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<title>The Gnome Chemistry Utils: gcu::Atom Class Reference</title>
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<h1>gcu::Atom Class Reference</h1><!-- doxytag: class="gcu::Atom" --><!-- doxytag: inherits="gcu::Object" -->
<p><code>#include <<a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>></code></p>
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Inheritance diagram for gcu::Atom:</div>
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<img src="classgcu_1_1Atom.gif" usemap="#gcu::Atom_map" alt=""/>
<map id="gcu::Atom_map" name="gcu::Atom_map">
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<p><a href="classgcu_1_1Atom-members.html">List of all members.</a></p>
<table border="0" cellpadding="0" cellspacing="0">
<tr><td colspan="2"><h2>Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#aa8943d4fa17eef381fd5d6b2b16cb3c5">Atom</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#aae941cba7af49c8b1a1d1bfc635a36b8">Atom</a> (int Z, double x, double y, double z=0.)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a7610b9679bf0dbfa6febefed539afc8d">Atom</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> &a)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Atom.html">Atom</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a73b1c38cbd4118c055720c7aec030b89">operator=</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> &a)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a6761fd5db008d0984e1fa056c385459b">~Atom</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a8e0470a96bc1fe3f1a2ceab7afc3fb63">Distance</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ab60ac47e3be8db95e1c9f2c2e986ff71">zoom</a> (double ZoomFactor)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a35d6470e8c8a3ea84cf69fef6decf656">GetCoords</a> (double *x, double *y, double *z=NULL) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ab9dbdfc744e2d8edf99f4009215866c6">SetCoords</a> (double x, double y, double z=0)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a3b5b44c467ea583adbaa77c263f33a8a">GetZ</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a38a15b6551a3eb6646206ba933af1fff">SetZ</a> (int Z)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ae22a3f7878ca7b08aa93004587303d9d">SetCharge</a> (char Charge)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">char </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#abdfd5d40227e19f53db6baee57c30260">GetCharge</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual const gchar * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a4371e488d9548ea7d9b6ee48c3be83bc">GetSymbol</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a374ed31f84f3400bf107c8fc5557acb3">AddBond</a> (<a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a687994b362c10a22a301aa12a960ce37">RemoveBond</a> (<a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a2c4b85fd9b08205696fc40d86ca1aebe">GetFirstBond</a> (std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::iterator &i)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#acb42e7980b0bc5a070324f1fc07fa989">GetNextBond</a> (std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::iterator &i)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a2eceb0aec2b8a0e30bba183af356d200">GetBond</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a026adef7ae137f92d2a4418dd94d1a30">GetBondsNumber</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a4d8e69e2c01645367c6c76c2d92c2433">Save</a> (xmlDocPtr xml) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a290a0a8c69ca6667d19e9d7f1d71d190">Load</a> (xmlNodePtr node)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a383a09c3d8bdbd0300bdc2b57b02e1ab">LoadNode</a> (xmlNodePtr node)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#af8a3a91412c9a585f60d49fb6e49280e">SaveNode</a> (xmlDocPtr xml, xmlNodePtr node) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#aab7ca2a758dc755d3da936cae82d1485">Move</a> (double x, double y, double z=0.)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a2ff6b67af11f6414fe8e972507e37f62">Transform2D</a> (<a class="el" href="classgcu_1_1Matrix2D.html">Matrix2D</a> &m, double x, double y)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ac9d2135007a4010d1e4ffffb9aec3227">SetProperty</a> (unsigned property, char const *value)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a759e64fd28f939c73a5130c49e876618">GetProperty</a> (unsigned property) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a8130046e2fd1ae7085935efe65c2ef94">IsInCycle</a> (<a class="el" href="classgcu_1_1Cycle.html">Cycle</a> *pCycle)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a3d8c5f65e203f23175c3422ef548e7f8">Match</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *atom, <a class="el" href="classgcu_1_1AtomMatchState.html">AtomMatchState</a> &state)</td></tr>
<tr><td colspan="2"><h2>Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a6fce7561c1e898b10dd418efbd2c7b1a">m_Z</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ab2c4ef4fd922120c4ff441c64aaa2ee1">m_x</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#af242ce3cb476a56ed16dc78ceeed6901">m_y</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a41a1b4161c01147c951c75f1ff4cae37">m_z</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">char </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a733db6db77be736879f983fbb11bcdaa">m_Charge</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a61f209632162c8553a7ebde3c4b194f9">m_Bonds</a></td></tr>
