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<title>The Gnome Chemistry Utils: gcu::Atom Class Reference</title>
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<div id="projectname">The Gnome Chemistry Utils
 <span id="projectnumber">0.14.2</span>
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<li class="navelem"><a class="el" href="namespacegcu.html">gcu</a></li><li class="navelem"><a class="el" href="classgcu_1_1Atom.html">Atom</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">gcu::Atom Class Reference</div> </div>
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<p><code>#include <<a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>></code></p>
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Inheritance diagram for gcu::Atom:</div>
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<area href="classgcu_1_1Object.html" alt="gcu::Object" shape="rect" coords="73,0,210,24"/>
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<area href="classgcr_1_1Atom.html" alt="gcr::Atom" shape="rect" coords="147,112,284,136"/>
<area href="classgcp_1_1FragmentAtom.html" alt="gcp::FragmentAtom" shape="rect" coords="0,168,137,192"/>
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<tr class="heading"><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:aa8943d4fa17eef381fd5d6b2b16cb3c5"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#aa8943d4fa17eef381fd5d6b2b16cb3c5">Atom</a> ()</td></tr>
<tr class="memitem:aae941cba7af49c8b1a1d1bfc635a36b8"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#aae941cba7af49c8b1a1d1bfc635a36b8">Atom</a> (int Z, double <a class="el" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a>, double <a class="el" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a>, double <a class="el" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a>=0.)</td></tr>
<tr class="memitem:a7610b9679bf0dbfa6febefed539afc8d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a7610b9679bf0dbfa6febefed539afc8d">Atom</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> &a)</td></tr>
<tr class="memitem:a73b1c38cbd4118c055720c7aec030b89"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Atom.html">Atom</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a73b1c38cbd4118c055720c7aec030b89">operator=</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> &a)</td></tr>
<tr class="memitem:a6761fd5db008d0984e1fa056c385459b"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a6761fd5db008d0984e1fa056c385459b">~Atom</a> ()</td></tr>
<tr class="memitem:a8e0470a96bc1fe3f1a2ceab7afc3fb63"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a8e0470a96bc1fe3f1a2ceab7afc3fb63">Distance</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom)</td></tr>
<tr class="memitem:ab60ac47e3be8db95e1c9f2c2e986ff71"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ab60ac47e3be8db95e1c9f2c2e986ff71">zoom</a> (double ZoomFactor)</td></tr>
<tr class="memitem:a8c63d0cca391f39f43f9f58fa7afc9f4"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a8c63d0cca391f39f43f9f58fa7afc9f4">GetCoords</a> (double *<a class="el" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a>, double *<a class="el" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a>, double *<a class="el" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a>=NULL) const </td></tr>
<tr class="memitem:ab9dbdfc744e2d8edf99f4009215866c6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ab9dbdfc744e2d8edf99f4009215866c6">SetCoords</a> (double <a class="el" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a>, double <a class="el" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a>, double <a class="el" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a>=0)</td></tr>
<tr class="memitem:a3b5b44c467ea583adbaa77c263f33a8a"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a3b5b44c467ea583adbaa77c263f33a8a">GetZ</a> () const </td></tr>
<tr class="memitem:a38a15b6551a3eb6646206ba933af1fff"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a38a15b6551a3eb6646206ba933af1fff">SetZ</a> (int Z)</td></tr>
<tr class="memitem:ae22a3f7878ca7b08aa93004587303d9d"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ae22a3f7878ca7b08aa93004587303d9d">SetCharge</a> (char Charge)</td></tr>
<tr class="memitem:abdfd5d40227e19f53db6baee57c30260"><td class="memItemLeft" align="right" valign="top">char </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#abdfd5d40227e19f53db6baee57c30260">GetCharge</a> ()</td></tr>
<tr class="memitem:a4371e488d9548ea7d9b6ee48c3be83bc"><td class="memItemLeft" align="right" valign="top">virtual const gchar * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a4371e488d9548ea7d9b6ee48c3be83bc">GetSymbol</a> () const </td></tr>
<tr class="memitem:a374ed31f84f3400bf107c8fc5557acb3"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a374ed31f84f3400bf107c8fc5557acb3">AddBond</a> (<a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond)</td></tr>
<tr class="memitem:a687994b362c10a22a301aa12a960ce37"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a687994b362c10a22a301aa12a960ce37">RemoveBond</a> (<a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond)</td></tr>
<tr class="memitem:a845f98c4e1bb2fe68dfa3fc61a83f79d"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a> () const </td></tr>
<tr class="memitem:a483d6aec85bb09acf681d0070f46149c"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a> () const </td></tr>
<tr class="memitem:aca911471b8848a4c78205c328557a7cc"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a> () const </td></tr>
<tr class="memitem:a4b693135365bae35648c96e6788407f0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Vector.html">Vector</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a4b693135365bae35648c96e6788407f0">GetVector</a> () const </td></tr>
<tr class="memitem:a2c4b85fd9b08205696fc40d86ca1aebe"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a2c4b85fd9b08205696fc40d86ca1aebe">GetFirstBond</a> (std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::iterator &i)</td></tr>
<tr class="memitem:aca168b840447f66d587d71d2aeafd274"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Bond.html">Bond</a> const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#aca168b840447f66d587d71d2aeafd274">GetFirstBond</a> (std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::const_iterator &i) const </td></tr>
<tr class="memitem:acb42e7980b0bc5a070324f1fc07fa989"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#acb42e7980b0bc5a070324f1fc07fa989">GetNextBond</a> (std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::iterator &i)</td></tr>
<tr class="memitem:ab853606fc4c4d0ec61cb205fa97f9544"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Bond.html">Bond</a> const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ab853606fc4c4d0ec61cb205fa97f9544">GetNextBond</a> (std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::const_iterator &i) const </td></tr>
<tr class="memitem:a2eceb0aec2b8a0e30bba183af356d200"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a2eceb0aec2b8a0e30bba183af356d200">GetBond</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom) const </td></tr>
