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<title>The Gnome Chemistry Utils: gcu::CrystalAtom Class Reference</title>
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<div class="navpath"><a class="el" href="namespacegcu.html">gcu</a>::<a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a>
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<h1>gcu::CrystalAtom Class Reference</h1><!-- doxytag: class="gcu::CrystalAtom" --><!-- doxytag: inherits="gcu::Atom" -->
<p><code>#include <<a class="el" href="crystalatom_8h_source.html">gcu/crystalatom.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for gcu::CrystalAtom:</div>
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<div class="center">
<img src="classgcu_1_1CrystalAtom.gif" usemap="#gcu::CrystalAtom_map" alt=""/>
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<area href="classgcu_1_1Atom.html" alt="gcu::Atom" shape="rect" coords="0,56,107,80"/>
<area href="classgcu_1_1Object.html" alt="gcu::Object" shape="rect" coords="0,0,107,24"/>
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<p><a href="classgcu_1_1CrystalAtom-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_1CrystalAtom.html#acb5dca290b7f5013a1dc14f86fd9756d">CrystalAtom</a> (<a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> &caAtom)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a45c2fc518b3e3e1f7a72db8fa31f4ed8">operator=</a> (<a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> &caAtom)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#ac3bac340bb89554a5cea833b6baa49e2">SetColor</a> (float red, float green, float blue, float alpha)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a79b7682b7cc89d0d394367992ea41293">SetDefaultColor</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a79e70af4f098470c871a03c37f12c326">HasCustomColor</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a6eb31ffbe30e731a80406f4854f6bcce">GetColor</a> (double *red, double *green, double *blue, double *alpha)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#ae103b582c0ddc3e5311abec1f323723d">SetSize</a> (double r)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#aee7bc25e8b2941efc49b9fcdcf8c0545">GetSize</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#ad040d5406d27abaa0943ef6c279ab82f">operator==</a> (<a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> &caAtom)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a7e15b918ceaaae39378152e7556aeab7">Cleave</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a92c8fdb148c1ac0051dce13c6c0741dd">ScalProd</a> (int h, int k, int l)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a3accb25403620077ff5ce14df80e1feb">NetToCartesian</a> (double a, double b, double c, double alpha, double beta, double gamma)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a105c8bc242de845415d06073fdf7d7fa">Distance</a> (double x, double y, double z, bool bFixed)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#aa1017cdd8a6ee24ee9bb13446cca642c">r</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const <a class="el" href="structGcuAtomicRadius.html">GcuAtomicRadius</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a88d750335ec805ebd0119eae5570d51c">GetRadius</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a57a87f97ad06f6b3e64743515d3230ce">SetRadius</a> (const <a class="el" href="structGcuAtomicRadius.html">GcuAtomicRadius</a> &r)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#ad3268872372d42328392ca2a829df15e">IsCleaved</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a21d46353f8315f4d2ffb4b7c8b2dfdc8">SaveNode</a> (xmlDocPtr xml, xmlNodePtr node) 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_1CrystalAtom.html#af598a763a41e4d74be9cf6c1ae7e3f09">LoadNode</a> (xmlNodePtr node)</td></tr>
<tr><td colspan="2"><h2>Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#acd9be65b37b7873e3fd248f7e407501b">m_fBlue</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#ad963587bca5555da806ed97854bd5be6">m_fRed</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#ada1bb25adb7fe5190bfda096904f919f">m_fGreen</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a0bbe37ae9fe9f8959b23bd373181fb9e">m_fAlpha</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#ae41dedc2e7aab818f12113dc22a910dc">m_bCustomColor</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structGcuAtomicRadius.html">GcuAtomicRadius</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a3249d1711608c6b10689895f6ceea800">m_Radius</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1CrystalAtom.html#a88d2c73d283d166e621aa3b18b83efd2">m_nCleave</a></td></tr>
</table>
<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>Used to represent atoms in a crystal. </p>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00043">43</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
<hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="acb5dca290b7f5013a1dc14f86fd9756d"></a><!-- doxytag: member="gcu::CrystalAtom::CrystalAtom" ref="acb5dca290b7f5013a1dc14f86fd9756d" args="(CrystalAtom &caAtom)" -->
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<td class="memname">gcu::CrystalAtom::CrystalAtom </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> & </td>
<td class="paramname"> <em>caAtom</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>caAtom,:</em> </td><td>the <a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> to duplicate.</td></tr>
</table>
</dd>
</dl>
