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<title>The Gnome Chemistry Utils: gcp::Atom Class Reference</title>
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<h1>gcp::Atom Class Reference</h1><!-- doxytag: class="gcp::Atom" --><!-- doxytag: inherits="gcu::Atom,gcu::DialogOwner" -->
<p><code>#include <<a class="el" href="gcp_2atom_8h_source.html">atom.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for gcp::Atom:</div>
<div class="dynsection">
<div class="center">
<img src="classgcp_1_1Atom.gif" usemap="#gcp::Atom_map" alt=""/>
<map id="gcp::Atom_map" name="gcp::Atom_map">
<area href="classgcu_1_1Atom.html" alt="gcu::Atom" shape="rect" coords="0,56,137,80"/>
<area href="classgcu_1_1DialogOwner.html" alt="gcu::DialogOwner" shape="rect" coords="147,56,284,80"/>
<area href="classgcu_1_1Object.html" alt="gcu::Object" shape="rect" coords="0,0,137,24"/>
<area href="classgcp_1_1FragmentAtom.html" alt="gcp::FragmentAtom" shape="rect" coords="73,168,210,192"/>
<area href="classgcp_1_1FragmentResidue.html" alt="gcp::FragmentResidue" shape="rect" coords="73,224,210,248"/>
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</div>
<p><a href="classgcp_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="classgcp_1_1Atom.html#a585be3b15c7324e813a09222f325bd05">Atom</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a16a9b2bca38d64c69e28f067005ecaa1">Atom</a> (int Z, double x, double y, double z)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#aea06d6c7b8c22a25f25422f2121318f1">Atom</a> (OpenBabel::OBAtom *atom)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a4ea961d1567b04333cf5a2d3ea2a3978">~Atom</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#ad3919236bd9ce0816e4a07712048e9df">SetZ</a> (int Z)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a009e0ce9ae2f156c2d292d1275d5f685">AddBond</a> (<a class="el" href="classgcu_1_1Bond.html">gcu::Bond</a> *pBond)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a41158b79556591cf4154ab0bed4139e4">RemoveBond</a> (<a class="el" href="classgcu_1_1Bond.html">gcu::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="classgcp_1_1Atom.html#af207aeb4fe1d8dfa90853c3f041d0d48">Update</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a2d89d6c843004252a85cec1b4e6f585d">Add</a> (GtkWidget *w) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a793c282d0db167ab92a88c37bf32adee">Update</a> (GtkWidget *w) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a52ab2c14845106a07497aea0ac7721f5">GetTotalBondsNumber</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a974d2026ac161b2fe3403c1151a64c74">GetAttachedHydrogens</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegcp.html#aa66e4b39c091a3385363101d7a55e7c2">HPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a17f84bebbf93dcfd8869b716eb245ed1">GetBestSide</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a1bd86ee23a823c7b016550eef1ab3f97">GetChargePosition</a> (unsigned char &Pos, double Angle, double &x, double &y)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#ab22695d2697b49885b5191680fcf7fe2">GetAvailablePosition</a> (double &x, double &y)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a58f2ad93c252d3aafda378510bae3fad">GetPosition</a> (double angle, double &x, double &y)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a67db585c20bdd33ac5ac071794b67dd5">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="classgcp_1_1Atom.html#a8eed490ca4ecc446a4a1cdc8aeb46f98">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="classgcp_1_1Atom.html#a5526b5a9b31aae0fe4d97f35680264d3">LoadNode</a> (xmlNodePtr node)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#aecbb80ded1850f8b7c73ee22e6777fed">SetSelected</a> (GtkWidget *w, int state)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#ad9a779a82911c075694a9f5e1d6a7494">AcceptNewBonds</a> (int nb=1)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#aa575936870844269806d17d31efb2835">AcceptCharge</a> (int charge)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#ac06b20c09e7568191922a2801d307fed">GetYAlign</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a2636a34f79bd72b0abb7c2e42fd016e0">Transform2D</a> (<a class="el" href="classgcu_1_1Matrix2D.html">gcu::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="classgcp_1_1Atom.html#a838d183449aae5b0b5903e1d531f2799">BuildContextualMenu</a> (GtkUIManager *UIManager, Object *object, double x, double y)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a8a7e7ce2a09f1d0de8b90e5e833580b8">AddToMolecule</a> (<a class="el" href="classgcp_1_1Molecule.html">Molecule</a> *Mol)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a24167266fe3074c314268f3f73399c9c">HasImplicitElectronPairs</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#abd47c0fcae9eaaf8622f22a442f347c2">MayHaveImplicitUnpairedElectrons</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a534a917f790b72f180216a922b79fd24">AddElectron</a> (<a class="el" href="classgcp_1_1Electron.html">Electron</a> *electron)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#aab3b25c01105e26c708bf121d2dfdbe6">RemoveElectron</a> (<a class="el" href="classgcp_1_1Electron.html">Electron</a> *electron)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a330a76649d4ca4b51c230f51c28274fe">NotifyPositionOccupation</a> (unsigned char pos, bool occupied)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a6fcc259201bcd5174f6432b89c9e7e0a">SetChargePosition</a> (unsigned char Pos, bool def, double angle=0., double distance=0.)