<tr class="memitem:a026adef7ae137f92d2a4418dd94d1a30"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a026adef7ae137f92d2a4418dd94d1a30">GetBondsNumber</a> () const </td></tr>
<tr class="memitem:a4d8e69e2c01645367c6c76c2d92c2433"><td class="memItemLeft" align="right" valign="top">virtual xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a4d8e69e2c01645367c6c76c2d92c2433">Save</a> (xmlDocPtr xml) const </td></tr>
<tr class="memitem:a290a0a8c69ca6667d19e9d7f1d71d190"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a290a0a8c69ca6667d19e9d7f1d71d190">Load</a> (xmlNodePtr node)</td></tr>
<tr class="memitem:a383a09c3d8bdbd0300bdc2b57b02e1ab"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a383a09c3d8bdbd0300bdc2b57b02e1ab">LoadNode</a> (xmlNodePtr node)</td></tr>
<tr class="memitem:af8a3a91412c9a585f60d49fb6e49280e"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#af8a3a91412c9a585f60d49fb6e49280e">SaveNode</a> (xmlDocPtr xml, xmlNodePtr node) const </td></tr>
<tr class="memitem:aab7ca2a758dc755d3da936cae82d1485"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#aab7ca2a758dc755d3da936cae82d1485">Move</a> (double <a class="el" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a>, double <a class="el" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a>, double <a class="el" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a>=0.)</td></tr>
<tr class="memitem:a2ff6b67af11f6414fe8e972507e37f62"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a2ff6b67af11f6414fe8e972507e37f62">Transform2D</a> (<a class="el" href="classgcu_1_1Matrix2D.html">Matrix2D</a> &m, double <a class="el" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a>, double <a class="el" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a>)</td></tr>
<tr class="memitem:ac9d2135007a4010d1e4ffffb9aec3227"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ac9d2135007a4010d1e4ffffb9aec3227">SetProperty</a> (unsigned property, char const *value)</td></tr>
<tr class="memitem:a759e64fd28f939c73a5130c49e876618"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a759e64fd28f939c73a5130c49e876618">GetProperty</a> (unsigned property) const </td></tr>
<tr class="memitem:a8130046e2fd1ae7085935efe65c2ef94"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a8130046e2fd1ae7085935efe65c2ef94">IsInCycle</a> (<a class="el" href="classgcu_1_1Cycle.html">Cycle</a> *pCycle)</td></tr>
<tr class="memitem:a3d8c5f65e203f23175c3422ef548e7f8"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a3d8c5f65e203f23175c3422ef548e7f8">Match</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *atom, <a class="el" href="classgcu_1_1AtomMatchState.html">AtomMatchState</a> &state)</td></tr>
<tr class="memitem:af41bf7c02e9a0dbf77156a9813fa1924"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#af41bf7c02e9a0dbf77156a9813fa1924">Name</a> ()</td></tr>
<tr class="memitem:a88f4565c7f8d1d8fd7575855655139bb"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a88f4565c7f8d1d8fd7575855655139bb">NetToCartesian</a> (double a, double b, double c, double alpha, double beta, double gamma)</td></tr>
<tr class="inherit_header pub_methods_classgcu_1_1Object"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classgcu_1_1Object')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classgcu_1_1Object.html">gcu::Object</a></td></tr>
<tr class="memitem:a6f15e766fdfb066008bd4b0779574549 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a6f15e766fdfb066008bd4b0779574549">Object</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id=OtherType)</td></tr>
<tr class="memitem:a3e575300e517594b0c2c161d6e704352 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a3e575300e517594b0c2c161d6e704352">~Object</a> ()</td></tr>
<tr class="memitem:a9c900a7a382cad4a995edbb10b8f179d inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a9c900a7a382cad4a995edbb10b8f179d">GetType</a> () const </td></tr>
<tr class="memitem:ac45cdb13cf013066a3704054c9d06ed0 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ac45cdb13cf013066a3704054c9d06ed0">SetId</a> (gchar const *Id)</td></tr>
<tr class="memitem:aef94f9435a51669a518b5a713f24e7ca inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">char const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aef94f9435a51669a518b5a713f24e7ca">GetId</a> () const </td></tr>
<tr class="memitem:ad054f1ae4f0cd697765aa4d2007521b2 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ad054f1ae4f0cd697765aa4d2007521b2">AddChild</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *object)</td></tr>
<tr class="memitem:adf610a8402000e9f9ae9ad0135c1d7da inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#adf610a8402000e9f9ae9ad0135c1d7da">GetMolecule</a> () const </td></tr>
<tr class="memitem:adaba7d20336b8036b6bfb7ef3884880a inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#adaba7d20336b8036b6bfb7ef3884880a">GetReaction</a> () const </td></tr>
<tr class="memitem:a841968632d00e5d879694ee84737225b inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a841968632d00e5d879694ee84737225b">GetGroup</a> () const </td></tr>
<tr class="memitem:a274432165e22fa89a375eded192631db inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Document.html">Document</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a274432165e22fa89a375eded192631db">GetDocument</a> () const </td></tr>
<tr class="memitem:ab65facd99621938dfbd6330ccee1e9f7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Application.html">Application</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ab65facd99621938dfbd6330ccee1e9f7">GetApplication</a> () const </td></tr>
<tr class="memitem:a158be0361aaadca1d03fdb5b5d3089b2 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a158be0361aaadca1d03fdb5b5d3089b2">GetParentOfType</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id) const </td></tr>
<tr class="memitem:a026b22b02b09f8f9f535197f2d936c07 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a026b22b02b09f8f9f535197f2d936c07">GetChild</a> (const gchar *Id) const </td></tr>
<tr class="memitem:a5fe8cfbfe83645c292f8895aba4a91d0 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a5fe8cfbfe83645c292f8895aba4a91d0">GetFirstChild</a> (std::map< std::string, <a class="el" href="classgcu_1_1Object.html">Object</a> * >::iterator &i)</td></tr>
<tr class="memitem:a70ff8a33f72e424f3c39b3d0edbe9903 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a70ff8a33f72e424f3c39b3d0edbe9903">GetNextChild</a> (std::map< std::string, <a class="el" href="classgcu_1_1Object.html">Object</a> * >::iterator &i)</td></tr>
<tr class="memitem:ab70083d7ebb2cf32180c5383b5bb428c inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ab70083d7ebb2cf32180c5383b5bb428c">GetDescendant</a> (const char *Id) const </td></tr>
<tr class="memitem:abacb2c2002726a3237ffbd0e50e3df52 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#abacb2c2002726a3237ffbd0e50e3df52">GetParent</a> () const </td></tr>