<p>Creates a new <a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> identical to caAtom. </p>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a7e15b918ceaaae39378152e7556aeab7"></a><!-- doxytag: member="gcu::CrystalAtom::Cleave" ref="a7e15b918ceaaae39378152e7556aeab7" args="()" -->
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<td class="memname">void gcu::CrystalAtom::Cleave </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [inline]</code></td>
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<p>Method used to cleave an atom. The inverse operation does not exist since the whole crystal must be recalculated after a change in the definition. </p>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00124">124</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
<p>References <a class="el" href="crystalatom_8h_source.html#l00220">m_nCleave</a>.</p>
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</div>
<a class="anchor" id="a105c8bc242de845415d06073fdf7d7fa"></a><!-- doxytag: member="gcu::CrystalAtom::Distance" ref="a105c8bc242de845415d06073fdf7d7fa" args="(double x, double y, double z, bool bFixed)" -->
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<td class="memname">double gcu::CrystalAtom::Distance </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>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"> <em>bFixed</em></td><td> </td>
</tr>
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<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>x,:</em> </td><td>the x coordinate of the center. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y,:</em> </td><td>the y coordinate of the center. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>z,:</em> </td><td>the z coordinate of the center. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>bFixed,:</em> </td><td>tells if cleaved atoms are taken into account.</td></tr>
</table>
</dd>
</dl>
<p>This helper method is called when searching for the size of the crystal. When some cleavages are defined, the procedure cn take into account atoms cleaved to get the same position in the view for the cleaved crystal than for the whole crystal. If bFixed is true, all atoms are taken into account.</p>
<dl class="return"><dt><b>Returns:</b></dt><dd>the distance of the atom to the center of the view or 0 if bFixed is false and the atom cleaved. </dd></dl>
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</div>
<a class="anchor" id="a6eb31ffbe30e731a80406f4854f6bcce"></a><!-- doxytag: member="gcu::CrystalAtom::GetColor" ref="a6eb31ffbe30e731a80406f4854f6bcce" args="(double *red, double *green, double *blue, double *alpha)" -->
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<td class="memname">void gcu::CrystalAtom::GetColor </td>
<td>(</td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>red</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>green</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>blue</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>alpha</em></td><td> </td>
</tr>
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<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>red,:</em> </td><td>a pointer to the red component. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>green,:</em> </td><td>a pointer to the green component. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>blue,:</em> </td><td>a pointer to the blue component. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>alpha,:</em> </td><td>a pointer to the alpha component.</td></tr>
</table>
</dd>
</dl>
<p>Used to retrieve the color used in the representation of the atom. Mainly useful for user defined colors. </p>
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<a class="anchor" id="a88d750335ec805ebd0119eae5570d51c"></a><!-- doxytag: member="gcu::CrystalAtom::GetRadius" ref="a88d750335ec805ebd0119eae5570d51c" args="()" -->
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<td class="memname">const <a class="el" href="structGcuAtomicRadius.html">GcuAtomicRadius</a>& gcu::CrystalAtom::GetRadius </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [inline]</code></td>
</tr>
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<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the <a class="el" href="structGcuAtomicRadius.html">GcuAtomicRadius</a> containing the caracteristics of the atom radius. </dd></dl>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00167">167</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
<p>References <a class="el" href="crystalatom_8h_source.html#l00214">m_Radius</a>.</p>
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<a class="anchor" id="aee7bc25e8b2941efc49b9fcdcf8c0545"></a><!-- doxytag: member="gcu::CrystalAtom::GetSize" ref="aee7bc25e8b2941efc49b9fcdcf8c0545" args="()" -->
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<td class="memname">double gcu::CrystalAtom::GetSize </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the value of the radius (in pm). </dd></dl>
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<a class="anchor" id="a79e70af4f098470c871a03c37f12c326"></a><!-- doxytag: member="gcu::CrystalAtom::HasCustomColor" ref="a79e70af4f098470c871a03c37f12c326" args="()" -->
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<td class="memname">bool gcu::CrystalAtom::HasCustomColor </td>
<td>(</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>: true if the color is user defined and false if it is the default color. </dd></dl>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00094">94</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
