42c5ce8ca479397b7743c">GetResidue</a> (char const *symbol, bool *ambiguous=NULL)</td></tr>
<tr class="memitem:a09a194c153d5262b378d1c8290325976"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classgcu_1_1Residue.html">Residue</a> const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a09a194c153d5262b378d1c8290325976">GetResiduebyName</a> (char const *name)</td></tr>
<tr class="memitem:afa1a0b80886c8d255deb7d7b10524a7f"><td class="memItemLeft" align="right" valign="top">static std::string const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#afa1a0b80886c8d255deb7d7b10524a7f">GetFirstResidueSymbol</a> (ResidueIterator &i)</td></tr>
<tr class="memitem:aaf275bb0e7b7d6afdda06d2d617c0730"><td class="memItemLeft" align="right" valign="top">static std::string const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#aaf275bb0e7b7d6afdda06d2d617c0730">GetNextResidueSymbol</a> (ResidueIterator &i)</td></tr>
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Static Public Attributes</h2></td></tr>
<tr class="memitem:a052795f0ebd6cd932e42bd50c6f2c412"><td class="memItemLeft" align="right" valign="top">static unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Residue.html#a052795f0ebd6cd932e42bd50c6f2c412">MaxSymbolLength</a></td></tr>
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<a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Represents the meaning of group symbols, such as Me, Ph or Bz. They have one or more associated symbols and a molecule which atoms and bonds are represented by the symbol. The molecule starts from a pseudo-atom with Z = 0, which represents the atom linked to the group. Currently only one pseudo-atom with one single bond to the group is allowed. </p>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00067">67</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
</div><h2>Constructor & Destructor Documentation</h2>
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<p>Creates a residue. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Residue.html#a8abffc8179331a68b93b281e81a64d56">gcp::Residue</a>.</p>
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<td class="memname">gcu::Residue::Residue </td>
<td>(</td>
<td class="paramtype">char const * </td>
<td class="paramname"><em>name</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Document.html">Document</a> * </td>
<td class="paramname"><em>doc</em> = <code>NULL</code> </td>
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<td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">name</td><td>the name of the residue. </td></tr>
<tr><td class="paramname">doc</td><td>the document owning the residue when it does not have global scope.</td></tr>
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<p>Creates a residue and sets its name. </p>
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<td class="memname">virtual gcu::Residue::~Residue </td>
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<p>The destructor. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Residue.html#a553f2f0eae1dc9e67ed224ff4a91e213">gcp::Residue</a>.</p>
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<h2>Member Function Documentation</h2>
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<td class="memname">void gcu::Residue::AddSymbol </td>
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<td class="paramtype">char const * </td>
<td class="paramname"><em>symbol</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">symbol</td><td>a chemical symbol.</td></tr>
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<p>Adds <em>symbol</em> to the list of valid symbols for the atoms group. </p>
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<p>Returns the <a class="el" href="classgcu_1_1Document.html">gcu::Document</a>* used to store the molecule associated with the atoms group. </p>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00209">209</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<td class="memname">static std::string const* gcu::Residue::GetFirstResidueSymbol </td>
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<td class="paramtype">ResidueIterator & </td>
<td class="paramname"><em>i</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">i</td><td>an iterator.</td></tr>
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<p>Used to iterate through all known atoms groups and their symbols. Initializes the iterator. </p>
<dl class="section return"><dt>Returns</dt><dd>the first known symbol. If not NULL, the iterator gives access to the associated <a class="el" href="classgcu_1_1Residue.html">Residue</a> througn a <a class="el" href="structgcu_1_1SymbolResidue.html">gcu::SymbolResidue</a> structure. </dd></dl>
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<dl class="section return"><dt>Returns</dt><dd>whether the symbol is a generic symbol or not. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00204">204</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<p>Returns the <a class="el" href="classgcu_1_1Molecule.html">gcu::Molecule</a>* describing the structure of the atoms group. </p>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00214">214</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>the name of the <a class="el" href="classgcu_1_1Residue.html">Residue</a> instance. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00189">189</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>the names of the atoms group, as a std::map indexed by the correspondig locale. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00111">111</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<td class="paramtype">ResidueIterator & </td>
<td class="paramname"><em>i</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">i</td><td>an iterator initialized by <a class="el" href="classgcu_1_1Residue.html#afa1a0b80886c8d255deb7d7b10524a7f">Residue::GetFirstResidueSymbol</a>.</td></tr>
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<p>Used to iterate through all known atoms groups and their symbols. Initializes the iterator. </p>
<dl class="section return"><dt>Returns</dt><dd>the next known symbol. If not NULL, the iterator gives access to the associated <a class="el" href="classgcu_1_1Residue.html">Residue</a> through a <a class="el" href="structgcu_1_1SymbolResidue.html">gcu::SymbolResidue</a> structure. </dd></dl>
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<td class="memname">gcu::Residue::GetOwner </td>