<tr class="memitem:a0ffe1f48151c92f167eeec303277e45c inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a0ffe1f48151c92f167eeec303277e45c">SetParent</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *Parent)</td></tr>
<tr class="memitem:a07de41cb137a650b51920d6186fc82d7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a07de41cb137a650b51920d6186fc82d7">SaveChildren</a> (xmlDocPtr xml, xmlNodePtr node) const </td></tr>
<tr class="memitem:a5f99b290d7e48c38738342dfc984865d inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a5f99b290d7e48c38738342dfc984865d">SaveId</a> (xmlNodePtr node) const </td></tr>
<tr class="memitem:ad533d866f1478a972a1896499e5659a5 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ad533d866f1478a972a1896499e5659a5">GetNodeByProp</a> (xmlNodePtr node, char const *Property, char const *Id)</td></tr>
<tr class="memitem:aa19f11cca83189a955f0a7bf2919562b inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aa19f11cca83189a955f0a7bf2919562b">GetNextNodeByProp</a> (xmlNodePtr node, char const *Property, char const *Id)</td></tr>
<tr class="memitem:a4e8712098d673c958fb0c72488058f80 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a4e8712098d673c958fb0c72488058f80">GetNodeByName</a> (xmlNodePtr node, char const *<a class="el" href="classgcu_1_1Object.html#ae19033807f4b7ee9321f308bb0ffd3b9">Name</a>)</td></tr>
<tr class="memitem:a2dc10bf48d3ebfe86853cace21e9abf2 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a2dc10bf48d3ebfe86853cace21e9abf2">GetNextNodeByName</a> (xmlNodePtr node, char const *<a class="el" href="classgcu_1_1Object.html#ae19033807f4b7ee9321f308bb0ffd3b9">Name</a>)</td></tr>
<tr class="memitem:a28f682a2891b17ae57c5f346c95d6f50 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a28f682a2891b17ae57c5f346c95d6f50">HasChildren</a> () const </td></tr>
<tr class="memitem:a5e3d6fbdc8b10a9dbf43de2c052fff05 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a5e3d6fbdc8b10a9dbf43de2c052fff05">GetChildrenNumber</a> () const </td></tr>
<tr class="memitem:aa47c38061c6a2e51947d89c86fbae630 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aa47c38061c6a2e51947d89c86fbae630">GetAtomAt</a> (double x, double y, double z=0.)</td></tr>
<tr class="memitem:af1da4274cbbf0ca56bf8d380743d49e7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#af1da4274cbbf0ca56bf8d380743d49e7">Build</a> (std::set< <a class="el" href="classgcu_1_1Object.html">Object</a> * > const &Children) throw (std::invalid_argument)</td></tr>
<tr class="memitem:aedeec6e6b66e1a35e6d2f3ef75c94a09 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aedeec6e6b66e1a35e6d2f3ef75c94a09">GetYAlign</a> ()</td></tr>
<tr class="memitem:acc55e92f84843058139d3a729aa6afcb inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#acc55e92f84843058139d3a729aa6afcb">BuildContextualMenu</a> (<a class="el" href="classgcu_1_1UIManager.html">UIManager</a> *uim, <a class="el" href="classgcu_1_1Object.html">Object</a> *object, double x, double y)</td></tr>
<tr class="memitem:acf16b429a6875e5620fa8051446ef34c inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#acf16b429a6875e5620fa8051446ef34c">EmitSignal</a> (<a class="el" href="namespacegcu.html#af13348b065987fa4ca74ca0fb1ffa48e">SignalId</a> Signal)</td></tr>
<tr class="memitem:a1ad183ecf7e5b5c42db100da03221e46 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a1ad183ecf7e5b5c42db100da03221e46">OnSignal</a> (<a class="el" href="namespacegcu.html#af13348b065987fa4ca74ca0fb1ffa48e">SignalId</a> Signal, <a class="el" href="classgcu_1_1Object.html">Object</a> *Child)</td></tr>
<tr class="memitem:a8b4da97be50a4ceea941ab8aa8ece825 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a8b4da97be50a4ceea941ab8aa8ece825">Lock</a> (bool state=true)</td></tr>
<tr class="memitem:a4094e3d8cf58a6f9de9cb6c6b6fed8c8 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a4094e3d8cf58a6f9de9cb6c6b6fed8c8">IsLocked</a> ()</td></tr>
<tr class="memitem:a79e87eb91afb57ebf188fdc3753cba7d inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a79e87eb91afb57ebf188fdc3753cba7d">GetFirstLink</a> (std::set< <a class="el" href="classgcu_1_1Object.html">Object</a> * >::iterator &i)</td></tr>
<tr class="memitem:a61b227220c2b831b7196d2bd61201bdc inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a61b227220c2b831b7196d2bd61201bdc">GetNextLink</a> (std::set< <a class="el" href="classgcu_1_1Object.html">Object</a> * >::iterator &i)</td></tr>
<tr class="memitem:a0173055f0ba60038d9d913b5f09bb354 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a0173055f0ba60038d9d913b5f09bb354">Link</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *object)</td></tr>
<tr class="memitem:a606a257c41cd9cc177c98958fdf2ae3d inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a606a257c41cd9cc177c98958fdf2ae3d">Unlink</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *object)</td></tr>
<tr class="memitem:a786610ff1992e4aa1acff883b5479ec7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a786610ff1992e4aa1acff883b5479ec7">OnUnlink</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *object)</td></tr>
<tr class="memitem:a97106b6ec695ac946d0a1d04293eef79 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a97106b6ec695ac946d0a1d04293eef79">GetPossibleAncestorTypes</a> (std::set< <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> > &types) const </td></tr>
<tr class="memitem:af972c30c9990923c34c54754654c3e72 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#af972c30c9990923c34c54754654c3e72">OnLoaded</a> ()</td></tr>
<tr class="memitem:a01ea0147ad675e139ddea7aaa2af503c inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a01ea0147ad675e139ddea7aaa2af503c">SetDirty</a> (bool dirty=true)</td></tr>
<tr class="memitem:adce3873de56ddf2abe7dba89e127fc06 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#adce3873de56ddf2abe7dba89e127fc06">Clear</a> ()</td></tr>
<tr class="memitem:a373cd8efa4af70cdbc4a77086aee82c7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a373cd8efa4af70cdbc4a77086aee82c7">Identity</a> ()</td></tr>
<tr class="memitem:aceff810bb8bfad7f9a7152eef3dfe46e inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual char const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aceff810bb8bfad7f9a7152eef3dfe46e">HasPropertiesDialog</a> () const </td></tr>
<tr class="memitem:a8f3da29ebe1fcc1534ac65b724f3582f inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a8f3da29ebe1fcc1534ac65b724f3582f">CanSelect</a> () const </td></tr>
<tr class="memitem:a67e3c8ee2104cd937aea48dabde7d319 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a67e3c8ee2104cd937aea48dabde7d319">NotifyEmpty</a> ()</td></tr>
<tr class="memitem:a45b59346e78b7a9927d379bb65df1710 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a45b59346e78b7a9927d379bb65df1710">ShowPropertiesDialog</a> ()</td></tr>
<tr class="memitem:a71e2333cf4d47abdd272a8709361829f inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a71e2333cf4d47abdd272a8709361829f">GetDirty</a> (void) const </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a6fce7561c1e898b10dd418efbd2c7b1a"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a6fce7561c1e898b10dd418efbd2c7b1a">m_Z</a></td></tr>