<p>References <a class="el" href="crystalatom_8h_source.html#l00210">m_bCustomColor</a>.</p>
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<a class="anchor" id="ad3268872372d42328392ca2a829df15e"></a><!-- doxytag: member="gcu::CrystalAtom::IsCleaved" ref="ad3268872372d42328392ca2a829df15e" args="()" -->
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<td class="memname">bool gcu::CrystalAtom::IsCleaved </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>true if the atom is cleaved by at least one cleavage or false if the atom is not cleaved at all. </dd></dl>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00175">175</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
<p>References <a class="el" href="crystalatom_8h_source.html#l00220">m_nCleave</a>.</p>
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<a class="anchor" id="af598a763a41e4d74be9cf6c1ae7e3f09"></a><!-- doxytag: member="gcu::CrystalAtom::LoadNode" ref="af598a763a41e4d74be9cf6c1ae7e3f09" args="(xmlNodePtr node)" -->
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<td class="memname">virtual bool gcu::CrystalAtom::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>
</table>
</dd>
</dl>
<p>Loads the color and the radius of the atom. </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="a3accb25403620077ff5ce14df80e1feb"></a><!-- doxytag: member="gcu::CrystalAtom::NetToCartesian" ref="a3accb25403620077ff5ce14df80e1feb" args="(double a, double b, double c, double alpha, double beta, double gamma)" -->
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<td class="memname">void gcu::CrystalAtom::NetToCartesian </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>a</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>b</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>c</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>alpha</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>beta</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>gamma</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>a,:</em> </td><td>the a parameter of the unit cell. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>b,:</em> </td><td>the b parameter of the unit cell. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>c,:</em> </td><td>the c parameter of the unit cell. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>alpha,:</em> </td><td>the alpha angle of the unit cell. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>beta,:</em> </td><td>the beta angle of the unit cell. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>gamma,:</em> </td><td>the gamma angle of the unit cell.</td></tr>
</table>
</dd>
</dl>
<p>Converts the coordinates of the atom from net related ones to cartesian. Initially, atoms are defined by their position relative to the unit cell and the coordinates must be transformed to the cartesian ones before displaying the atom. </p>
</div>
</div>
<a class="anchor" id="a45c2fc518b3e3e1f7a72db8fa31f4ed8"></a><!-- doxytag: member="gcu::CrystalAtom::operator=" ref="a45c2fc518b3e3e1f7a72db8fa31f4ed8" args="(CrystalAtom &caAtom)" -->
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<td class="memname"><a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a>& gcu::CrystalAtom::operator= </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> & </td>
<td class="paramname"> <em>a</em></td>
<td> ) </td>
<td></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>a</em> </td><td>the <a class="el" href="classgcu_1_1Atom.html">Atom</a> to copy.</td></tr>
</table>
</dd>
</dl>
<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 from <a class="el" href="classgcu_1_1Atom.html#a73b1c38cbd4118c055720c7aec030b89">gcu::Atom</a>.</p>
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<a class="anchor" id="ad040d5406d27abaa0943ef6c279ab82f"></a><!-- doxytag: member="gcu::CrystalAtom::operator==" ref="ad040d5406d27abaa0943ef6c279ab82f" args="(CrystalAtom &caAtom)" -->
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<td class="memname">bool gcu::CrystalAtom::operator== </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> & </td>
<td class="paramname"> <em>caAtom</em></td>
<td> ) </td>
<td></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>caAtom,:</em> </td><td>a <a class="el" href="classgcu_1_1CrystalAtom.html">CrystalAtom</a> instance. </td></tr>
</table>
</dd>
</dl>
<dl class="return"><dt><b>Returns:</b></dt><dd>true if the atoms are at the same position and false if their positions are different. </dd></dl>
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</div>
<a class="anchor" id="aa1017cdd8a6ee24ee9bb13446cca642c"></a><!-- doxytag: member="gcu::CrystalAtom::r" ref="aa1017cdd8a6ee24ee9bb13446cca642c" args="()" -->
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<td class="memname">double gcu::CrystalAtom::r </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [inline]</code></td>
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</table>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the value of the radius (in pm). </dd></dl>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00163">163</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
<p>References <a class="el" href="crystalatom_8h_source.html#l00214">m_Radius</a>, <a class="el" href="chemistry_8h_source.html#l00121">GcuDimensionalValue::value</a>, and <a class="el" href="chemistry_8h_source.html#l00140">GcuAtomicRadius::value</a>.</p>