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<dl class="section return"><dt>Returns</dt><dd>the <a class="el" href="classgcu_1_1Document.html">Document</a> for which the <a class="el" href="classgcu_1_1Residue.html">Residue</a> is valid. If NULL, the <a class="el" href="classgcu_1_1Residue.html">Residue</a> is of global scope. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00219">219</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<td class="memname">std::map<int,int> const& gcu::Residue::GetRawFormula </td>
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<dl class="section return"><dt>Returns</dt><dd>the raw formula of the residue as a map of integers (number of atoms of an element) indexed by the atomic number of the element.</dd></dl>
<p>The following code gives the number of carbon atoms: </p>
<div class="fragment"><div class="line"><a class="code" href="classgcu_1_1Residue.html#a72f5130fa5fd589db8a28aca5f90524e">Residue</a> *residue;</div>
<div class="line">... <span class="comment">// initialize the residue</span></div>
<div class="line">cout << <span class="stringliteral">"the residue has "</span> << residue->GetRawFormula ()[6] << <span class="stringliteral">" carbon atoms."</span> << endl;</div>
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<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00099">99</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<td class="memname">gcu::Residue::GetRefGeneric </td>
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<dl class="section return"><dt>Returns</dt><dd>whether the symbol is a generic symbol or not as a reference to a boolean variable. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00204">204</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<td class="memname">static <a class="el" href="classgcu_1_1Residue.html">Residue</a> const* gcu::Residue::GetResidue </td>
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<td class="paramtype">bool * </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">symbol</td><td>the symbol for which a Residue* is searched. </td></tr>
<tr><td class="paramname">ambiguous</td><td>where to store the boolean telling if the symbol is ambiguous or NULL.</td></tr>
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<dl class="section return"><dt>Returns</dt><dd>the Residue* found or NULL. </dd></dl>
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<td class="memname">static <a class="el" href="classgcu_1_1Residue.html">Residue</a> const* gcu::Residue::GetResiduebyName </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">name</td><td>the name for which a Residue* is searched.</td></tr>
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<dl class="section return"><dt>Returns</dt><dd>the Residue* found or NULL. </dd></dl>
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<dl class="section return"><dt>Returns</dt><dd>the symbols of the atoms group as a std::map. The symbols index boolean values telling whether the symbol is ambiguous or not.</dd></dl>
<p>A symbol is ambiguous if it can also represent a single atom, such as Ac, or Pr. </p>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00106">106</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<td class="memname">virtual void gcu::Residue::Load </td>
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<td class="paramtype">xmlNodePtr </td>
<td class="paramname"><em>node</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Application.html">Application</a> * </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">node</td><td>a XMLNode* representing the residue. </td></tr>
<tr><td class="paramname">app</td><td>the <a class="el" href="classgcu_1_1Application.html">Application</a> owning the residue.</td></tr>
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<p>loads the residu from an XML file. </p>
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<td class="memname">virtual bool gcu::Residue::operator== </td>
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<td class="paramtype">G_GNUC_UNUSED <a class="el" href="classgcu_1_1Molecule.html">Molecule</a> const & </td>
<td class="paramname"><em>mol</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">mol</td><td>a molecule to compare to the atoms group. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>true if the molecule is the same as the one associated with <em>this</em>. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00172">172</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<td class="memname">void gcu::Residue::RemoveSymbol </td>
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<td class="paramname"><em>symbol</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">symbol</td><td>a chemical symbol.</td></tr>
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<p>Removes <em>symbol</em> from the list of valid symbols for the atoms group. </p>
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<td class="memname">gcu::Residue::SetGeneric </td>
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<td class="paramname"><em>Generic</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">Generic</td><td>whether the symbol is a generic symbol or not.</td></tr>
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<p>Generic symbols are such symbols as R, Ar, or X which might represent various atoms or groups of atoms. When expanded, they will be replaced by a default value, for example, R will expand to a methyl, and Ar to a phenyl group. </p>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00204">204</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<td class="memname">void gcu::Residue::SetName </td>
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<td class="paramname"><em>name</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">name</td><td>the name to give to the <a class="el" href="classgcu_1_1Residue.html">Residue</a>. </td></tr>
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<h2>Member Data Documentation</h2>
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<td class="memname">unsigned gcu::Residue::MaxSymbolLength</td>
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<dl class="section return"><dt>Returns</dt><dd>the maxium length of all known symbols. This is used by the framework when parsing a string formula. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2residue_8h_source.html#l00179">179</a> of file <a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a>.</p>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="gcu_2residue_8h_source.html">gcu/residue.h</a></li>
</ul>
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