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<div class="title">gcu/residue.h</div> </div>
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<a href="gcu_2residue_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"> * residue.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) 2007-2008 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_RESIDUE_H</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor"></span><span class="preprocessor">#define GCU_RESIDUE_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="macros_8h.html">macros.h</a>"</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor">#include <libxml/parser.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 <set></span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="preprocessor">#include <string></span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">namespace </span>gcu {</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>Application;</div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="keyword">class </span>Residue;</div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="keyword">class </span>Molecule;</div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">class </span>Document;</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a name="l00045"></a><span class="lineno"><a class="code" href="structgcu_1_1SymbolResidue.html"> 45</a></span> <span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
<div class="line"><a name="l00051"></a><span class="lineno"><a class="code" href="structgcu_1_1SymbolResidue.html#a057d153e52066b23e051b5c1b0536433"> 51</a></span>  <a class="code" href="classgcu_1_1Residue.html">Residue</a> *<a class="code" href="structgcu_1_1SymbolResidue.html#a057d153e52066b23e051b5c1b0536433">res</a>;</div>
<div class="line"><a name="l00055"></a><span class="lineno"><a class="code" href="structgcu_1_1SymbolResidue.html#a2016ca0bea9f9acb6a5fe9726e38515d"> 55</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structgcu_1_1SymbolResidue.html#a2016ca0bea9f9acb6a5fe9726e38515d">ambiguous</a>;</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> } <a class="code" href="structgcu_1_1SymbolResidue.html">SymbolResidue</a>;</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="keyword">typedef</span> std::map<std::string, SymbolResidue>::iterator ResidueIterator;</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> </div>
<div class="line"><a name="l00067"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html"> 67</a></span> <span class="keyword">class </span><a class="code" href="classgcu_1_1Residue.html">Residue</a></div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> {</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <a class="code" href="classgcu_1_1Residue.html#a72f5130fa5fd589db8a28aca5f90524e">Residue</a> ();</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <a class="code" href="classgcu_1_1Residue.html#a72f5130fa5fd589db8a28aca5f90524e">Residue</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *name, <a class="code" href="classgcu_1_1Document.html">Document</a> *doc = NULL);</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1Residue.html#a62b6b69527e5db5bbb70b9fefa64cba8">~Residue</a> ();</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#a1a861fa8e57112b8025fc640b6f885ae"> 99</a></span>  std::map<int,int> <span class="keyword">const</span> &<a class="code" href="classgcu_1_1Residue.html#a1a861fa8e57112b8025fc640b6f885ae">GetRawFormula</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> m_Raw;}</div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#ad4d8a7d85d659bf901c597fea3793683"> 106</a></span>  std::map<std::string, bool> <span class="keyword">const</span> &<a class="code" href="classgcu_1_1Residue.html#ad4d8a7d85d659bf901c597fea3793683">GetSymbols</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> m_Symbols;}</div>
<div class="line"><a name="l00111"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#a1871b94a8f5bcec18e4ffa38c6f36c1f"> 111</a></span>  std::map<std::string, std::string> <span class="keyword">const</span> &<a class="code" href="classgcu_1_1Residue.html#a1871b94a8f5bcec18e4ffa38c6f36c1f">GetNames</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> m_Names;}</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Residue.html#ae088f4d7d8c67d2cddfb91b4b6a7ce25">SetName</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *name);</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Residue.html#aec88c7c40f56373bff9a87934d43476b">AddSymbol</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *symbol);</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Residue.html#a22551d87f7bd3429ab7f9e9b81f91319">RemoveSymbol</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *symbol);</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Residue.html#a92052b6044adf168b01ae8031e3ba3b9">Load</a> (xmlNodePtr node, <a class="code" href="classgcu_1_1Application.html">Application</a> *app);</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keyword">static</span> <a class="code" href="classgcu_1_1Residue.html">Residue</a> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Residue.html#a4591a80941c42c5ce8ca479397b7743c">GetResidue</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *symbol, <span class="keywordtype">bool</span> *ambiguous = NULL);</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keyword">static</span> <a class="code" href="classgcu_1_1Residue.html">Residue</a> <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Residue.html#a09a194c153d5262b378d1c8290325976">GetResiduebyName</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *name);</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="keyword">static</span> std::string <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Residue.html#afa1a0b80886c8d255deb7d7b10524a7f">GetFirstResidueSymbol</a> (ResidueIterator &i);</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keyword">static</span> std::string <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Residue.html#aaf275bb0e7b7d6afdda06d2d617c0730">GetNextResidueSymbol</a> (ResidueIterator &i);</div>
<div class="line"><a name="l00172"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#ade70b99416f4e0f23ffd84f093f2dd92"> 172</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Residue.html#ade70b99416f4e0f23ffd84f093f2dd92">operator== </a>(G_GNUC_UNUSED <a class="code" href="classgcu_1_1Molecule.html">Molecule</a> <span class="keyword">const</span> &mol)<span class="keyword"> const </span>{<span class="keywordflow">return</span> <span class="keyword">false</span>;}</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span> </div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00179"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#a052795f0ebd6cd932e42bd50c6f2c412"> 179</a></span>  <span class="keyword">static</span> <span class="keywordtype">unsigned</span> <a class="code" href="classgcu_1_1Residue.html#a052795f0ebd6cd932e42bd50c6f2c412">MaxSymbolLength</a>;</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span> </div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  std::map<int,int> m_Raw;</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  std::map<std::string, bool> m_Symbols; <span class="comment">// boolean is true if the symbol is ambiguous</span></div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  std::map<std::string, std::string> m_Names;</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span> </div>
<div class="line"><a name="l00189"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#a05cbc14c6089d25d809d39a9d591fdbd"> 189</a></span> <a class="code" href="macros_8h.html#ae59df402113b58e8e28a7898e09a19a2">GCU_RO_PROP</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *, Name)</div>
<div class="line"><a name="l00204"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#a3a75e74ef6c8f6816a6d2dd22961c965"> 204</a></span> <a class="code" href="macros_8h.html#a2e6e8322502a538f4583d41206cea297">GCU_PROP</a> (<span class="keywordtype">bool</span>, Generic)</div>
<div class="line"><a name="l00209"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#acc4b9089357090d0cc1c484e5874f775"> 209</a></span> <a class="code" href="macros_8h.html#ad52419f8ee19ed3a6e49ca7db37e6a47">GCU_PROT_POINTER_PROP</a> (<a class="code" href="classgcu_1_1Document.html">Document</a>, Document);</div>
<div class="line"><a name="l00214"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#adfd41c037e534060849b2332464a2fdb"> 214</a></span> <a class="code" href="macros_8h.html#ad52419f8ee19ed3a6e49ca7db37e6a47">GCU_PROT_POINTER_PROP</a> (<a class="code" href="classgcu_1_1Molecule.html">Molecule</a>, Molecule);</div>
<div class="line"><a name="l00219"></a><span class="lineno"><a class="code" href="classgcu_1_1Residue.html#ad8674695234f709328305da3855b12ae"> 219</a></span> <a class="code" href="macros_8h.html#ae59df402113b58e8e28a7898e09a19a2">GCU_RO_PROP</a> (Document *, Owner)</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span> };</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span> } <span class="comment">// namespace gcu</span></div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> </div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span> <span class="preprocessor">#endif // GCU_RESIDUE_H</span></div>
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