</table>
<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>This class is used to represent atoms. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00045">45</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="aa8943d4fa17eef381fd5d6b2b16cb3c5"></a><!-- doxytag: member="gcu::Atom::Atom" ref="aa8943d4fa17eef381fd5d6b2b16cb3c5" args="()" -->
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<td class="memname">gcu::Atom::Atom </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
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<div class="memdoc">
<p>The default constructor. Creates an atom with atomic number set to 0. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a585be3b15c7324e813a09222f325bd05">gcp::Atom</a>.</p>
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</div>
<a class="anchor" id="aae941cba7af49c8b1a1d1bfc635a36b8"></a><!-- doxytag: member="gcu::Atom::Atom" ref="aae941cba7af49c8b1a1d1bfc635a36b8" args="(int Z, double x, double y, double z=0.)" -->
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<td class="memname">gcu::Atom::Atom </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>Z</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>y</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>z</em> = <code>0.</code></td><td> </td>
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<td></td>
<td>)</td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>Z</em> </td><td>the atomic number of the new atom. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>the x coordinate of the new atom. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the y coordinate of the new atom. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>z</em> </td><td>the z coordinate of the new atom.</td></tr>
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</dd>
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<p>Creates an atom. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a16a9b2bca38d64c69e28f067005ecaa1">gcp::Atom</a>.</p>
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<a class="anchor" id="a7610b9679bf0dbfa6febefed539afc8d"></a><!-- doxytag: member="gcu::Atom::Atom" ref="a7610b9679bf0dbfa6febefed539afc8d" args="(Atom &a)" -->
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<td class="memname">gcu::Atom::Atom </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> & </td>
<td class="paramname"> <em>a</em></td>
<td> ) </td>
<td></td>
</tr>
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<div class="memdoc">
<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>a</em> </td><td>the <a class="el" href="classgcu_1_1Atom.html">Atom</a> to duplicate.</td></tr>
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</dd>
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<p>Creates a new atom identical to a without any bond. </p>
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<a class="anchor" id="a6761fd5db008d0984e1fa056c385459b"></a><!-- doxytag: member="gcu::Atom::~Atom" ref="a6761fd5db008d0984e1fa056c385459b" args="()" -->
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<td class="memname">virtual gcu::Atom::~Atom </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<p>The destructor of <a class="el" href="classgcu_1_1Atom.html">Atom</a>. It removes bonds but do not delete the associated <a class="el" href="classgcu_1_1Bond.html">Bond</a> instances. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a4ea961d1567b04333cf5a2d3ea2a3978">gcp::Atom</a>.</p>
</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a374ed31f84f3400bf107c8fc5557acb3"></a><!-- doxytag: member="gcu::Atom::AddBond" ref="a374ed31f84f3400bf107c8fc5557acb3" args="(Bond *pBond)" -->
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<td class="memname">virtual void gcu::Atom::AddBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td>
<td class="paramname"> <em>pBond</em></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<div class="memdoc">
<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pBond</em> </td><td>a pointer to the new <a class="el" href="classgcu_1_1Bond.html">Bond</a> to this <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
</table>
</dd>
</dl>
<p>Adds a <a class="el" href="classgcu_1_1Bond.html">Bond</a>. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a009e0ce9ae2f156c2d292d1275d5f685">gcp::Atom</a>.</p>
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</div>
<a class="anchor" id="a8e0470a96bc1fe3f1a2ceab7afc3fb63"></a><!-- doxytag: member="gcu::Atom::Distance" ref="a8e0470a96bc1fe3f1a2ceab7afc3fb63" args="(Atom *pAtom)" -->
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<td class="memname">double gcu::Atom::Distance </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"> <em>pAtom</em></td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pAtom</em> </td><td>a pointer to an <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
</table>