<tr class="memitem:ab2c4ef4fd922120c4ff441c64aaa2ee1"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#ab2c4ef4fd922120c4ff441c64aaa2ee1">m_x</a></td></tr>
<tr class="memitem:af242ce3cb476a56ed16dc78ceeed6901"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#af242ce3cb476a56ed16dc78ceeed6901">m_y</a></td></tr>
<tr class="memitem:a41a1b4161c01147c951c75f1ff4cae37"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a41a1b4161c01147c951c75f1ff4cae37">m_z</a></td></tr>
<tr class="memitem:a733db6db77be736879f983fbb11bcdaa"><td class="memItemLeft" align="right" valign="top">char </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a733db6db77be736879f983fbb11bcdaa">m_Charge</a></td></tr>
<tr class="memitem:a61f209632162c8553a7ebde3c4b194f9"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Atom.html#a61f209632162c8553a7ebde3c4b194f9">m_Bonds</a></td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_static_methods_classgcu_1_1Object"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classgcu_1_1Object')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classgcu_1_1Object.html">gcu::Object</a></td></tr>
<tr class="memitem:aea6734ca6bde8ae3e0788db43928f42e inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aea6734ca6bde8ae3e0788db43928f42e">AddType</a> (std::string TypeName, <a class="el" href="classgcu_1_1Object.html">Object</a> *(*CreateFunc)(), <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> id=OtherType)</td></tr>
<tr class="memitem:a3645f28b3df32308f135ec5b0aac0793 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a3645f28b3df32308f135ec5b0aac0793">AddAlias</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> id, std::string TypeName)</td></tr>
<tr class="memitem:a0d3837f66eccae5ce73573ca95930dbc inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a0d3837f66eccae5ce73573ca95930dbc">CreateObject</a> (const std::string &TypeName, <a class="el" href="classgcu_1_1Object.html">Object</a> *parent=NULL)</td></tr>
<tr class="memitem:a6038f7f7c0f58cd1aa12bd8237ac1024 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a6038f7f7c0f58cd1aa12bd8237ac1024">GetTypeId</a> (const std::string &<a class="el" href="classgcu_1_1Object.html#ae19033807f4b7ee9321f308bb0ffd3b9">Name</a>)</td></tr>
<tr class="memitem:a9e57005d5129e341ce3dcd4d3c188eaf inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a9e57005d5129e341ce3dcd4d3c188eaf">GetTypeName</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id)</td></tr>
<tr class="memitem:a47d2dd181c9934ab4671c526a251295f inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a47d2dd181c9934ab4671c526a251295f">AddMenuCallback</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id, <a class="el" href="namespacegcu.html#aea85ee1e0ab66342f28448b2e7a9174d">BuildMenuCb</a> cb)</td></tr>
<tr class="memitem:a3eb4fd4787f224f5e7e3e5f8d1fc2abb inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a3eb4fd4787f224f5e7e3e5f8d1fc2abb">AddRule</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> type1, <a class="el" href="namespacegcu.html#a19c49d12e7c0a96ae2be6c6c33c44b47">RuleId</a> rule, <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> type2)</td></tr>
<tr class="memitem:a13348c710f80100519c94d10dff3d0e0 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a13348c710f80100519c94d10dff3d0e0">AddRule</a> (const std::string &type1, <a class="el" href="namespacegcu.html#a19c49d12e7c0a96ae2be6c6c33c44b47">RuleId</a> rule, const std::string &type2)</td></tr>
<tr class="memitem:a96a3ea77a33f4721399f00e6b341cde2 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static const std::set< <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a96a3ea77a33f4721399f00e6b341cde2">GetRules</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> type, <a class="el" href="namespacegcu.html#a19c49d12e7c0a96ae2be6c6c33c44b47">RuleId</a> rule)</td></tr>
<tr class="memitem:a44d44e134f05976140e8e4686b0cd936 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static const std::set< <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a44d44e134f05976140e8e4686b0cd936">GetRules</a> (const std::string &type, <a class="el" href="namespacegcu.html#a19c49d12e7c0a96ae2be6c6c33c44b47">RuleId</a> rule)</td></tr>
<tr class="memitem:a8159c48a642f3410913e635e23d77f24 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a8159c48a642f3410913e635e23d77f24">SetCreationLabel</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id, std::string Label)</td></tr>
<tr class="memitem:a90c6d068fdbea8cffe8690f177b5c939 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static const std::string & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a90c6d068fdbea8cffe8690f177b5c939">GetCreationLabel</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id)</td></tr>
<tr class="memitem:a591fb1674ad415be983b6810ef484326 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static const std::string & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a591fb1674ad415be983b6810ef484326">GetCreationLabel</a> (const std::string &TypeName)</td></tr>
<tr class="memitem:a380275771a250b94785e43286525c74e inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="namespacegcu.html#af13348b065987fa4ca74ca0fb1ffa48e">SignalId</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a380275771a250b94785e43286525c74e">CreateNewSignalId</a> ()</td></tr>
<tr class="inherit_header pro_methods_classgcu_1_1Object"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classgcu_1_1Object')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classgcu_1_1Object.html">gcu::Object</a></td></tr>
<tr class="memitem:a98a9025b609f6ba46ab3b273792ee51e inherit pro_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classgcu_1_1Dialog.html">Dialog</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a98a9025b609f6ba46ab3b273792ee51e">BuildPropertiesDialog</a> ()</td></tr>
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<a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>This class is used to represent atoms. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00046">46</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
</div><h2>Constructor & Destructor Documentation</h2>
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<p>The default constructor. Creates an atom with atomic number set to 0. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a585be3b15c7324e813a09222f325bd05">gcp::Atom</a>, and <a class="el" href="classgcr_1_1Atom.html#a98d209e08beb455c8d051512c08ce5c9">gcr::Atom</a>.</p>
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<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>Z</em>, </td>
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<td class="paramtype">double </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">Z</td><td>the atomic number of the new atom. </td></tr>
<tr><td class="paramname">x</td><td>the x coordinate of the new atom. </td></tr>
<tr><td class="paramname">y</td><td>the y coordinate of the new atom. </td></tr>
<tr><td class="paramname">z</td><td>the z coordinate of the new atom.</td></tr>