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">char </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a88e79387c06c5b559a115dd16485c97c">GetChargePosition</a> (double *Angle, double *Dist) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a1d0a59d6ffd19a170164138bbcde223f">SetCharge</a> (int charge)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a6afc5b1b3a3d09a5c369f3e4d04fca6b">GetCharge</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#aeb5384777a0771e6e79b6f495602f0a3">ForceChanged</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#ab19ede9511483d34fb841c98e13491a0">Match</a> (<a class="el" href="classgcu_1_1Atom.html">gcu::Atom</a> *atom, <a class="el" href="classgcu_1_1AtomMatchState.html">gcu::AtomMatchState</a> &state)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a2f2f6468dfaa1ad29dcfb650d51f987f">GetSymbolGeometry</a> (double &width, double &height, double &angle, bool up) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a85164bd7e0d5e93934b7f0c9ea59fc52">SetShowSymbol</a> (bool val)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a63932af2d6c6a5542068428dbe29a62e">GetShowSymbol</a> (void) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a55adbd6d3e8f0fa0d5c8284615784ff5">GetRefShowSymbol</a> (void)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a608bcf3065c2936b488c6b8dcfcad057">SetHPosStyle</a> (<a class="el" href="namespacegcp.html#aa66e4b39c091a3385363101d7a55e7c2">HPos</a> val)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegcp.html#aa66e4b39c091a3385363101d7a55e7c2">HPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a0d71acc02f732409fa082b2be4281632">GetHPosStyle</a> (void) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegcp.html#aa66e4b39c091a3385363101d7a55e7c2">HPos</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a64440f6035576571733be6357a8800f5">GetRefHPosStyle</a> (void)</td></tr>
<tr><td colspan="2"><h2>Protected Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a4784ed328b09666189095aabe78413b3">BuildSymbolGeometry</a> (double width, double height, double ascent)</td></tr>
<tr><td colspan="2"><h2>Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Atom.html#a1f354e6337f550d02fccff5ebef6de5a">m_CHeight</a></td></tr>
</table>
<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>Represents atoms in GChemPaint. </p>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00113">113</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
<hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="a585be3b15c7324e813a09222f325bd05"></a><!-- doxytag: member="gcp::Atom::Atom" ref="a585be3b15c7324e813a09222f325bd05" args="()" -->
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<div class="memproto">
<table class="memname">
<tr>
<td class="memname">gcp::Atom::Atom </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Default construtor. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#aa8943d4fa17eef381fd5d6b2b16cb3c5">gcu::Atom</a>.</p>
</div>
</div>
<a class="anchor" id="a16a9b2bca38d64c69e28f067005ecaa1"></a><!-- doxytag: member="gcp::Atom::Atom" ref="a16a9b2bca38d64c69e28f067005ecaa1" args="(int Z, double x, double y, double z)" -->
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<div class="memproto">
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<td class="memname">gcp::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>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>y</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>z</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></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>Z</em> </td><td>the atomic number. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>the x coordinate. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the y coordinate. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>z</em> </td><td>the z coordinate. </td></tr>
</table>
</dd>
</dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#aae941cba7af49c8b1a1d1bfc635a36b8">gcu::Atom</a>.</p>
</div>
</div>
<a class="anchor" id="aea06d6c7b8c22a25f25422f2121318f1"></a><!-- doxytag: member="gcp::Atom::Atom" ref="aea06d6c7b8c22a25f25422f2121318f1" args="(OpenBabel::OBAtom *atom)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
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<td class="memname">gcp::Atom::Atom </td>
<td>(</td>
<td class="paramtype">OpenBabel::OBAtom * </td>
<td class="paramname"> <em>atom</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>atom</em> </td><td>an OpenBabel <a class="el" href="classgcp_1_1Atom.html">Atom</a> instance.</td></tr>
</table>
</dd>
</dl>
<p>Builds an atom importing as many properties from an existing OpenBabel <a class="el" href="classgcp_1_1Atom.html">Atom</a> instance. </p>
</div>
</div>
<a class="anchor" id="a4ea961d1567b04333cf5a2d3ea2a3978"></a><!-- doxytag: member="gcp::Atom::~Atom" ref="a4ea961d1567b04333cf5a2d3ea2a3978" args="()" -->
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<td class="memname">virtual gcp::Atom::~Atom </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>The destructor. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#a6761fd5db008d0984e1fa056c385459b">gcu::Atom</a>.</p>
</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="aa575936870844269806d17d31efb2835"></a><!-- doxytag: member="gcp::Atom::AcceptCharge" ref="aa575936870844269806d17d31efb2835" args="(int charge)" -->
<div class="memitem">
<div class="memproto">
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<td class="memname">virtual bool gcp::Atom::AcceptCharge </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>charge</em></td>
<td> ) </td>
<td><code> [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 charge that might be set.</td></tr>
</table>
</dd>
</dl>
<dl class="return"><dt><b>Returns:</b></dt><dd>true if the charge is acceptable. </dd></dl>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#a93fde84c232703f5b33a28e7791f186d">gcp::FragmentAtom</a>.</p>
</div>
</div>
<a class="anchor" id="ad9a779a82911c075694a9f5e1d6a7494"></a><!-- doxytag: member="gcp::Atom::AcceptNewBonds" ref="ad9a779a82911c075694a9f5e1d6a7494" args="(int nb=1)" -->
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<td class="memname">virtual bool gcp::Atom::AcceptNewBonds </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nb</em> = <code>1</code></td>
<td> ) </td>