</dd>
</dl>
<dl class="return"><dt><b>Returns:</b></dt><dd>the distance between the <a class="el" href="classgcu_1_1Atom.html">Atom</a> at pAtom and this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
</div>
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<a class="anchor" id="a2eceb0aec2b8a0e30bba183af356d200"></a><!-- doxytag: member="gcu::Atom::GetBond" ref="a2eceb0aec2b8a0e30bba183af356d200" args="(Atom *pAtom) const " -->
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<td class="memname"><a class="el" href="classgcu_1_1Bond.html">Bond</a>* gcu::Atom::GetBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"> <em>pAtom</em></td>
<td> ) </td>
<td> const</td>
</tr>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pAtom</em> </td><td>a pointer to an <a class="el" href="classgcu_1_1Atom.html">Atom</a> instance. </td></tr>
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</dd>
</dl>
<dl class="return"><dt><b>Returns:</b></dt><dd>a pointer to the <a class="el" href="classgcu_1_1Bond.html">Bond</a> shared by pAtom and this <a class="el" href="classgcu_1_1Atom.html">Atom</a> if it exists or NULL. </dd></dl>
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<a class="anchor" id="a026adef7ae137f92d2a4418dd94d1a30"></a><!-- doxytag: member="gcu::Atom::GetBondsNumber" ref="a026adef7ae137f92d2a4418dd94d1a30" args="() const " -->
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<td class="memname">int gcu::Atom::GetBondsNumber </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td> const<code> [inline]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the number of <a class="el" href="classgcu_1_1Bond.html">Bond</a> instances shared by this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. It does not take multiplicity of bonds into account. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00178">178</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00282">m_Bonds</a>.</p>
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<a class="anchor" id="abdfd5d40227e19f53db6baee57c30260"></a><!-- doxytag: member="gcu::Atom::GetCharge" ref="abdfd5d40227e19f53db6baee57c30260" args="()" -->
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<td class="memname">char gcu::Atom::GetCharge </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [inline]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the formal charge of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00127">127</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00278">m_Charge</a>.</p>
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<a class="anchor" id="a35d6470e8c8a3ea84cf69fef6decf656"></a><!-- doxytag: member="gcu::Atom::GetCoords" ref="a35d6470e8c8a3ea84cf69fef6decf656" args="(double *x, double *y, double *z=NULL) const " -->
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<td class="memname">virtual bool gcu::Atom::GetCoords </td>
<td>(</td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>x</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>y</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>z</em> = <code>NULL</code></td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td> const<code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>a pointer to the double value which will receive the x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>a pointer to the double value which will receive the y coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>z</em> </td><td>a pointer to the double value which will receive the z coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL for 2D representations.</td></tr>
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<p>Retrieves the coordinates of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>true if successful and false if an error occurs (if x or y is NULL). </dd></dl>
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<a class="anchor" id="a2c4b85fd9b08205696fc40d86ca1aebe"></a><!-- doxytag: member="gcu::Atom::GetFirstBond" ref="a2c4b85fd9b08205696fc40d86ca1aebe" args="(std::map< Atom *, Bond * >::iterator &i)" -->
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<td class="memname"><a class="el" href="classgcu_1_1Bond.html">Bond</a>* gcu::Atom::GetFirstBond </td>
<td>(</td>
<td class="paramtype">std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::iterator & </td>
<td class="paramname"> <em>i</em></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>i</em> </td><td>a C++ std::map iterator.</td></tr>
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<p>Use this function to retrieve the first <a class="el" href="classgcu_1_1Bond.html">Bond</a> of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> and initialize the iterator. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>the first <a class="el" href="classgcu_1_1Bond.html">Bond</a> of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL if the <a class="el" href="classgcu_1_1Atom.html">Atom</a> has is not bonded. </dd></dl>
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<a class="anchor" id="acb42e7980b0bc5a070324f1fc07fa989"></a><!-- doxytag: member="gcu::Atom::GetNextBond" ref="acb42e7980b0bc5a070324f1fc07fa989" args="(std::map< Atom *, Bond * >::iterator &i)" -->