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<p>Creates an atom. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a16a9b2bca38d64c69e28f067005ecaa1">gcp::Atom</a>, and <a class="el" href="classgcr_1_1Atom.html#a24d690baa560aab0ffc66a2a2669148e">gcr::Atom</a>.</p>
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<td class="memname">gcu::Atom::Atom </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> & </td>
<td class="paramname"><em>a</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">a</td><td>the <a class="el" href="classgcu_1_1Atom.html">Atom</a> to duplicate.</td></tr>
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<p>Creates a new atom identical to a without any bond. </p>
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<td class="memname">virtual gcu::Atom::~Atom </td>
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<p>The destructor of <a class="el" href="classgcu_1_1Atom.html">Atom</a>. It removes bonds but do not delete the associated <a class="el" href="classgcu_1_1Bond.html">Bond</a> instances. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a4ea961d1567b04333cf5a2d3ea2a3978">gcp::Atom</a>, and <a class="el" href="classgcr_1_1Atom.html#a73697f87aee4cfb68f98b536755bab88">gcr::Atom</a>.</p>
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<h2>Member Function Documentation</h2>
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<td class="memname">virtual void gcu::Atom::AddBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td>
<td class="paramname"><em>pBond</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pBond</td><td>a pointer to the new <a class="el" href="classgcu_1_1Bond.html">Bond</a> to this <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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<p>Adds a <a class="el" href="classgcu_1_1Bond.html">Bond</a>. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a009e0ce9ae2f156c2d292d1275d5f685">gcp::Atom</a>.</p>
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<td class="memname">double gcu::Atom::Distance </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>pAtom</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pAtom</td><td>a pointer to an <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>the distance between the <a class="el" href="classgcu_1_1Atom.html">Atom</a> at pAtom and this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
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<td class="memname"><a class="el" href="classgcu_1_1Bond.html">Bond</a>* gcu::Atom::GetBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>pAtom</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pAtom</td><td>a pointer to an <a class="el" href="classgcu_1_1Atom.html">Atom</a> instance. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>a pointer to the <a class="el" href="classgcu_1_1Bond.html">Bond</a> shared by pAtom and this <a class="el" href="classgcu_1_1Atom.html">Atom</a> if it exists or NULL. </dd></dl>
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<td class="memname">int gcu::Atom::GetBondsNumber </td>
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<dl class="section return"><dt>Returns</dt><dd>the number of <a class="el" href="classgcu_1_1Bond.html">Bond</a> instances shared by this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. It does not take multiplicity of bonds into account. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00200">200</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00323">m_Bonds</a>.</p>
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<td class="memname">char gcu::Atom::GetCharge </td>
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<dl class="section return"><dt>Returns</dt><dd>the formal charge of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00128">128</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00319">m_Charge</a>.</p>
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<td class="memname">bool gcu::Atom::GetCoords </td>
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<td class="paramtype">double * </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">x</td><td>a pointer to the double value which will receive the x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
<tr><td class="paramname">y</td><td>a pointer to the double value which will receive the y coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
<tr><td class="paramname">z</td><td>a pointer to the double value which will receive the z coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL for 2D representations.</td></tr>
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<p>Retrieves the coordinates of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
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<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#a7ae5e90dd76580aee332c6ef59e89298">gcu::Object</a>.</p>
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<td class="memname"><a class="el" href="classgcu_1_1Bond.html">Bond</a>* gcu::Atom::GetFirstBond </td>
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<p>Use this function to retrieve the first <a class="el" href="classgcu_1_1Bond.html">Bond</a> of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> and initialize the iterator. </p>
<dl class="section return"><dt>Returns</dt><dd>the first <a class="el" href="classgcu_1_1Bond.html">Bond</a> of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL if the <a class="el" href="classgcu_1_1Atom.html">Atom</a> has is not bonded. </dd></dl>
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<td>(</td>
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<td class="paramname"><em>i</em></td><td>)</td>
<td> const</td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">i</td><td>a C++ std::map constant iterator.</td></tr>
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</dd>
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<p>Use this function to retrieve the first <a class="el" href="classgcu_1_1Bond.html">Bond</a> of this constant <a class="el" href="classgcu_1_1Atom.html">Atom</a> and initialize the iterator. </p>
<dl class="section return"><dt>Returns</dt><dd>the first <a class="el" href="classgcu_1_1Bond.html">Bond</a> of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL if the <a class="el" href="classgcu_1_1Atom.html">Atom</a> has is not bonded. </dd></dl>
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<td class="memname"><a class="el" href="classgcu_1_1Bond.html">Bond</a>* gcu::Atom::GetNextBond </td>
<td>(</td>
<td class="paramtype">std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::iterator & </td>
<td class="paramname"><em>i</em></td><td>)</td>
<td></td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">i</td><td>a C++ std::map iterator initialized by <a class="el" href="classgcu_1_1Atom.html#a2c4b85fd9b08205696fc40d86ca1aebe">Atom::GetFirstBond</a>.</td></tr>
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</dd>
