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<a href="gcu_2molecule_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"> * libs/gcu/molecule.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) 2001-2012 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_MOLECULE_H</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor"></span><span class="preprocessor">#define GCU_MOLECULE_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 "<a class="code" href="gcu_2structs_8h.html">structs.h</a>"</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> </div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="keyword">namespace </span>gcu {</div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">class </span>Atom;</div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">class </span>Bond;</div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">class </span>Chain;</div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keyword">class </span>Cycle;</div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="keyword">class </span>Formula;</div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div>
<div class="line"><a name="l00043"></a><span class="lineno"><a class="code" href="classgcu_1_1Molecule.html"> 43</a></span> <span class="keyword">class </span><a class="code" href="classgcu_1_1Molecule.html">Molecule</a>: <span class="keyword">public</span> <a class="code" href="classgcu_1_1Object.html">Object</a></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> {</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="keyword">friend</span> <span class="keyword">class </span><a class="code" href="classgcu_1_1Chain.html">Chain</a>;</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <a class="code" href="classgcu_1_1Molecule.html#a5c80e950f8a9d02283d8b04c1c89f3f7">Molecule</a> (<a class="code" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Type = MoleculeType, <a class="code" href="namespacegcu.html#a662cb06e31132a49034b70b48a5f2b8f">ContentType</a> ct = <a class="code" href="namespacegcu.html#a662cb06e31132a49034b70b48a5f2b8fa4684bb2abdb70d1ce573189f1419ca8e">ContentType3D</a>);</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <a class="code" href="classgcu_1_1Molecule.html#a5c80e950f8a9d02283d8b04c1c89f3f7">Molecule</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom, <a class="code" href="namespacegcu.html#a662cb06e31132a49034b70b48a5f2b8f">ContentType</a> ct = <a class="code" href="namespacegcu.html#a662cb06e31132a49034b70b48a5f2b8fa4684bb2abdb70d1ce573189f1419ca8e">ContentType3D</a>);</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1Molecule.html#a27d96d88547230d32ea7f8bfc6601742">~Molecule</a> ();</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#ab9ec078566194173ab67d60074b6b245">AddChild</a> (<a class="code" href="classgcu_1_1Object.html">Object</a>* <span class="keywordtype">object</span>);</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#a2f277cc2b9f40b2ece88df56c1fe5c95">AddAtom</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom);</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#a30a68fe89c3c1f81497ec1498acc1012">AddBond</a> (<a class="code" href="classgcu_1_1Bond.html">Bond</a>* pBond);</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#aff43b05c6f575fefda0c13a181181379">Remove</a> (<a class="code" href="classgcu_1_1Object.html">gcu::Object</a>* pObject);</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#abb8dc72dc84a7c22a553425f0c447195">UpdateCycles</a> (<a class="code" href="classgcu_1_1Bond.html">Bond</a>* pBond);</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#abb8dc72dc84a7c22a553425f0c447195">UpdateCycles</a> ();</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Molecule.html#a8e2afa9634a94587b3fc6bb01da41784">operator== </a>(<a class="code" href="classgcu_1_1Molecule.html">Molecule</a> <span class="keyword">const</span>& molecule) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00113"></a><span class="lineno"><a class="code" href="classgcu_1_1Molecule.html#a6ad0da2f365b11e8693fae4d24b45030"> 113</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">unsigned</span> <a class="code" href="classgcu_1_1Molecule.html#a6ad0da2f365b11e8693fae4d24b45030">GetAtomsNumber</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classgcu_1_1Molecule.html#adcad89ca2f5c358068b466a99ce9a7cd">m_Atoms</a>.size ();}</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keyword">static</span> <a class="code" href="classgcu_1_1Molecule.html">Molecule</a> *<a class="code" href="classgcu_1_1Molecule.html#a9a41f121b26ddb33a88cdba1302d0644">MoleculeFromFormula</a> (<a class="code" href="classgcu_1_1Document.html">Document</a> *Doc, <a class="code" href="classgcu_1_1Formula.html">Formula</a> <span class="keyword">const</span> &formula, <span class="keywordtype">bool</span> add_pseudo = <span class="keyword">true</span>);</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span> </div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#a7b1eb4f9ab32d992e6185f7e395025f1">Clear</a> ();</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <a class="code" href="classgcu_1_1Atom.html">Atom</a> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Molecule.html#a3c19f4e9a34dbe0a8138a08c5c5fccc5">GetFirstAtom</a> (std::list<Atom*>::const_iterator &i) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <a class="code" href="classgcu_1_1Atom.html">Atom</a> *<a class="code" href="classgcu_1_1Molecule.html#a3c19f4e9a34dbe0a8138a08c5c5fccc5">GetFirstAtom</a> (std::list<Atom*>::iterator &i);</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <a class="code" href="classgcu_1_1Atom.html">Atom</a> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Molecule.html#a0b77aea73cf2936f596842643c32a211">GetNextAtom</a> (std::list<Atom*>::const_iterator &i) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <a class="code" href="classgcu_1_1Atom.html">Atom</a> *<a class="code" href="classgcu_1_1Molecule.html#a0b77aea73cf2936f596842643c32a211">GetNextAtom</a> (std::list<Atom*>::iterator &i);</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <a class="code" href="classgcu_1_1Bond.html">Bond</a> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Molecule.html#ac5b1209db07da379fd093a8422ffe568">GetFirstBond</a> (std::list<Bond*>::const_iterator &i) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <a class="code" href="classgcu_1_1Bond.html">Bond</a> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Molecule.html#ac2f28b51b9236b869ad4abb2f6ad0a77">GetNextBond</a>(std::list<Bond*>::const_iterator &i) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#a77aef9f22d2aabf21a237deace2f86b2">SetName</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *name, <span class="keywordtype">char</span> <span class="keyword">const</span> *convention);</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordtype">char</span> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Molecule.html#a1d497f446c24f935a5c9e786f05788ad">GetName</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *convention = NULL);</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  std::string <a class="code" href="classgcu_1_1Molecule.html#a4254a7135bdf0265a6199f2a8707ddd0">Name</a> ();</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span> </div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#ad93bfcfae597bf78ac655801319dbd49">ResetIndentifiers</a> ();</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> </div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  std::string <span class="keyword">const</span> &<a class="code" href="classgcu_1_1Molecule.html#a914e97b43bcdf0262cc71f3e576d6a98">GetCML</a> ();</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Molecule.html#a87f086317cf795225793431eb77754db">ClearCycles</a> ();</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span> </div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  std::string <span class="keyword">const</span> &<a class="code" href="classgcu_1_1Molecule.html#a440907f7a0b9e8467aaa97c56866c392">GetInChI</a> ();</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> </div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  std::string <span class="keyword">const</span> &<a class="code" href="classgcu_1_1Molecule.html#a3d16f78ffa1a8fe340cd555f2b12ec20">GetInChIKey</a> ();</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  std::string <span class="keyword">const</span> &<a class="code" href="classgcu_1_1Molecule.html#aa49799eef938ec7f1794000ddce01c51">GetSMILES</a> ();</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="keyword">virtual</span> std::string <a class="code" href="classgcu_1_1Molecule.html#aa4e0698faf9877b572f621492c82fac0">GetRawFormula</a> () <span class="keyword">const</span>;</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span> </div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00216"></a><span class="lineno"><a class="code" href="classgcu_1_1Molecule.html#a936ef484763b9a9ace3ced4a847eb251"> 216</a></span>  std::list<Cycle*> <a class="code" href="classgcu_1_1Molecule.html#a936ef484763b9a9ace3ced4a847eb251">m_Cycles</a>;</div>
<div class="line"><a name="l00220"></a><span class="lineno"><a class="code" href="classgcu_1_1Molecule.html#aa9d30f8cfd6f87fdd84fd07aef21f4b0"> 220</a></span>  std::list<Chain*> <a class="code" href="classgcu_1_1Molecule.html#aa9d30f8cfd6f87fdd84fd07aef21f4b0">m_Chains</a>;</div>
<div class="line"><a name="l00224"></a><span class="lineno"><a class="code" href="classgcu_1_1Molecule.html#adcad89ca2f5c358068b466a99ce9a7cd"> 224</a></span>  std::list<Atom*> <a class="code" href="classgcu_1_1Molecule.html#adcad89ca2f5c358068b466a99ce9a7cd">m_Atoms</a>;</div>
<div class="line"><a name="l00228"></a><span class="lineno"><a class="code" href="classgcu_1_1Molecule.html#ab939115e2e636a22de80176dbed6811c"> 228</a></span>  std::list<Bond*> <a class="code" href="classgcu_1_1Molecule.html#ab939115e2e636a22de80176dbed6811c">m_Bonds</a>;</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> </div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  std::map <std::string, std::string> m_Names;</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  std::string m_CML;</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  std::string m_InChI;</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  std::string m_InChIKey;</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  std::string m_SMILES;</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <a class="code" href="namespacegcu.html#a662cb06e31132a49034b70b48a5f2b8f">ContentType</a> m_Content;</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span> };</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span> </div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span> } <span class="comment">// namespace gcu</span></div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span> </div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span> <span class="preprocessor">#endif // GCU_MOLECULE_H</span></div>
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