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<td class="memname"><a class="el" href="classgcu_1_1Bond.html">Bond</a>* gcu::Atom::GetNextBond </td>
<td>(</td>
<td class="paramtype">std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::iterator & </td>
<td class="paramname"> <em>i</em></td>
<td> ) </td>
<td></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>i</em> </td><td>a C++ std::map iterator initialized by <a class="el" href="classgcu_1_1Atom.html#a2c4b85fd9b08205696fc40d86ca1aebe">Atom::GetFirstBond</a>.</td></tr>
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<p>Use this method to iterate through the list of <a class="el" href="classgcu_1_1Bond.html">Bond</a> instances of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>the next <a class="el" href="classgcu_1_1Bond.html">Bond</a> of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL. </dd></dl>
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<a class="anchor" id="a759e64fd28f939c73a5130c49e876618"></a><!-- doxytag: member="gcu::Atom::GetProperty" ref="a759e64fd28f939c73a5130c49e876618" args="(unsigned property) const " -->
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<td class="memname">std::string gcu::Atom::GetProperty </td>
<td>(</td>
<td class="paramtype">unsigned </td>
<td class="paramname"> <em>property</em></td>
<td> ) </td>
<td> const<code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>property</em> </td><td>the identity of the property as defined in <a class="el" href="objprops_8h.html">objprops.h</a>.</td></tr>
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<p>Used by the <a class="el" href="classgcu_1_1Loader.html" title="class used to implement serialization engines.">gcu::Loader</a> mechanism to retrieve properties of atoms. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>the value of the property as a string. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#a9f612121600c791abbee16bb539975d7">gcu::Object</a>.</p>
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<a class="anchor" id="a4371e488d9548ea7d9b6ee48c3be83bc"></a><!-- doxytag: member="gcu::Atom::GetSymbol" ref="a4371e488d9548ea7d9b6ee48c3be83bc" args="() const " -->
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<td class="memname">virtual const gchar* gcu::Atom::GetSymbol </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td> const<code> [virtual]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the atomic symbol of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL if the element is unknown. </dd></dl>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentResidue.html#a83de50e53fbc175fbcc8026ec77c7d4a">gcp::FragmentResidue</a>.</p>
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<a class="anchor" id="a3b5b44c467ea583adbaa77c263f33a8a"></a><!-- doxytag: member="gcu::Atom::GetZ" ref="a3b5b44c467ea583adbaa77c263f33a8a" args="() const " -->
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<td class="memname">int gcu::Atom::GetZ </td>
<td>(</td>
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<td> ) </td>
<td> const<code> [inline]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the atomic number of the atom. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00110">110</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00262">m_Z</a>.</p>
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<a class="anchor" id="a8130046e2fd1ae7085935efe65c2ef94"></a><!-- doxytag: member="gcu::Atom::IsInCycle" ref="a8130046e2fd1ae7085935efe65c2ef94" args="(Cycle *pCycle)" -->
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<td class="memname">bool gcu::Atom::IsInCycle </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Cycle.html">Cycle</a> * </td>
<td class="paramname"> <em>pCycle</em></td>
<td> ) </td>
<td></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pCycle</em> </td><td>a cycle in which the atom might be.</td></tr>
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<dl class="return"><dt><b>Returns:</b></dt><dd>true if the atom lies in the cycle, false otherwise. </dd></dl>
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<a class="anchor" id="a290a0a8c69ca6667d19e9d7f1d71d190"></a><!-- doxytag: member="gcu::Atom::Load" ref="a290a0a8c69ca6667d19e9d7f1d71d190" args="(xmlNodePtr node)" -->
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<td class="memname">virtual bool gcu::Atom::Load </td>
<td>(</td>
<td class="paramtype">xmlNodePtr </td>
<td class="paramname"> <em>node</em></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>node</em> </td><td>a pointer to the xmlNode containing the serialized <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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</dd>
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<p>Loads an atom from an xmlNode. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#aa3ee33c25154d8e7bbe1e39de970c489">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a8eed490ca4ecc446a4a1cdc8aeb46f98">gcp::Atom</a>, <a class="el" href="classgcp_1_1FragmentAtom.html#aca577c2cb21b8fcb47fe0790cc41458a">gcp::FragmentAtom</a>, and <a class="el" href="classgcp_1_1FragmentResidue.html#add2c5572e5eed7d7d88d30f44c76226a">gcp::FragmentResidue</a>.</p>