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<p>Use this method to iterate through the list of <a class="el" href="classgcu_1_1Bond.html">Bond</a> instances of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<dl class="section return"><dt>Returns</dt><dd>the next <a class="el" href="classgcu_1_1Bond.html">Bond</a> of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL. </dd></dl>
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<td class="memname"><a class="el" href="classgcu_1_1Bond.html">Bond</a> const* gcu::Atom::GetNextBond </td>
<td>(</td>
<td class="paramtype">std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="classgcu_1_1Bond.html">Bond</a> * >::const_iterator & </td>
<td class="paramname"><em>i</em></td><td>)</td>
<td> const</td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">i</td><td>a C++ std::map constant iterator initialized by Atom::GetFirstBond(std::map< Atom *, Bond * >::const_iterator&).</td></tr>
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</dd>
</dl>
<p>Use this method to iterate through the list of <a class="el" href="classgcu_1_1Bond.html">Bond</a> instances of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<dl class="section return"><dt>Returns</dt><dd>the next <a class="el" href="classgcu_1_1Bond.html">Bond</a> of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL. </dd></dl>
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<td class="memname">std::string gcu::Atom::GetProperty </td>
<td>(</td>
<td class="paramtype">unsigned </td>
<td class="paramname"><em>property</em></td><td>)</td>
<td> const</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">property</td><td>the identity of the property as defined in <a class="el" href="objprops_8h.html">objprops.h</a>.</td></tr>
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</dd>
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<p>Used by the <a class="el" href="classgcu_1_1Loader.html" title="class used to implement serialization engines.">gcu::Loader</a> mechanism to retrieve properties of atoms. </p>
<dl class="section return"><dt>Returns</dt><dd>the value of the property as a string. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#a9f612121600c791abbee16bb539975d7">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcr_1_1Atom.html#ac7a91f0accef35a1539ac09ca7b54d1b">gcr::Atom</a>.</p>
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<td class="memname">virtual const gchar* gcu::Atom::GetSymbol </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<dl class="section return"><dt>Returns</dt><dd>the atomic symbol of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL if the element is unknown. </dd></dl>
<p>Reimplemented in <a class="el" href="classgcp_1_1FragmentResidue.html#a83de50e53fbc175fbcc8026ec77c7d4a">gcp::FragmentResidue</a>.</p>
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<td class="memname"><a class="el" href="classgcu_1_1Vector.html">Vector</a> gcu::Atom::GetVector </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>a <a class="el" href="classgcu_1_1Vector.html" title="3D vector.">Vector</a> with the three <a class="el" href="classgcu_1_1Atom.html">Atom</a> space coordinates. </dd></dl>
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<td class="memname">int gcu::Atom::GetZ </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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<span class="mlabels"><span class="mlabel">inline</span></span> </td>
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<dl class="section return"><dt>Returns</dt><dd>the atomic number of the atom. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00111">111</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00303">m_Z</a>.</p>
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<td class="memname">bool gcu::Atom::IsInCycle </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Cycle.html">Cycle</a> * </td>
<td class="paramname"><em>pCycle</em></td><td>)</td>
<td></td>
</tr>
</table>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pCycle</td><td>a cycle in which the atom might be.</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>true if the atom lies in the cycle, false otherwise. </dd></dl>
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<td class="memname">virtual bool gcu::Atom::Load </td>
<td>(</td>
<td class="paramtype">xmlNodePtr </td>
<td class="paramname"><em>node</em></td><td>)</td>
<td></td>
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</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">node</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 an atom from an xmlNode. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#aa3ee33c25154d8e7bbe1e39de970c489">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a8eed490ca4ecc446a4a1cdc8aeb46f98">gcp::Atom</a>, <a class="el" href="classgcp_1_1FragmentAtom.html#aca577c2cb21b8fcb47fe0790cc41458a">gcp::FragmentAtom</a>, and <a class="el" href="classgcp_1_1FragmentResidue.html#add2c5572e5eed7d7d88d30f44c76226a">gcp::FragmentResidue</a>.</p>
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<td class="memname">virtual bool gcu::Atom::LoadNode </td>
<td>(</td>
<td class="paramtype">xmlNodePtr </td>
<td class="paramname"><em>node</em></td><td>)</td>
<td></td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">node</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>This virtual method is called at the end of the <a class="el" href="classgcu_1_1Atom.html#a290a0a8c69ca6667d19e9d7f1d71d190">Atom::Load</a> method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the <a class="el" href="classgcu_1_1Atom.html#a290a0a8c69ca6667d19e9d7f1d71d190">Atom::Load</a> method. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a5526b5a9b31aae0fe4d97f35680264d3">gcp::Atom</a>, and <a class="el" href="classgcr_1_1Atom.html#a8cb2a40703531143af35e4ea7bf35953">gcr::Atom</a>.</p>
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<td class="memname">virtual bool gcu::Atom::Match </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>atom</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classgcu_1_1AtomMatchState.html">AtomMatchState</a> & </td>
<td class="paramname"><em>state</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">atom</td><td>the atom to which the this instance is to be compared. </td></tr>
<tr><td class="paramname">state</td><td>the <a class="el" href="classgcu_1_1AtomMatchState.html">AtomMatchState</a> representing the current comparison state.</td></tr>
</table>
</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="section return"><dt>Returns</dt><dd>true if the atoms match, false otherwise. </dd></dl>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#ab19ede9511483d34fb841c98e13491a0">gcp::Atom</a>, and <a class="el" href="classgcp_1_1FragmentAtom.html#a56baed02ef40ab67c4d7ba50b25394e3">gcp::FragmentAtom</a>.</p>
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<td class="memname">virtual void gcu::Atom::Move </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"><em>x</em>, </td>
</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> = <code>0.</code> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">x</td><td>the x component of the transation vector. </td></tr>