<td><code> [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>nb</em> </td><td>the number of bonds to add, taking orders into account. </td></tr>
</table>
</dd>
</dl>
<dl class="return"><dt><b>Returns:</b></dt><dd>true if the operation is allowed, false if the new bonds would exceed the maximum valence for the element. </dd></dl>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#a989c1215fe116dc30c6b819b8135b7dc">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="a2d89d6c843004252a85cec1b4e6f585d"></a><!-- doxytag: member="gcp::Atom::Add" ref="a2d89d6c843004252a85cec1b4e6f585d" args="(GtkWidget *w) const " -->
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<td class="memname">virtual void gcp::Atom::Add </td>
<td>(</td>
<td class="paramtype">GtkWidget * </td>
<td class="paramname"> <em>w</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>w</em> </td><td>a GtkWidget.</td></tr>
</table>
</dd>
</dl>
<p>Adds the representation of the atom to the canvas widget. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#afcd1e6f8bc15be563bd33429757d9d21">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#ad9bc7efd23f280d6f7e18ee3b4d3bb44">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="a009e0ce9ae2f156c2d292d1275d5f685"></a><!-- doxytag: member="gcp::Atom::AddBond" ref="a009e0ce9ae2f156c2d292d1275d5f685" args="(gcu::Bond *pBond)" -->
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<td class="memname">void gcp::Atom::AddBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">gcu::Bond</a> * </td>
<td class="paramname"> <em>pBond</em></td>
<td> ) </td>
<td><code> [virtual]</code></td>
</tr>
</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>pBond</em> </td><td>a bond.</td></tr>
</table>
</dd>
</dl>
<p>Adds a bond to the atom. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#a374ed31f84f3400bf107c8fc5557acb3">gcu::Atom</a>.</p>
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<a class="anchor" id="a534a917f790b72f180216a922b79fd24"></a><!-- doxytag: member="gcp::Atom::AddElectron" ref="a534a917f790b72f180216a922b79fd24" args="(Electron *electron)" -->
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<td class="memname">void gcp::Atom::AddElectron </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcp_1_1Electron.html">Electron</a> * </td>
<td class="paramname"> <em>electron</em></td>
<td> ) </td>
<td></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>electron</em> </td><td>a pointer to an <a class="el" href="classgcp_1_1Electron.html">Electron</a> instance.</td></tr>
</table>
</dd>
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<p>Adds the <a class="el" href="classgcp_1_1Electron.html">Electron</a> (representing either a single electron or a pair) to the <a class="el" href="classgcp_1_1Atom.html">Atom</a>. </p>
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<a class="anchor" id="a8a7e7ce2a09f1d0de8b90e5e833580b8"></a><!-- doxytag: member="gcp::Atom::AddToMolecule" ref="a8a7e7ce2a09f1d0de8b90e5e833580b8" args="(Molecule *Mol)" -->
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<td class="memname">virtual void gcp::Atom::AddToMolecule </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcp_1_1Molecule.html">Molecule</a> * </td>
<td class="paramname"> <em>Mol</em></td>
<td> ) </td>
<td><code> [virtual]</code></td>
</tr>
</table>
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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>Mol,:</em> </td><td>a pointer to a molecule</td></tr>
</table>
</dd>
</dl>
<p>Adds the atom to the molecule calling gcpMolecule::AddAtom() </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#a4e8dba4b0e4e27309ef30d6036b344f9">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="a838d183449aae5b0b5903e1d531f2799"></a><!-- doxytag: member="gcp::Atom::BuildContextualMenu" ref="a838d183449aae5b0b5903e1d531f2799" args="(GtkUIManager *UIManager, Object *object, double x, double y)" -->
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<td class="memname">bool gcp::Atom::BuildContextualMenu </td>
<td>(</td>
<td class="paramtype">GtkUIManager * </td>
<td class="paramname"> <em>UIManager</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Object * </td>
<td class="paramname"> <em>object</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>y</em></td><td> </td>
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<tr>
<td></td>
<td>)</td>
<td></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>UIManager,:</em> </td><td>the GtkUIManager to populate. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>object</em> </td><td>the atom on which occured the mouse click. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>x coordinate of the mouse click. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>y coordinate of the mouse click.</td></tr>
</table>
</dd>
</dl>
<p>This method is called to build a contextual menu for the atom. </p>
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<a class="anchor" id="a4784ed328b09666189095aabe78413b3"></a><!-- doxytag: member="gcp::Atom::BuildSymbolGeometry" ref="a4784ed328b09666189095aabe78413b3" args="(double width, double height, double ascent)" -->
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<td class="memname">void gcp::Atom::BuildSymbolGeometry </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>width</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>height</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>ascent</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td><code> [protected]</code></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>width</em> </td><td>the witdh of the atomic symbol. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>height</em> </td><td>the height of the atomic symbol. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>ascent</em> </td><td>the ascent of the atomic symbol.</td></tr>
</table>
</dd>
</dl>
<p>Evaluates where lines representing bonds should end to not overload the symbol. </p>