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<td class="memname">virtual bool gcu::Atom::LoadNode </td>
<td>(</td>
<td class="paramtype">xmlNodePtr </td>
<td class="paramname"> <em>node</em></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>node</em> </td><td>a pointer to the xmlNode containing the serialized <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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<p>This virtual method is called at the end of the <a class="el" href="classgcu_1_1Atom.html#a290a0a8c69ca6667d19e9d7f1d71d190">Atom::Load</a> method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the <a class="el" href="classgcu_1_1Atom.html#a290a0a8c69ca6667d19e9d7f1d71d190">Atom::Load</a> method. </p>
<p>Reimplemented in <a class="el" href="classgcu_1_1CrystalAtom.html#af598a763a41e4d74be9cf6c1ae7e3f09">gcu::CrystalAtom</a>, and <a class="el" href="classgcp_1_1Atom.html#a5526b5a9b31aae0fe4d97f35680264d3">gcp::Atom</a>.</p>
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<td class="memname">virtual bool gcu::Atom::Match </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classgcu_1_1AtomMatchState.html">AtomMatchState</a> & </td>
<td class="paramname"> <em>state</em></td><td> </td>
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<td>)</td>
<td></td><td></td><td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>atom</em> </td><td>the atom to which the this instance is to be compared. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>state</em> </td><td>the <a class="el" href="classgcu_1_1AtomMatchState.html">AtomMatchState</a> representing the current comparison state.</td></tr>
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<p>Try to match atoms from two molecules which are compared. This function calls itself recursively until all atoms from the two molecules have been matched or until an difference is found. Overriden methods should call this base function and return its result. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>true if the atoms match, false otherwise. </dd></dl>
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<a class="anchor" id="aab7ca2a758dc755d3da936cae82d1485"></a><!-- doxytag: member="gcu::Atom::Move" ref="aab7ca2a758dc755d3da936cae82d1485" args="(double x, double y, double z=0.)" -->
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<td class="memname">virtual void gcu::Atom::Move </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>y</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>z</em> = <code>0.</code></td><td> </td>
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<td>)</td>
<td></td><td></td><td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>the x component of the transation vector. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the y component of the transation vector. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>z</em> </td><td>the z component of the transation vector.</td></tr>
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<p>Used to move an <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#af5505430c421604ff7e26e4414197fbc">gcu::Object</a>.</p>
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<a class="anchor" id="a73b1c38cbd4118c055720c7aec030b89"></a><!-- doxytag: member="gcu::Atom::operator=" ref="a73b1c38cbd4118c055720c7aec030b89" args="(Atom &a)" -->
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<td class="memname"><a class="el" href="classgcu_1_1Atom.html">Atom</a>& gcu::Atom::operator= </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> & </td>
<td class="paramname"> <em>a</em></td>
<td> ) </td>
<td></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>a</em> </td><td>the <a class="el" href="classgcu_1_1Atom.html">Atom</a> to copy.</td></tr>
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<dl class="return"><dt><b>Returns:</b></dt><dd>an <a class="el" href="classgcu_1_1Atom.html">Atom</a> identical to a without any bond. </dd></dl>
<p>Reimplemented in <a class="el" href="classgcu_1_1CrystalAtom.html#a45c2fc518b3e3e1f7a72db8fa31f4ed8">gcu::CrystalAtom</a>.</p>
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<a class="anchor" id="a687994b362c10a22a301aa12a960ce37"></a><!-- doxytag: member="gcu::Atom::RemoveBond" ref="a687994b362c10a22a301aa12a960ce37" args="(Bond *pBond)" -->
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<td class="memname">virtual void gcu::Atom::RemoveBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td>
<td class="paramname"> <em>pBond</em></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pBond</em> </td><td>a pointer to the <a class="el" href="classgcu_1_1Bond.html">Bond</a> to remove from this <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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<p>Removes a <a class="el" href="classgcu_1_1Bond.html">Bond</a>. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a41158b79556591cf4154ab0bed4139e4">gcp::Atom</a>.</p>
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<a class="anchor" id="a4d8e69e2c01645367c6c76c2d92c2433"></a><!-- doxytag: member="gcu::Atom::Save" ref="a4d8e69e2c01645367c6c76c2d92c2433" args="(xmlDocPtr xml) const " -->
