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<a href="gcu_2atom_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// -*- C++ -*-</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> </div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">/*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * Gnome Chemistry Utils</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> * atom.h</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * Copyright (C) 2002-2011 Jean Bréfort <jean.brefort@normalesup.org></span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * This program is free software; you can redistribute it and/or</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * modify it under the terms of the GNU General Public License as</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * published by the Free Software Foundation; either version 3 of the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> * License, or (at your option) any later version.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * This program is distributed in the hope that it will be useful,</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment"> * GNU General Public License for more details.</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment"> * You should have received a copy of the GNU General Public License</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment"> * along with this program; if not, write to the Free Software</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment"> * USA</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#ifndef GCU_ATOM_H</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor"></span><span class="preprocessor">#define GCU_ATOM_H</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="preprocessor">#include "<a class="code" href="object_8h.html">object.h</a>"</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor">#include <glib.h></span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor">#include <map></span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> </div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">namespace </span>gcu</div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> {</div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> </div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keyword">class </span>Bond;</div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="keyword">class </span>Cycle;</div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="keyword">class </span>AtomMatchState;</div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">class </span>Vector;</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a name="l00046"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html"> 46</a></span> <span class="keyword">class </span><a class="code" href="classgcu_1_1Atom.html">Atom</a>: <span class="keyword">public</span> <a class="code" href="classgcu_1_1Object.html">Object</a></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> {</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <a class="code" href="classgcu_1_1Atom.html#aa8943d4fa17eef381fd5d6b2b16cb3c5">Atom</a> ();</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <a class="code" href="classgcu_1_1Atom.html#aa8943d4fa17eef381fd5d6b2b16cb3c5">Atom</a> (<span class="keywordtype">int</span> Z, <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a>, <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a>, <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a> = 0.);</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <a class="code" href="classgcu_1_1Atom.html#aa8943d4fa17eef381fd5d6b2b16cb3c5">Atom</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>& a);</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <a class="code" href="classgcu_1_1Atom.html">Atom</a>& <a class="code" href="classgcu_1_1Atom.html#a73b1c38cbd4118c055720c7aec030b89">operator= </a>(<a class="code" href="classgcu_1_1Atom.html">Atom</a>& a);</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1Atom.html#a6761fd5db008d0984e1fa056c385459b">~Atom</a> ();</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="keyword">public</span> :</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#a8e0470a96bc1fe3f1a2ceab7afc3fb63">Distance</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom);</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Atom.html#ab60ac47e3be8db95e1c9f2c2e986ff71">zoom</a> (<span class="keywordtype">double</span> ZoomFactor);</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Atom.html#a8c63d0cca391f39f43f9f58fa7afc9f4">GetCoords</a> (<span class="keywordtype">double</span> *x, <span class="keywordtype">double</span> *y, <span class="keywordtype">double</span> *<a