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<a class="anchor" id="aeb5384777a0771e6e79b6f495602f0a3"></a><!-- doxytag: member="gcp::Atom::ForceChanged" ref="aeb5384777a0771e6e79b6f495602f0a3" args="()" -->
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<td class="memname">void gcp::Atom::ForceChanged </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [inline]</code></td>
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<p>Forces an update. </p>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00351">351</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
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<a class="anchor" id="a974d2026ac161b2fe3403c1151a64c74"></a><!-- doxytag: member="gcp::Atom::GetAttachedHydrogens" ref="a974d2026ac161b2fe3403c1151a64c74" args="() const " -->
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<td class="memname">int gcp::Atom::GetAttachedHydrogens </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 implicit hydrogens lnked to the atom. </dd></dl>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00183">183</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
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<a class="anchor" id="ab22695d2697b49885b5191680fcf7fe2"></a><!-- doxytag: member="gcp::Atom::GetAvailablePosition" ref="ab22695d2697b49885b5191680fcf7fe2" args="(double &x, double &y)" -->
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<td class="memname">virtual int gcp::Atom::GetAvailablePosition </td>
<td>(</td>
<td class="paramtype">double & </td>
<td class="paramname"> <em>x</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double & </td>
<td class="paramname"> <em>y</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>x</em> </td><td>the x position. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the y position.</td></tr>
</table>
</dd>
</dl>
<p>This method finds an available position for drawing a charge sign or electrons and returns it as a symbolic value (see POSITION_E, POSITION_N,...). The <em>x</em> and <em>y</em> are updated so that they give the absolute position. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>an available position. </dd></dl>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#afbe19aaf182c6520377dafb08e983bef">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="a17f84bebbf93dcfd8869b716eb245ed1"></a><!-- doxytag: member="gcp::Atom::GetBestSide" ref="a17f84bebbf93dcfd8869b716eb245ed1" args="()" -->
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<td class="memname"><a class="el" href="namespacegcp.html#aa66e4b39c091a3385363101d7a55e7c2">HPos</a> gcp::Atom::GetBestSide </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the position of the attached hydrogen atoms symbol when automatically arranged. </dd></dl>
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<a class="anchor" id="a6afc5b1b3a3d09a5c369f3e4d04fca6b"></a><!-- doxytag: member="gcp::Atom::GetCharge" ref="a6afc5b1b3a3d09a5c369f3e4d04fca6b" args="() const " -->
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<td class="memname">int gcp::Atom::GetCharge </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 current formal local charge. </dd></dl>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00347">347</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00278">gcu::Atom::m_Charge</a>.</p>
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<a class="anchor" id="a88e79387c06c5b559a115dd16485c97c"></a><!-- doxytag: member="gcp::Atom::GetChargePosition" ref="a88e79387c06c5b559a115dd16485c97c" args="(double *Angle, double *Dist) const " -->
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<td class="memname">char gcp::Atom::GetChargePosition </td>
<td>(</td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>Angle</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>Dist</em></td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td> const</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>Angle</em> </td><td>where to store the angle from east direction in the trigonometric convention. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>Dist</em> </td><td>where to store the distance from the center of the atom.</td></tr>
</table>
</dd>
</dl>
<dl class="return"><dt><b>Returns:</b></dt><dd>the charge position as one of POSITION_E, POSITION_N,... </dd></dl>
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<a class="anchor" id="a1bd86ee23a823c7b016550eef1ab3f97"></a><!-- doxytag: member="gcp::Atom::GetChargePosition" ref="a1bd86ee23a823c7b016550eef1ab3f97" args="(unsigned char &Pos, double Angle, double &x, double &y)" -->
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<td class="memname">virtual int gcp::Atom::GetChargePosition </td>
<td>(</td>
<td class="paramtype">unsigned char & </td>
<td class="paramname"> <em>Pos</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>Angle</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double & </td>
<td class="paramname"> <em>x</em>, </td>
</tr>
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<td></td>
<td class="paramtype">double & </td>
<td class="paramname"> <em>y</em></td><td> </td>
</tr>
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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>Pos</em> </td><td>the approximate position of the charge. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>Angle</em> </td><td>the angle from horizontal left. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>the x position of the charge symbol. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the y position of the charge symbol.</td></tr>
</table>
</dd>
</dl>
<p>On input <em>Pos</em> can be one of POSITION_E, POSITION_N,... or 0xff, in which case, it will be given a default value. <em>x</em> and <em>y</em> are set to the position where the charge sign should be displayed usding the alignment code returned by this method. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>a number to set how the charge symbol should be aligned relative to its position. Possible values are:<ul>