<tr><td class="paramname">y</td><td>the y component of the transation vector. </td></tr>
<tr><td class="paramname">z</td><td>the z component of the transation vector.</td></tr>
</table>
</dd>
</dl>
<p>Used to move an <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#af5505430c421604ff7e26e4414197fbc">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#ab74a17bd03ec01c84a96d54c48ef48ea">gcp::Atom</a>.</p>
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<td class="memname">std::string gcu::Atom::Name </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
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</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<dl class="section return"><dt>Returns</dt><dd>the localized object generic name. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#ae19033807f4b7ee9321f308bb0ffd3b9">gcu::Object</a>.</p>
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<td class="memname">void gcu::Atom::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>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>alpha</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>beta</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>gamma</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">a,:</td><td>the a parameter of the unit cell. </td></tr>
<tr><td class="paramname">b,:</td><td>the b parameter of the unit cell. </td></tr>
<tr><td class="paramname">c,:</td><td>the c parameter of the unit cell. </td></tr>
<tr><td class="paramname">alpha,:</td><td>the alpha angle of the unit cell. </td></tr>
<tr><td class="paramname">beta,:</td><td>the beta angle of the unit cell. </td></tr>
<tr><td class="paramname">gamma,:</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>
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<td class="memname"><a class="el" href="classgcu_1_1Atom.html">Atom</a>& gcu::Atom::operator= </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> & </td>
<td class="paramname"><em>a</em></td><td>)</td>
<td></td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">a</td><td>the <a class="el" href="classgcu_1_1Atom.html">Atom</a> to copy.</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>an <a class="el" href="classgcu_1_1Atom.html">Atom</a> identical to a without any bond. </dd></dl>
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<td class="memname">virtual void gcu::Atom::RemoveBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td>
<td class="paramname"><em>pBond</em></td><td>)</td>
<td></td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pBond</td><td>a pointer to the <a class="el" href="classgcu_1_1Bond.html">Bond</a> to remove from this <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
</table>
</dd>
</dl>
<p>Removes a <a class="el" href="classgcu_1_1Bond.html">Bond</a>. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a41158b79556591cf4154ab0bed4139e4">gcp::Atom</a>.</p>
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<td class="memname">virtual xmlNodePtr gcu::Atom::Save </td>
<td>(</td>
<td class="paramtype">xmlDocPtr </td>
<td class="paramname"><em>xml</em></td><td>)</td>
<td> const</td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">xml</td><td>the xmlDoc used to save the document. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>a pointer to the xmlNode representing this <a class="el" href="classgcu_1_1Atom.html">Atom</a> or NULL if an error occured. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#aad462441e79fbd93e158f8294a198d11">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a67db585c20bdd33ac5ac071794b67dd5">gcp::Atom</a>, <a class="el" href="classgcp_1_1FragmentAtom.html#a143e33f55d77547cc9be39f2c5e248d0">gcp::FragmentAtom</a>, and <a class="el" href="classgcp_1_1FragmentResidue.html#aa9860847b53b41355982dc5d1d6c058a">gcp::FragmentResidue</a>.</p>
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<td class="memname">virtual bool gcu::Atom::SaveNode </td>
<td>(</td>
<td class="paramtype">xmlDocPtr </td>
<td class="paramname"><em>xml</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">xmlNodePtr </td>
<td class="paramname"><em>node</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td> const</td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">xml</td><td>the xmlDoc used to save the document. </td></tr>
<tr><td class="paramname">node</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>
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<p>This virtual method is called at the end of the <a class="el" href="classgcu_1_1Atom.html#a4d8e69e2c01645367c6c76c2d92c2433">Atom::Save</a> method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the <a class="el" href="classgcu_1_1Atom.html#a4d8e69e2c01645367c6c76c2d92c2433">Atom::Save</a> method. </p>
<p>Reimplemented in <a class="el" href="classgcr_1_1Atom.html#a6a4524b878ab19098e22070277e356a7">gcr::Atom</a>.</p>
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<td class="memname">virtual void gcu::Atom::SetCharge </td>
<td>(</td>
<td class="paramtype">char </td>
<td class="paramname"><em>Charge</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">Charge</td><td>the new formal charge of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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</dd>
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<p>Changes the formal charge of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00124">124</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00319">m_Charge</a>.</p>
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<td class="memname">void gcu::Atom::SetCoords </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"><em>x</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>y</em>, </td>
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<td class="paramkey"></td>
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<td class="paramname"><em>z</em> = <code>0</code> </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">x</td><td>the new x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
<tr><td class="paramname">y</td><td>the new y coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </td></tr>
<tr><td class="paramname">z</td><td>the new z coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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<p>Changes the position of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00107">107</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00307">m_x</a>, <a class="el" href="gcu_2atom_8h_source.html#l00311">m_y</a>, <a class="el" href="gcu_2atom_8h_source.html#l00315">m_z</a>, <a class="el" href="gcu_2atom_8h_source.html#l00148">x()</a>, <a class="el" href="gcu_2atom_8h_source.html#l00153">y()</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00158">z()</a>.</p>
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<td class="memname">bool gcu::Atom::SetProperty </td>
<td>(</td>
<td class="paramtype">unsigned </td>
<td class="paramname"><em>property</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">char const * </td>
<td class="paramname"><em>value</em> </td>