class="code" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a> = NULL) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#ab9dbdfc744e2d8edf99f4009215866c6"> 107</a></span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Atom.html#ab9dbdfc744e2d8edf99f4009215866c6">SetCoords</a> (<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> y, <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a> = 0) {<a class="code" href="classgcu_1_1Atom.html#ab2c4ef4fd922120c4ff441c64aaa2ee1">m_x</a> = <a class="code" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a>; <a class="code" href="classgcu_1_1Atom.html#af242ce3cb476a56ed16dc78ceeed6901">m_y</a> = <a class="code" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a>; <a class="code" href="classgcu_1_1Atom.html#a41a1b4161c01147c951c75f1ff4cae37">m_z</a> = <a class="code" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a>;}</div>
<div class="line"><a name="l00111"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#a3b5b44c467ea583adbaa77c263f33a8a"> 111</a></span>  <span class="keywordtype">int</span> <a class="code" href="classgcu_1_1Atom.html#a3b5b44c467ea583adbaa77c263f33a8a">GetZ</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Atom.html#a6fce7561c1e898b10dd418efbd2c7b1a">m_Z</a>;}</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Atom.html#a38a15b6551a3eb6646206ba933af1fff">SetZ</a> (<span class="keywordtype">int</span> Z);</div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#ae22a3f7878ca7b08aa93004587303d9d"> 124</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Atom.html#ae22a3f7878ca7b08aa93004587303d9d">SetCharge</a> (<span class="keywordtype">char</span> Charge) {<a class="code" href="classgcu_1_1Atom.html#a733db6db77be736879f983fbb11bcdaa">m_Charge</a> = Charge;}</div>
<div class="line"><a name="l00128"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#abdfd5d40227e19f53db6baee57c30260"> 128</a></span>  <span class="keywordtype">char</span> <a class="code" href="classgcu_1_1Atom.html#abdfd5d40227e19f53db6baee57c30260">GetCharge</a> () {<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Atom.html#a733db6db77be736879f983fbb11bcdaa">m_Charge</a>;}</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keyword">virtual</span> <span class="keyword">const</span> gchar* <a class="code" href="classgcu_1_1Atom.html#a4371e488d9548ea7d9b6ee48c3be83bc">GetSymbol</a> () <span class="keyword">const</span>;</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Atom.html#a374ed31f84f3400bf107c8fc5557acb3">AddBond</a> (<a class="code" href="classgcu_1_1Bond.html">Bond</a>* pBond);</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Atom.html#a687994b362c10a22a301aa12a960ce37">RemoveBond</a> (<a class="code" href="classgcu_1_1Bond.html">Bond</a>* pBond);</div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d"> 148</a></span>  <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Atom.html#ab2c4ef4fd922120c4ff441c64aaa2ee1">m_x</a>;}</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keywordtype">double</span> &<a class="code" href="classgcu_1_1Atom.html#a845f98c4e1bb2fe68dfa3fc61a83f79d">x</a> () {<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Atom.html#ab2c4ef4fd922120c4ff441c64aaa2ee1">m_x</a>;}</div>
<div class="line"><a name="l00153"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c"> 153</a></span>  <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Atom.html#af242ce3cb476a56ed16dc78ceeed6901">m_y</a>;}</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keywordtype">double</span> &<a class="code" href="classgcu_1_1Atom.html#a483d6aec85bb09acf681d0070f46149c">y</a> () {<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Atom.html#af242ce3cb476a56ed16dc78ceeed6901">m_y</a>;}</div>
<div class="line"><a name="l00158"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc"> 158</a></span>  <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Atom.html#a41a1b4161c01147c951c75f1ff4cae37">m_z</a>;}</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordtype">double</span> &<a class="code" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a> () {<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Atom.html#a41a1b4161c01147c951c75f1ff4cae37">m_z</a>;}</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  Vector <a class="code" href="classgcu_1_1Atom.html#a4b693135365bae35648c96e6788407f0">GetVector</a> () <span class="keyword">const</span>;</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  Bond *<a class="code" href="classgcu_1_1Atom.html#a2c4b85fd9b08205696fc40d86ca1aebe">GetFirstBond</a> (std::map < Atom *, Bond * >::iterator& i);</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  Bond <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Atom.html#a2c4b85fd9b08205696fc40d86ca1aebe">GetFirstBond</a> (std::map< Atom *, Bond * >::const_iterator& i) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  Bond *<a class="code" href="classgcu_1_1Atom.html#acb42e7980b0bc5a070324f1fc07fa989">GetNextBond</a> (std::map<Atom*, Bond*>::iterator& i);</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  Bond <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Atom.html#acb42e7980b0bc5a070324f1fc07fa989">GetNextBond</a> (std::map< Atom *, Bond * >::const_iterator& i) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  Bond* <a class="code" href="classgcu_1_1Atom.html#a2eceb0aec2b8a0e30bba183af356d200">GetBond</a> (<a class="code" href="classgcu_1_1Atom.html#aa8943d4fa17eef381fd5d6b2b16cb3c5">Atom</a>* pAtom) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00200"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#a026adef7ae137f92d2a4418dd94d1a30"> 200</a></span>  <span class="keywordtype">int</span> <a class="code" href="classgcu_1_1Atom.html#a026adef7ae137f92d2a4418dd94d1a30">GetBondsNumber</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Atom.html#a61f209632162c8553a7ebde3c4b194f9">m_Bonds</a>.size();}</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="keyword">virtual</span> xmlNodePtr <a class="code" href="classgcu_1_1Atom.html#a4d8e69e2c01645367c6c76c2d92c2433">Save</a> (xmlDocPtr xml) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Atom.html#a290a0a8c69ca6667d19e9d7f1d71d190">Load</a> (xmlNodePtr node);</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Atom.html#a383a09c3d8bdbd0300bdc2b57b02e1ab">LoadNode</a> (xmlNodePtr node);</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Atom.html#af8a3a91412c9a585f60d49fb6e49280e">SaveNode</a> (xmlDocPtr xml, xmlNodePtr node) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Atom.html#aab7ca2a758dc755d3da936cae82d1485">Move</a> (<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> y, <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#aca911471b8848a4c78205c328557a7cc">z</a> = 0.);</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Atom.html#a2ff6b67af11f6414fe8e972507e37f62">Transform2D</a> (<a class="code" href="classgcu_1_1Matrix2D.html">Matrix2D</a>& m, <span class="keywordtype">double</span> x, <span class="keywordtype">double</span> y);</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span> </div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Atom.html#ac9d2135007a4010d1e4ffffb9aec3227">SetProperty</a> (<span class="keywordtype">unsigned</span> property, <span class="keywordtype">char</span> <span class="keyword">const</span> *value);</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span> </div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  std::string <a class="code" href="classgcu_1_1Atom.html#a759e64fd28f939c73a5130c49e876618">GetProperty</a> (<span class="keywordtype">unsigned</span> property) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> </div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Atom.html#a8130046e2fd1ae7085935efe65c2ef94">IsInCycle</a> (<a class="code" href="classgcu_1_1Cycle.html">Cycle</a>* pCycle);</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span> </div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Atom.html#a3d8c5f65e203f23175c3422ef548e7f8">Match</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a> *atom, <a class="code" href="classgcu_1_1AtomMatchState.html">AtomMatchState</a> &state);</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span> </div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  std::string <a class="code" href="classgcu_1_1Atom.html#af41bf7c02e9a0dbf77156a9813fa1924">Name</a> ();</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Atom.html#a88f4565c7f8d1d8fd7575855655139bb">NetToCartesian</a> (<span class="keywordtype">double</span> a, <span class="keywordtype">double</span> b, <span class="keywordtype">double</span> c, <span class="keywordtype">double</span> alpha, <span class="keywordtype">double</span> beta, <span class="keywordtype">double</span> gamma);</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span> </div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00303"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#a6fce7561c1e898b10dd418efbd2c7b1a"> 303</a></span>  <span class="keywordtype">int</span> <a class="code" href="classgcu_1_1Atom.html#a6fce7561c1e898b10dd418efbd2c7b1a">m_Z</a>;</div>
<div class="line"><a name="l00307"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#ab2c4ef4fd922120c4ff441c64aaa2ee1"> 307</a></span>  <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#ab2c4ef4fd922120c4ff441c64aaa2ee1">m_x</a>;</div>