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<td class="memname">virtual xmlNodePtr gcu::Atom::Save </td>
<td>(</td>
<td class="paramtype">xmlDocPtr </td>
<td class="paramname"> <em>xml</em></td>
<td> ) </td>
<td> const<code> [virtual]</code></td>
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</table>
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<div class="memdoc">
<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>xml</em> </td><td>the xmlDoc used to save the document. </td></tr>
</table>
</dd>
</dl>
<dl class="return"><dt><b>Returns:</b></dt><dd>a pointer to the xmlNode representing this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL if an error occured. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#aad462441e79fbd93e158f8294a198d11">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a67db585c20bdd33ac5ac071794b67dd5">gcp::Atom</a>, <a class="el" href="classgcp_1_1FragmentAtom.html#a143e33f55d77547cc9be39f2c5e248d0">gcp::FragmentAtom</a>, and <a class="el" href="classgcp_1_1FragmentResidue.html#aa9860847b53b41355982dc5d1d6c058a">gcp::FragmentResidue</a>.</p>
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<a class="anchor" id="af8a3a91412c9a585f60d49fb6e49280e"></a><!-- doxytag: member="gcu::Atom::SaveNode" ref="af8a3a91412c9a585f60d49fb6e49280e" args="(xmlDocPtr xml, xmlNodePtr node) const " -->
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<td class="memname">virtual bool gcu::Atom::SaveNode </td>
<td>(</td>
<td class="paramtype">xmlDocPtr </td>
<td class="paramname"> <em>xml</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">xmlNodePtr </td>
<td class="paramname"> <em>node</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td> const<code> [virtual]</code></td>
</tr>
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<div class="memdoc">
<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>xml</em> </td><td>the xmlDoc used to save the document. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>node</em> </td><td>a pointer to the xmlNode to which this <a class="el" href="classgcu_1_1Atom.html">Atom</a> is serialized.</td></tr>
</table>
</dd>
</dl>
<p>This virtual method is called at the end of the <a class="el" href="classgcu_1_1Atom.html#a4d8e69e2c01645367c6c76c2d92c2433">Atom::Save</a> method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the <a class="el" href="classgcu_1_1Atom.html#a4d8e69e2c01645367c6c76c2d92c2433">Atom::Save</a> method. </p>
<p>Reimplemented in <a class="el" href="classgcu_1_1CrystalAtom.html#a21d46353f8315f4d2ffb4b7c8b2dfdc8">gcu::CrystalAtom</a>.</p>
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<a class="anchor" id="ae22a3f7878ca7b08aa93004587303d9d"></a><!-- doxytag: member="gcu::Atom::SetCharge" ref="ae22a3f7878ca7b08aa93004587303d9d" args="(char Charge)" -->
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<td class="memname">virtual void gcu::Atom::SetCharge </td>
<td>(</td>
<td class="paramtype">char </td>
<td class="paramname"> <em>Charge</em></td>
<td> ) </td>
<td><code> [inline, virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>Charge</em> </td><td>the new formal charge of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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</dd>
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<p>Changes the formal charge of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00123">123</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00278">m_Charge</a>.</p>
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<a class="anchor" id="ab9dbdfc744e2d8edf99f4009215866c6"></a><!-- doxytag: member="gcu::Atom::SetCoords" ref="ab9dbdfc744e2d8edf99f4009215866c6" args="(double x, double y, double z=0)" -->
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<td class="memname">void gcu::Atom::SetCoords </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>y</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>z</em> = <code>0</code></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td><code> [inline]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>the new x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the new y coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>z</em> </td><td>the new z coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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</dd>
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<p>Changes the position of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00106">106</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00266">m_x</a>, <a class="el" href="gcu_2atom_8h_source.html#l00270">m_y</a>, <a class="el" href="gcu_2atom_8h_source.html#l00274">m_z</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00155">z()</a>.</p>
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<a class="anchor" id="ac9d2135007a4010d1e4ffffb9aec3227"></a><!-- doxytag: member="gcu::Atom::SetProperty" ref="ac9d2135007a4010d1e4ffffb9aec3227" args="(unsigned property, char const *value)" -->
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<td class="memname">bool gcu::Atom::SetProperty </td>
<td>(</td>
<td class="paramtype">unsigned </td>
<td class="paramname"> <em>property</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">char const * </td>