<li>−2: center top.</li>
<li>−1: right.</li>
<li>0: center.</li>
<li>1: left.</li>
<li>2: center bottom. </li>
</ul>
</dd></dl>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#a30641bc4d2527f30ec6559d7a757e8fa">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="a0d71acc02f732409fa082b2be4281632"></a><!-- doxytag: member="gcp::Atom::GetHPosStyle" ref="a0d71acc02f732409fa082b2be4281632" args="(void) const " -->
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<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td>
<td> ) </td>
<td> const<code> [inline]</code></td>
</tr>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the position of attached hydrogen atoms symbol. </dd></dl>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00455">455</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
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<a class="anchor" id="a58f2ad93c252d3aafda378510bae3fad"></a><!-- doxytag: member="gcp::Atom::GetPosition" ref="a58f2ad93c252d3aafda378510bae3fad" args="(double angle, double &x, double &y)" -->
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<td class="memname">virtual bool gcp::Atom::GetPosition </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>angle</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double & </td>
<td class="paramname"> <em>x</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double & </td>
<td class="paramname"> <em>y</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td><code> [virtual]</code></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>angle</em> </td><td>the angle at which a charge sign or an electron should be displayed. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>the x position. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the y position.</td></tr>
</table>
</dd>
</dl>
<p>Updates <em>x</em> and <em>y</em> so that they become the absolute position corresponding to the angle when the position is available. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>true on success, false otherwise. </dd></dl>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#a244bdf880fedfaa77666b5f6224aea5f">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="a64440f6035576571733be6357a8800f5"></a><!-- doxytag: member="gcp::Atom::GetRefHPosStyle" ref="a64440f6035576571733be6357a8800f5" args="(void)" -->
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<td class="memname">gcp::Atom::GetRefHPosStyle </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [inline]</code></td>
</tr>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the position of attached hydrogen atoms symbol as a reference. </dd></dl>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00455">455</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
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<a class="anchor" id="a55adbd6d3e8f0fa0d5c8284615784ff5"></a><!-- doxytag: member="gcp::Atom::GetRefShowSymbol" ref="a55adbd6d3e8f0fa0d5c8284615784ff5" args="(void)" -->
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<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [inline]</code></td>
</tr>
</table>
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<dl class="return"><dt><b>Returns:</b></dt><dd>whether the symbol of a carbon atom is displayed or not as a reference. </dd></dl>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00442">442</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
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<a class="anchor" id="a63932af2d6c6a5542068428dbe29a62e"></a><!-- doxytag: member="gcp::Atom::GetShowSymbol" ref="a63932af2d6c6a5542068428dbe29a62e" args="(void) const " -->
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<td class="memname">gcp::Atom::GetShowSymbol </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td>
<td> ) </td>
<td> const<code> [inline]</code></td>
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<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>whether the symbol of a carbon atom is displayed or not. </dd></dl>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00442">442</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
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<a class="anchor" id="a2f2f6468dfaa1ad29dcfb650d51f987f"></a><!-- doxytag: member="gcp::Atom::GetSymbolGeometry" ref="a2f2f6468dfaa1ad29dcfb650d51f987f" args="(double &width, double &height, double &angle, bool up) const " -->
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<td class="memname">void gcp::Atom::GetSymbolGeometry </td>
<td>(</td>
<td class="paramtype">double & </td>
<td class="paramname"> <em>width</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double & </td>
<td class="paramname"> <em>height</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double & </td>
<td class="paramname"> <em>angle</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"> <em>up</em></td><td> </td>
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<tr>
<td></td>
<td>)</td>
<td></td><td></td><td> const</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>width</em> </td><td>where to store the width. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>height</em> </td><td>where to store the height. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>angle</em> </td><td>where to store the limit angle. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>up</em> </td><td>whether considering the top half or the bottom half</td></tr>
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</dd>
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<p>Used to retrieve the size of the ink rectangle of the atom symbol (if displayed). <em>angle</em> is absolute value of the angle between an horizontal line and the line joining the center and the top left or the bottom left vertex. The returned width value is actually half the full width. Height is the height. This method is used to avoid bonds lines extyending over their atoms symbols. </p>