<div class="line"><a name="l00311"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#af242ce3cb476a56ed16dc78ceeed6901"> 311</a></span>  <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#af242ce3cb476a56ed16dc78ceeed6901">m_y</a>;</div>
<div class="line"><a name="l00315"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#a41a1b4161c01147c951c75f1ff4cae37"> 315</a></span>  <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Atom.html#a41a1b4161c01147c951c75f1ff4cae37">m_z</a>;</div>
<div class="line"><a name="l00319"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#a733db6db77be736879f983fbb11bcdaa"> 319</a></span>  <span class="keywordtype">char</span> <a class="code" href="classgcu_1_1Atom.html#a733db6db77be736879f983fbb11bcdaa">m_Charge</a>;</div>
<div class="line"><a name="l00323"></a><span class="lineno"><a class="code" href="classgcu_1_1Atom.html#a61f209632162c8553a7ebde3c4b194f9"> 323</a></span>  std::map<Atom*, Bond*> <a class="code" href="classgcu_1_1Atom.html#a61f209632162c8553a7ebde3c4b194f9">m_Bonds</a>;</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span> };</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span> </div>
<div class="line"><a name="l00331"></a><span class="lineno"><a class="code" href="classgcu_1_1AtomPair.html"> 331</a></span> <span class="keyword">class </span><a class="code" href="classgcu_1_1AtomPair.html">AtomPair</a> {</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span> </div>
<div class="line"><a name="l00340"></a><span class="lineno"><a class="code" href="classgcu_1_1AtomPair.html#aa0b9033915e6eb9029955e76f0c35759"> 340</a></span>  <a class="code" href="classgcu_1_1AtomPair.html#aa0b9033915e6eb9029955e76f0c35759">AtomPair</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a> *at1, <a class="code" href="classgcu_1_1Atom.html">Atom</a> *at2) {<a class="code" href="classgcu_1_1AtomPair.html#add5e93679f70f26ba6875ee3fdf41298">atom1</a> = at1; <a class="code" href="classgcu_1_1AtomPair.html#a9d0a5da2b8deaea7bedaaf663a0b77b0">atom2</a> = at2;}</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span> </div>
<div class="line"><a name="l00345"></a><span class="lineno"><a class="code" href="classgcu_1_1AtomPair.html#add5e93679f70f26ba6875ee3fdf41298"> 345</a></span>  <a class="code" href="classgcu_1_1Atom.html">Atom</a> *<a class="code" href="classgcu_1_1AtomPair.html#add5e93679f70f26ba6875ee3fdf41298">atom1</a>;</div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span> </div>
<div class="line"><a name="l00350"></a><span class="lineno"><a class="code" href="classgcu_1_1AtomPair.html#a9d0a5da2b8deaea7bedaaf663a0b77b0"> 350</a></span>  <a class="code" href="classgcu_1_1Atom.html">Atom</a> *<a class="code" href="classgcu_1_1AtomPair.html#a9d0a5da2b8deaea7bedaaf663a0b77b0">atom2</a>;</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span> };</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span> </div>
<div class="line"><a name="l00358"></a><span class="lineno"><a class="code" href="classgcu_1_1AtomMatchState.html"> 358</a></span> <span class="keyword">class </span><a class="code" href="classgcu_1_1AtomMatchState.html">AtomMatchState</a></div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> {</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span> </div>
<div class="line"><a name="l00365"></a><span class="lineno"><a class="code" href="classgcu_1_1AtomMatchState.html#ab0c9f96cb951d4916d34de0e7a5f52b2"> 365</a></span>  std::map <Atom*, int> <a class="code" href="classgcu_1_1AtomMatchState.html#ab0c9f96cb951d4916d34de0e7a5f52b2">mol1</a>;</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> </div>
<div class="line"><a name="l00370"></a><span class="lineno"><a class="code" href="classgcu_1_1AtomMatchState.html#ac128db673118b0f92591983e8927ae8f"> 370</a></span>  std::map <Atom*, int> <a class="code" href="classgcu_1_1AtomMatchState.html#ac128db673118b0f92591983e8927ae8f">mol2</a>;</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span> </div>
<div class="line"><a name="l00375"></a><span class="lineno"><a class="code" href="classgcu_1_1AtomMatchState.html#a63dd459c90617beef93a3639ae2c02e5"> 375</a></span>  std::vector <AtomPair> <a class="code" href="classgcu_1_1AtomMatchState.html#a63dd459c90617beef93a3639ae2c02e5">atoms</a>;</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span> };</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span> </div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span> } <span class="comment">//namespace gcu</span></div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span> <span class="preprocessor">#endif // GCU_ATOM_H</span></div>
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