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<a class="anchor" id="a21d46353f8315f4d2ffb4b7c8b2dfdc8"></a><!-- doxytag: member="gcu::CrystalAtom::SaveNode" ref="a21d46353f8315f4d2ffb4b7c8b2dfdc8" args="(xmlDocPtr xml, xmlNodePtr node) const " -->
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<td class="memname">virtual bool gcu::CrystalAtom::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>
</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>
<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>Saves the color and the radius of the atom. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Atom.html#af8a3a91412c9a585f60d49fb6e49280e">gcu::Atom</a>.</p>
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</div>
<a class="anchor" id="a92c8fdb148c1ac0051dce13c6c0741dd"></a><!-- doxytag: member="gcu::CrystalAtom::ScalProd" ref="a92c8fdb148c1ac0051dce13c6c0741dd" args="(int h, int k, int l)" -->
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<td class="memname">double gcu::CrystalAtom::ScalProd </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>h</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>k</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>l</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>h,:</em> </td><td>the h Miller index of a plane. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>k,:</em> </td><td>the k Miller index of a plane. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>l,:</em> </td><td>the l Miller index of a plane.</td></tr>
</table>
</dd>
</dl>
<dl class="return"><dt><b>Returns:</b></dt><dd>the product hx+ky+lz where x, y and z are the coordinates of the atom. This makes sense only if coordinates are related to the net and are not the cartesian coordinates. This method should not be called after <a class="el" href="classgcu_1_1CrystalAtom.html#a3accb25403620077ff5ce14df80e1feb">NetToCartesian()</a>. </dd></dl>
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</div>
<a class="anchor" id="ac3bac340bb89554a5cea833b6baa49e2"></a><!-- doxytag: member="gcu::CrystalAtom::SetColor" ref="ac3bac340bb89554a5cea833b6baa49e2" args="(float red, float green, float blue, float alpha)" -->
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<td class="memname">void gcu::CrystalAtom::SetColor </td>
<td>(</td>
<td class="paramtype">float </td>
<td class="paramname"> <em>red</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">float </td>
<td class="paramname"> <em>green</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">float </td>
<td class="paramname"> <em>blue</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">float </td>
<td class="paramname"> <em>alpha</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></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>red,:</em> </td><td>the red component of the color. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>green,:</em> </td><td>the green component of the color. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>blue,:</em> </td><td>the blue component of the color. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>alpha,:</em> </td><td>the alpha component of the color.</td></tr>
</table>
</dd>
</dl>
<p>Sets a custom color to the atom. </p>
</div>
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<a class="anchor" id="a79b7682b7cc89d0d394367992ea41293"></a><!-- doxytag: member="gcu::CrystalAtom::SetDefaultColor" ref="a79b7682b7cc89d0d394367992ea41293" args="()" -->
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<td class="memname">void gcu::CrystalAtom::SetDefaultColor </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td></td>
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<p>Gives the atom the default color. </p>
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<a class="anchor" id="a57a87f97ad06f6b3e64743515d3230ce"></a><!-- doxytag: member="gcu::CrystalAtom::SetRadius" ref="a57a87f97ad06f6b3e64743515d3230ce" args="(const GcuAtomicRadius &r)" -->
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<td class="memname">void gcu::CrystalAtom::SetRadius </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structGcuAtomicRadius.html">GcuAtomicRadius</a> & </td>
<td class="paramname"> <em>r</em></td>
<td> ) </td>
<td></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>r,:</em> </td><td>a <a class="el" href="structGcuAtomicRadius.html">GcuAtomicRadius</a> with the caracteristics of the atom radius. </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a class="anchor" id="ae103b582c0ddc3e5311abec1f323723d"></a><!-- doxytag: member="gcu::CrystalAtom::SetSize" ref="ae103b582c0ddc3e5311abec1f323723d" args="(double r)" -->
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<td class="memname">void gcu::CrystalAtom::SetSize </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"> <em>r</em></td>
<td> ) </td>
<td></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>r,:</em> </td><td>the new value of the atomic radius.</td></tr>
</table>
</dd>
</dl>
<p>Sets the value of the radius (in pm). </p>
</div>
</div>
<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="ae41dedc2e7aab818f12113dc22a910dc"></a><!-- doxytag: member="gcu::CrystalAtom::m_bCustomColor" ref="ae41dedc2e7aab818f12113dc22a910dc" args="" -->
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<td class="memname">bool <a class="el" href="classgcu_1_1CrystalAtom.html#ae41dedc2e7aab818f12113dc22a910dc">gcu::CrystalAtom::m_bCustomColor</a><code> [protected]</code></td>