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<a class="anchor" id="a52ab2c14845106a07497aea0ac7721f5"></a><!-- doxytag: member="gcp::Atom::GetTotalBondsNumber" ref="a52ab2c14845106a07497aea0ac7721f5" args="() const " -->
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<td class="memname">int gcp::Atom::GetTotalBondsNumber </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td> const</td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the bonds number for this atom taking bond order into account </dd></dl>
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<a class="anchor" id="ac06b20c09e7568191922a2801d307fed"></a><!-- doxytag: member="gcp::Atom::GetYAlign" ref="ac06b20c09e7568191922a2801d307fed" args="()" -->
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<td class="memname">virtual double gcp::Atom::GetYAlign </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the y coordinate at half height of the atom symbol if it was carbon. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#aedeec6e6b66e1a35e6d2f3ef75c94a09">gcu::Object</a>.</p>
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<a class="anchor" id="a24167266fe3074c314268f3f73399c9c"></a><!-- doxytag: member="gcp::Atom::HasImplicitElectronPairs" ref="a24167266fe3074c314268f3f73399c9c" args="()" -->
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<td class="memname">bool gcp::Atom::HasImplicitElectronPairs </td>
<td>(</td>
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<td> ) </td>
<td></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>true if the atom has implicit electron pairs, false otherwise. </dd></dl>
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<a class="anchor" id="a8eed490ca4ecc446a4a1cdc8aeb46f98"></a><!-- doxytag: member="gcp::Atom::Load" ref="a8eed490ca4ecc446a4a1cdc8aeb46f98" args="(xmlNodePtr node)" -->
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<td class="memname">virtual bool gcp::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 atom.</td></tr>
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</dd>
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<p>Used to load an atom in memory. The <a class="el" href="classgcp_1_1Atom.html">Atom</a> must already exist. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>true on succes, false otherwise. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#a290a0a8c69ca6667d19e9d7f1d71d190">gcu::Atom</a>.</p>
<p>Reimplemented in <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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<a class="anchor" id="a5526b5a9b31aae0fe4d97f35680264d3"></a><!-- doxytag: member="gcp::Atom::LoadNode" ref="a5526b5a9b31aae0fe4d97f35680264d3" args="(xmlNodePtr node)" -->
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<td class="memname">virtual bool gcp::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="classgcp_1_1Atom.html">Atom</a>.</td></tr>
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</dd>
</dl>
<p>Used in this class to correctly set the atomic number. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#a383a09c3d8bdbd0300bdc2b57b02e1ab">gcu::Atom</a>.</p>
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<a class="anchor" id="ab19ede9511483d34fb841c98e13491a0"></a><!-- doxytag: member="gcp::Atom::Match" ref="ab19ede9511483d34fb841c98e13491a0" args="(gcu::Atom *atom, gcu::AtomMatchState &state)" -->
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<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">gcu::Atom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classgcu_1_1AtomMatchState.html">gcu::AtomMatchState</a> & </td>
<td class="paramname"> <em>state</em></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>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 AtomMatchState representing the current comparison state.</td></tr>
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</dd>
</dl>
<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>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#a56baed02ef40ab67c4d7ba50b25394e3">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="abd47c0fcae9eaaf8622f22a442f347c2"></a><!-- doxytag: member="gcp::Atom::MayHaveImplicitUnpairedElectrons" ref="abd47c0fcae9eaaf8622f22a442f347c2" args="()" -->
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<td class="memname">bool gcp::Atom::MayHaveImplicitUnpairedElectrons </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>true if the atom has implcit electrons that might be unpaired. </dd></dl>
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<a class="anchor" id="a330a76649d4ca4b51c230f51c28274fe"></a><!-- doxytag: member="gcp::Atom::NotifyPositionOccupation" ref="a330a76649d4ca4b51c230f51c28274fe" args="(unsigned char pos, bool occupied)" -->
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<td class="memname">void gcp::Atom::NotifyPositionOccupation </td>
<td>(</td>
<td class="paramtype">unsigned char </td>
<td class="paramname"> <em>pos</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"> <em>occupied</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></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>pos</em> </td><td>one of POSITION_E, POSITION_N,... </td></tr>
<tr><td valign="top"></td><td valign="top"><em>occupied</em> </td><td>true if occupied, false otherwise.</td></tr>
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</dd>
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<p>Notifies if a position is occupied or not. </p>
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<a class="anchor" id="a41158b79556591cf4154ab0bed4139e4"></a><!-- doxytag: member="gcp::Atom::RemoveBond" ref="a41158b79556591cf4154ab0bed4139e4" args="(gcu::Bond *pBond)" -->
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<td class="memname">void gcp::Atom::RemoveBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">gcu::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 bond.</td></tr>