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<td></td>
<td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">property</td><td>the identity of the property as defined in <a class="el" href="objprops_8h.html">objprops.h</a>. </td></tr>
<tr><td class="paramname">value</td><td>the value of the property as a string.</td></tr>
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<p>Used by the <a class="el" href="classgcu_1_1Loader.html" title="class used to implement serialization engines.">gcu::Loader</a> mechanism to load properties of atoms. </p>
<dl class="section return"><dt>Returns</dt><dd>true on success. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#a47862fe83b1c3739ee37b8af81550644">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#ae39a3fe66e5bf72ecdf54eb2e08bd8dc">gcp::Atom</a>, and <a class="el" href="classgcr_1_1Atom.html#a3c343958bee49282b671a343218ae165">gcr::Atom</a>.</p>
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<td class="memname">virtual void gcu::Atom::SetZ </td>
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<td class="paramname"><em>Z</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">Z</td><td>the new atomic number of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>.</td></tr>
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<p>This method might be overrided by derived class since changing the atomic number generally changes most properties. The default behavior is just to change the atomic number and nothing else. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#ad3919236bd9ce0816e4a07712048e9df">gcp::Atom</a>, and <a class="el" href="classgcp_1_1FragmentAtom.html#aebd1c27ec2490d2b8d313a1aef819616">gcp::FragmentAtom</a>.</p>
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<td class="memname">virtual void gcu::Atom::Transform2D </td>
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<td class="paramname"><em>m</em>, </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">m</td><td>the 2D <a class="el" href="classgcu_1_1Matrix.html">Matrix</a> of the transformation. </td></tr>
<tr><td class="paramname">x</td><td>the x component of the center of the transformation. </td></tr>
<tr><td class="paramname">y</td><td>the y component of the center of the transformation.</td></tr>
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</dd>
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<p>Used to move and/or transform an atom. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#a69ad6edf7d50950b036f09d9ff86f849">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Atom.html#a2636a34f79bd72b0abb7c2e42fd016e0">gcp::Atom</a>.</p>
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<td class="memname">double gcu::Atom::x </td>
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<td class="paramname"></td><td>)</td>
<td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the x coordinate of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00148">148</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00307">m_x</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00107">SetCoords()</a>.</p>
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<td class="memname">double gcu::Atom::y </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the y coordinate of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00153">153</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00311">m_y</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00107">SetCoords()</a>.</p>
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<td class="memname">double gcu::Atom::z </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the z coordinate of this <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </dd></dl>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00158">158</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>References <a class="el" href="gcu_2atom_8h_source.html#l00315">m_z</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00107">SetCoords()</a>.</p>
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<td class="memname">void gcu::Atom::zoom </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"><em>ZoomFactor</em></td><td>)</td>
<td></td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">ZoomFactor</td><td>the zoom factor.</td></tr>
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</dd>
</dl>
<p>Multiplies all three coordinates of this <a class="el" href="classgcu_1_1Atom.html">Atom</a> by ZoomFactor. </p>
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<h2>Member Data Documentation</h2>
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<td class="memname">std::map<<a class="el" href="classgcu_1_1Atom.html">Atom</a>*, <a class="el" href="classgcu_1_1Bond.html">Bond</a>*> gcu::Atom::m_Bonds</td>
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<p>The <a class="el" href="classgcu_1_1Bond.html">Bond</a> instances of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. The index of the map is a pointer to the other end of the <a class="el" href="classgcu_1_1Bond.html">Bond</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00323">323</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00200">GetBondsNumber()</a>.</p>
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<p>The charge of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00319">319</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00128">GetCharge()</a>, <a class="el" href="gcp_2atom_8h_source.html#l00344">gcp::Atom::GetCharge()</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00124">SetCharge()</a>.</p>
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<td class="memname">double gcu::Atom::m_x</td>
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<p>The x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00307">307</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00107">SetCoords()</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00148">x()</a>.</p>
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<p>The x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00311">311</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00107">SetCoords()</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00153">y()</a>.</p>
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<td class="memname">int gcu::Atom::m_Z</td>
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<p>The atomic number of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00303">303</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00111">GetZ()</a>.</p>
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<p>The x coordinate of the <a class="el" href="classgcu_1_1Atom.html">Atom</a>. </p>
<p>Definition at line <a class="el" href="gcu_2atom_8h_source.html#l00315">315</a> of file <a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2atom_8h_source.html#l00107">SetCoords()</a>, and <a class="el" href="gcu_2atom_8h_source.html#l00158">z()</a>.</p>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="gcu_2atom_8h_source.html">gcu/atom.h</a></li>
</ul>
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