<td class="paramname"> <em>value</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>property</em> </td><td>the identity of the property as defined in <a class="el" href="objprops_8h.html">objprops.h</a>. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>value</em> </td><td>the value of the property as a string.</td></tr>
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</dd>
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<p>Used by the <a class="el" href="classgcu_1_1Loader.html" title="class used to implement serialization engines.">gcu::Loader</a> mechanism to load properties of atoms. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>true on success. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#a47862fe83b1c3739ee37b8af81550644">gcu::Object</a>.</p>
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<a class="anchor" id="a38a15b6551a3eb6646206ba933af1fff"></a><!-- doxytag: member="gcu::Atom::SetZ" ref="a38a15b6551a3eb6646206ba933af1fff" args="(int Z)" -->
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<td class="memname">virtual void gcu::Atom::SetZ </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>Z</em></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>Z</em> </td><td>the new atomic number of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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<p>This method might be overrided by derived class since changing the atomic number generally changes most properties. The default behavior is just to change the atomic number and nothing else. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#ad3919236bd9ce0816e4a07712048e9df">gcp::Atom</a>, and <a class="el" href="classgcp_1_1FragmentAtom.html#aebd1c27ec2490d2b8d313a1aef819616">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="a2ff6b67af11f6414fe8e972507e37f62"></a><!-- doxytag: member="gcu::Atom::Transform2D" ref="a2ff6b67af11f6414fe8e972507e37f62" args="(Matrix2D &m, double x, double y)" -->
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<td class="memname">virtual void gcu::Atom::Transform2D </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Matrix2D.html">Matrix2D</a> & </td>
<td class="paramname"> <em>m</em>, </td>
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<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>y</em></td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>m</em> </td><td>the 2D <a class="el" href="classgcu_1_1Matrix.html">Matrix</a> of the transformation. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>the x component of the center of the transformation. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the y component of the center of the transformation.</td></tr>
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</dd>
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<p>Used to move and/or transform an atom. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#a69ad6edf7d50950b036f09d9ff86f849">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a2636a34f79bd72b0abb7c2e42fd016e0">gcp::Atom</a>.</p>
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<a class="anchor" id="a845f98c4e1bb2fe68dfa3fc61a83f79d"></a><!-- doxytag: member="gcu::Atom::x" ref="a845f98c4e1bb2fe68dfa3fc61a83f79d" args="() const " -->
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<td class="memname">double gcu::Atom::x </td>
<td>(</td>
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<td> ) </td>
<td> const<code> [inline]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the x coordinate of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00147">147</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00266">m_x</a>.</p>
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<a class="anchor" id="a483d6aec85bb09acf681d0070f46149c"></a><!-- doxytag: member="gcu::Atom::y" ref="a483d6aec85bb09acf681d0070f46149c" args="() const " -->
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<td class="memname">double gcu::Atom::y </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td> const<code> [inline]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the y coordinate of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00151">151</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00270">m_y</a>.</p>
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<a class="anchor" id="aca911471b8848a4c78205c328557a7cc"></a><!-- doxytag: member="gcu::Atom::z" ref="aca911471b8848a4c78205c328557a7cc" args="() const " -->
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<td class="memname">double gcu::Atom::z </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td> const<code> [inline]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the z coordinate of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00155">155</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00274">m_z</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00106">SetCoords()</a>.</p>
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<a class="anchor" id="ab60ac47e3be8db95e1c9f2c2e986ff71"></a><!-- doxytag: member="gcu::Atom::zoom" ref="ab60ac47e3be8db95e1c9f2c2e986ff71" args="(double ZoomFactor)" -->