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</dd>
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<p>Removes a bond from the atom. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#a687994b362c10a22a301aa12a960ce37">gcu::Atom</a>.</p>
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<a class="anchor" id="aab3b25c01105e26c708bf121d2dfdbe6"></a><!-- doxytag: member="gcp::Atom::RemoveElectron" ref="aab3b25c01105e26c708bf121d2dfdbe6" args="(Electron *electron)" -->
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<td class="memname">void gcp::Atom::RemoveElectron </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcp_1_1Electron.html">Electron</a> * </td>
<td class="paramname"> <em>electron</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>electron</em> </td><td>a pointer to an <a class="el" href="classgcp_1_1Electron.html">Electron</a> instance.</td></tr>
</table>
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<p>Removes the <a class="el" href="classgcp_1_1Electron.html">Electron</a> (representing either a single electron or a pair) from the <a class="el" href="classgcp_1_1Atom.html">Atom</a>. </p>
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<a class="anchor" id="a67db585c20bdd33ac5ac071794b67dd5"></a><!-- doxytag: member="gcp::Atom::Save" ref="a67db585c20bdd33ac5ac071794b67dd5" args="(xmlDocPtr xml) const " -->
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<td class="memname">virtual xmlNodePtr gcp::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>
</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>xml</em> </td><td>the xmlDoc used to save the document.</td></tr>
</table>
</dd>
</dl>
<p>Used to save the <a class="el" href="classgcp_1_1Atom.html">Atom</a> to the xmlDoc. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>the xmlNode containing the serialized atom. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#a4d8e69e2c01645367c6c76c2d92c2433">gcu::Atom</a>.</p>
<p>Reimplemented in <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="a1d0a59d6ffd19a170164138bbcde223f"></a><!-- doxytag: member="gcp::Atom::SetCharge" ref="a1d0a59d6ffd19a170164138bbcde223f" args="(int charge)" -->
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<td class="memname">void gcp::Atom::SetCharge </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>charge</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>charge</em> </td><td>the charge to set.</td></tr>
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<p>Sets the formal local charge of an atom. </p>
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<a class="anchor" id="a6fcc259201bcd5174f6432b89c9e7e0a"></a><!-- doxytag: member="gcp::Atom::SetChargePosition" ref="a6fcc259201bcd5174f6432b89c9e7e0a" args="(unsigned char Pos, bool def, double angle=0., double distance=0.)" -->
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<td class="memname">void gcp::Atom::SetChargePosition </td>
<td>(</td>
<td class="paramtype">unsigned char </td>
<td class="paramname"> <em>Pos</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"> <em>def</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>angle</em> = <code>0.</code>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>distance</em> = <code>0.</code></td><td> </td>
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<tr>
<td></td>
<td>)</td>
<td></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>Pos</em> </td><td>one of POSITION_E, POSITION_N,... </td></tr>
<tr><td valign="top"></td><td valign="top"><em>def</em> </td><td>true if the position is automatic. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>angle</em> </td><td>the angle from the east direction in the trigonometric convention. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>distance</em> </td><td>the distance from the center of the atom, or 0. if automatic.</td></tr>
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<p>Sets the relative position of a charge sign. </p>
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<a class="anchor" id="a608bcf3065c2936b488c6b8dcfcad057"></a><!-- doxytag: member="gcp::Atom::SetHPosStyle" ref="a608bcf3065c2936b488c6b8dcfcad057" args="(HPos val)" -->
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<td class="memname">gcp::Atom::SetHPosStyle </td>
<td>(</td>
<td class="paramtype"><a class="el" href="namespacegcp.html#aa66e4b39c091a3385363101d7a55e7c2">HPos</a> </td>
<td class="paramname"> <em>val</em></td>
<td> ) </td>
<td><code> [inline]</code></td>
</tr>
</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>val</em> </td><td>the new position.</td></tr>
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</dd>
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<p>Sets the position of attached hydrogen atoms symbol. </p>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00455">455</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
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<a class="anchor" id="aecbb80ded1850f8b7c73ee22e6777fed"></a><!-- doxytag: member="gcp::Atom::SetSelected" ref="aecbb80ded1850f8b7c73ee22e6777fed" args="(GtkWidget *w, int state)" -->
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<td class="memname">virtual void gcp::Atom::SetSelected </td>
<td>(</td>
<td class="paramtype">GtkWidget * </td>
<td class="paramname"> <em>w</em>, </td>
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<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>state</em></td><td> </td>
</tr>
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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>w</em> </td><td>the GtkWidget inside which the atom is displayed. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>state</em> </td><td>the selection state of the atom.</td></tr>
</table>
</dd>