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<p>False if the color used is the default color and true if it is a user defined color. </p>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00210">210</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
<p>Referenced by <a class="el" href="crystalatom_8h_source.html#l00094">HasCustomColor()</a>.</p>
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<a class="anchor" id="a0bbe37ae9fe9f8959b23bd373181fb9e"></a><!-- doxytag: member="gcu::CrystalAtom::m_fAlpha" ref="a0bbe37ae9fe9f8959b23bd373181fb9e" args="" -->
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<td class="memname">float <a class="el" href="classgcu_1_1CrystalAtom.html#a0bbe37ae9fe9f8959b23bd373181fb9e">gcu::CrystalAtom::m_fAlpha</a><code> [protected]</code></td>
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<p>The alpha component of the color of the sphere representing the atom. </p>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00206">206</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
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<a class="anchor" id="acd9be65b37b7873e3fd248f7e407501b"></a><!-- doxytag: member="gcu::CrystalAtom::m_fBlue" ref="acd9be65b37b7873e3fd248f7e407501b" args="" -->
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<td class="memname">float <a class="el" href="classgcu_1_1CrystalAtom.html#acd9be65b37b7873e3fd248f7e407501b">gcu::CrystalAtom::m_fBlue</a><code> [protected]</code></td>
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<p>The blue component of the color of the sphere representing the atom. </p>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00194">194</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
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<a class="anchor" id="ada1bb25adb7fe5190bfda096904f919f"></a><!-- doxytag: member="gcu::CrystalAtom::m_fGreen" ref="ada1bb25adb7fe5190bfda096904f919f" args="" -->
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<td class="memname">float <a class="el" href="classgcu_1_1CrystalAtom.html#ada1bb25adb7fe5190bfda096904f919f">gcu::CrystalAtom::m_fGreen</a><code> [protected]</code></td>
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<p>The green component of the color of the sphere representing the atom. </p>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00202">202</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
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</div>
<a class="anchor" id="ad963587bca5555da806ed97854bd5be6"></a><!-- doxytag: member="gcu::CrystalAtom::m_fRed" ref="ad963587bca5555da806ed97854bd5be6" args="" -->
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<td class="memname">float <a class="el" href="classgcu_1_1CrystalAtom.html#ad963587bca5555da806ed97854bd5be6">gcu::CrystalAtom::m_fRed</a><code> [protected]</code></td>
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<p>The red component of the color of the sphere representing the atom. </p>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00198">198</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
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<a class="anchor" id="a88d2c73d283d166e621aa3b18b83efd2"></a><!-- doxytag: member="gcu::CrystalAtom::m_nCleave" ref="a88d2c73d283d166e621aa3b18b83efd2" args="" -->
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<td class="memname">int <a class="el" href="classgcu_1_1CrystalAtom.html#a88d2c73d283d166e621aa3b18b83efd2">gcu::CrystalAtom::m_nCleave</a><code> [protected]</code></td>
</tr>
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<p>When cleavages (see <a class="el" href="classgcu_1_1CrystalCleavage.html">CrystalCleavage</a> class documentation) are defined, the atom might be cleaved. m_nCleave is the number of <a class="el" href="classgcu_1_1CrystalCleavage.html">CrystalCleavage</a> instances which remove the atom. If this member is not 0, the atom will not be displayed. </p>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00220">220</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
<p>Referenced by <a class="el" href="crystalatom_8h_source.html#l00124">Cleave()</a>, and <a class="el" href="crystalatom_8h_source.html#l00175">IsCleaved()</a>.</p>
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<a class="anchor" id="a3249d1711608c6b10689895f6ceea800"></a><!-- doxytag: member="gcu::CrystalAtom::m_Radius" ref="a3249d1711608c6b10689895f6ceea800" args="" -->
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<td class="memname"><a class="el" href="structGcuAtomicRadius.html">GcuAtomicRadius</a> <a class="el" href="classgcu_1_1CrystalAtom.html#a3249d1711608c6b10689895f6ceea800">gcu::CrystalAtom::m_Radius</a><code> [protected]</code></td>
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<div class="memdoc">
<p>The <a class="el" href="structGcuAtomicRadius.html">GcuAtomicRadius</a> containing the radius caracteristics of the atom. </p>
<p>Definition at line <a class="el" href="crystalatom_8h_source.html#l00214">214</a> of file <a class="el" href="crystalatom_8h_source.html">crystalatom.h</a>.</p>
<p>Referenced by <a class="el" href="crystalatom_8h_source.html#l00167">GetRadius()</a>, and <a class="el" href="crystalatom_8h_source.html#l00163">r()</a>.</p>
</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="crystalatom_8h_source.html">crystalatom.h</a></li>
</ul>
</div>
<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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