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<td class="memname">void gcu::Atom::zoom </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>ZoomFactor</em></td>
<td> ) </td>
<td></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>ZoomFactor</em> </td><td>the zoom factor.</td></tr>
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</dd>
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<p>Multiplies all three coordinates of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> by ZoomFactor. </p>
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<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a61f209632162c8553a7ebde3c4b194f9"></a><!-- doxytag: member="gcu::Atom::m_Bonds" ref="a61f209632162c8553a7ebde3c4b194f9" args="" -->
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<td class="memname">std::map<<a class="el" href="classgcu_1_1Atom.html">Atom</a>*, <a class="el" href="classgcu_1_1Bond.html">Bond</a>*> <a class="el" href="classgcu_1_1Atom.html#a61f209632162c8553a7ebde3c4b194f9">gcu::Atom::m_Bonds</a><code> [protected]</code></td>
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<p>The <a class="el" href="classgcu_1_1Bond.html">Bond</a> instances of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. The index of the map is a pointer to the other end of the <a class="el" href="classgcu_1_1Bond.html">Bond</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00282">282</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00178">GetBondsNumber()</a>.</p>
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<a class="anchor" id="a733db6db77be736879f983fbb11bcdaa"></a><!-- doxytag: member="gcu::Atom::m_Charge" ref="a733db6db77be736879f983fbb11bcdaa" args="" -->
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<td class="memname">char <a class="el" href="classgcu_1_1Atom.html#a733db6db77be736879f983fbb11bcdaa">gcu::Atom::m_Charge</a><code> [protected]</code></td>
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<p>The charge of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00278">278</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcp_2atom_8h_source.html#l00347">gcp::Atom::GetCharge()</a>, <a class="el" href="gcu_2atom_8h_source.html#l00127">GetCharge()</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00123">SetCharge()</a>.</p>
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<a class="anchor" id="ab2c4ef4fd922120c4ff441c64aaa2ee1"></a><!-- doxytag: member="gcu::Atom::m_x" ref="ab2c4ef4fd922120c4ff441c64aaa2ee1" args="" -->
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<td class="memname">double <a class="el" href="classgcu_1_1Atom.html#ab2c4ef4fd922120c4ff441c64aaa2ee1">gcu::Atom::m_x</a><code> [protected]</code></td>
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<p>The x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00266">266</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00106">SetCoords()</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00147">x()</a>.</p>
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<a class="anchor" id="af242ce3cb476a56ed16dc78ceeed6901"></a><!-- doxytag: member="gcu::Atom::m_y" ref="af242ce3cb476a56ed16dc78ceeed6901" args="" -->
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<td class="memname">double <a class="el" href="classgcu_1_1Atom.html#af242ce3cb476a56ed16dc78ceeed6901">gcu::Atom::m_y</a><code> [protected]</code></td>
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<p>The x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00270">270</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00106">SetCoords()</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00151">y()</a>.</p>
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<a class="anchor" id="a41a1b4161c01147c951c75f1ff4cae37"></a><!-- doxytag: member="gcu::Atom::m_z" ref="a41a1b4161c01147c951c75f1ff4cae37" args="" -->
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<td class="memname">double <a class="el" href="classgcu_1_1Atom.html#a41a1b4161c01147c951c75f1ff4cae37">gcu::Atom::m_z</a><code> [protected]</code></td>
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<p>The x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00274">274</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00106">SetCoords()</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00155">z()</a>.</p>
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<a class="anchor" id="a6fce7561c1e898b10dd418efbd2c7b1a"></a><!-- doxytag: member="gcu::Atom::m_Z" ref="a6fce7561c1e898b10dd418efbd2c7b1a" args="" -->
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<td class="memname">int <a class="el" href="classgcu_1_1Atom.html#a6fce7561c1e898b10dd418efbd2c7b1a">gcu::Atom::m_Z</a><code> [protected]</code></td>
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<p>The atomic number of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00262">262</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00110">GetZ()</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_2atom_8h_source.html">gcu/atom.h</a></li>
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<hr size="1"/><address style="text-align: right;"><small>Generated on Sun Sep 6 18:33:55 2009 for The Gnome Chemistry Utils by
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