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<p>Used to set the selection state of the atom inside the widget. The values of state might be <a class="el" href="namespacegcp.html#a2873f45c769a642340cfd80eff3dde74abd6a663c786e2d2b135a74d52f0cd552">gcp::SelStateUnselected</a>, <a class="el" href="namespacegcp.html#a2873f45c769a642340cfd80eff3dde74a94b317915b52f90cbc98b15a577b25d8">gcp::SelStateSelected</a>, <a class="el" href="namespacegcp.html#a2873f45c769a642340cfd80eff3dde74adcae1871fb81a60e980331b689fe3ce0">gcp::SelStateUpdating</a>, or <a class="el" href="namespacegcp.html#a2873f45c769a642340cfd80eff3dde74a2d4e3b5f28ae0af00b9381c2548dea00">gcp::SelStateErasing</a>. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#a9a751a51b887de4a4035ff1927c2aede">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#a4e6f8c633b698e96d2710ac16fcf3656">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="a85164bd7e0d5e93934b7f0c9ea59fc52"></a><!-- doxytag: member="gcp::Atom::SetShowSymbol" ref="a85164bd7e0d5e93934b7f0c9ea59fc52" args="(bool val)" -->
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<td class="memname">gcp::Atom::SetShowSymbol </td>
<td>(</td>
<td class="paramtype">bool </td>
<td class="paramname"> <em>ShowSymbol</em></td>
<td> ) </td>
<td><code> [inline]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
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<tr><td valign="top"></td><td valign="top"><em>ShowSymbol</em> </td><td>whether the symbol of a carbon atom is to be displayed or not.</td></tr>
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<p>Sets the visibility of a carbon atom symbol in a chain. </p>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00442">442</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
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<a class="anchor" id="ad3919236bd9ce0816e4a07712048e9df"></a><!-- doxytag: member="gcp::Atom::SetZ" ref="ad3919236bd9ce0816e4a07712048e9df" args="(int Z)" -->
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<td class="memname">virtual void gcp::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>
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<tr><td valign="top"></td><td valign="top"><em>Z</em> </td><td>the new atomic number.</td></tr>
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<p>Changes the atomic number of the atom. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#a38a15b6551a3eb6646206ba933af1fff">gcu::Atom</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#aebd1c27ec2490d2b8d313a1aef819616">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="a2636a34f79bd72b0abb7c2e42fd016e0"></a><!-- doxytag: member="gcp::Atom::Transform2D" ref="a2636a34f79bd72b0abb7c2e42fd016e0" args="(gcu::Matrix2D &m, double x, double y)" -->
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<td class="memname">virtual void gcp::Atom::Transform2D </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Matrix2D.html">gcu::Matrix2D</a> & </td>
<td class="paramname"> <em>m</em>, </td>
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<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><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>
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<tr><td valign="top"></td><td valign="top"><em>m</em> </td><td>the Matrix2D 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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<p>Used to move and/or transform an object. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#a2ff6b67af11f6414fe8e972507e37f62">gcu::Atom</a>.</p>
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<a class="anchor" id="a793c282d0db167ab92a88c37bf32adee"></a><!-- doxytag: member="gcp::Atom::Update" ref="a793c282d0db167ab92a88c37bf32adee" args="(GtkWidget *w) const " -->
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<td class="memname">virtual void gcp::Atom::Update </td>
<td>(</td>
<td class="paramtype">GtkWidget * </td>
<td class="paramname"> <em>w</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>w</em> </td><td>a GtkWidget.</td></tr>
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</dd>
</dl>
<p>Updates the representation of the atom in the canvas widget. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#af2fffc10644e8cb8a18da68c8e18e24c">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#a57b91204844ebab1ad33c54cda61d4c0">gcp::FragmentAtom</a>.</p>
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<a class="anchor" id="af207aeb4fe1d8dfa90853c3f041d0d48"></a><!-- doxytag: member="gcp::Atom::Update" ref="af207aeb4fe1d8dfa90853c3f041d0d48" args="()" -->
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<td class="memname">virtual void gcp::Atom::Update </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<p>Updates the atom after changing its bonds, charge or explicit electrons. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentAtom.html#ad42dc61198d0b1dcd4d0b529e83d43aa">gcp::FragmentAtom</a>.</p>
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<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a1f354e6337f550d02fccff5ebef6de5a"></a><!-- doxytag: member="gcp::Atom::m_CHeight" ref="a1f354e6337f550d02fccff5ebef6de5a" args="" -->
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<td class="memname">double <a class="el" href="classgcp_1_1Atom.html#a1f354e6337f550d02fccff5ebef6de5a">gcp::Atom::m_CHeight</a><code> [protected]</code></td>
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<p>Half the height of the "C" character. </p>
<p>Definition at line <a class="el" href="gcp_2atom_8h_source.html#l00429">429</a> of file <a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a>.</p>
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</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="gcp_2atom_8h_source.html">gcp/atom.h</a></li>
</ul>
</div>
<hr size="1"/><address style="text-align: right;"><small>Generated on Sun Sep 6 18:33:54 2009 for The Gnome Chemistry Utils by
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