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gnome-chemistry-utils-devel-0.10.8-3mdv2010.0.i586.rpm

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<h1>gcu/residue.h</h1><a href="gcu_2residue_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">// -*- C++ -*-</span>
<a name="l00002"></a>00002 
<a name="l00003"></a>00003 <span class="comment">/* </span>
<a name="l00004"></a>00004 <span class="comment"> * Gnome Chemistry Utils</span>
<a name="l00005"></a>00005 <span class="comment"> * residue.h </span>
<a name="l00006"></a>00006 <span class="comment"> *</span>
<a name="l00007"></a>00007 <span class="comment"> * Copyright (C) 2007-2008 Jean Bréfort &lt;jean.brefort@normalesup.org&gt;</span>
<a name="l00008"></a>00008 <span class="comment"> *</span>
<a name="l00009"></a>00009 <span class="comment"> * This program is free software; you can redistribute it and/or </span>
<a name="l00010"></a>00010 <span class="comment"> * modify it under the terms of the GNU General Public License as </span>
<a name="l00011"></a>00011 <span class="comment"> * published by the Free Software Foundation; either version 2 of the</span>
<a name="l00012"></a>00012 <span class="comment"> * License, or (at your option) any later version.</span>
<a name="l00013"></a>00013 <span class="comment"> *</span>
<a name="l00014"></a>00014 <span class="comment"> * This program is distributed in the hope that it will be useful,</span>
<a name="l00015"></a>00015 <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00016"></a>00016 <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00017"></a>00017 <span class="comment"> * GNU General Public License for more details.</span>
<a name="l00018"></a>00018 <span class="comment"> *</span>
<a name="l00019"></a>00019 <span class="comment"> * You should have received a copy of the GNU General Public License</span>
<a name="l00020"></a>00020 <span class="comment"> * along with this program; if not, write to the Free Software</span>
<a name="l00021"></a>00021 <span class="comment"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301</span>
<a name="l00022"></a>00022 <span class="comment"> * USA</span>
<a name="l00023"></a>00023 <span class="comment"> */</span>
<a name="l00024"></a>00024 
<a name="l00025"></a>00025 <span class="preprocessor">#ifndef GCU_RESIDUE_H</span>
<a name="l00026"></a>00026 <span class="preprocessor"></span><span class="preprocessor">#define GCU_RESIDUE_H</span>
<a name="l00027"></a>00027 <span class="preprocessor"></span>
<a name="l00028"></a>00028 <span class="preprocessor">#include &quot;<a class="code" href="macros_8h.html">macros.h</a>&quot;</span>
<a name="l00029"></a>00029 <span class="preprocessor">#include &lt;libxml/parser.h&gt;</span>
<a name="l00030"></a>00030 <span class="preprocessor">#include &lt;map&gt;</span>
<a name="l00031"></a>00031 <span class="preprocessor">#include &lt;set&gt;</span>
<a name="l00032"></a>00032 <span class="preprocessor">#include &lt;string&gt;</span>
<a name="l00033"></a>00033 
<a name="l00035"></a>00035 <span class="keyword">namespace </span>gcu {
<a name="l00036"></a>00036 
<a name="l00037"></a>00037 <span class="keyword">class </span>Residue;
<a name="l00038"></a>00038 <span class="keyword">class </span>Molecule;
<a name="l00039"></a>00039 <span class="keyword">class </span>Document;
<a name="l00040"></a>00040 
<a name="l00044"></a><a class="code" href="structgcu_1_1SymbolResidue.html">00044</a> <span class="keyword">typedef</span> <span class="keyword">struct </span>{
<a name="l00050"></a><a class="code" href="structgcu_1_1SymbolResidue.html#a057d153e52066b23e051b5c1b0536433">00050</a>         <a class="code" href="classgcu_1_1Residue.html">Residue</a> *res;
<a name="l00054"></a><a class="code" href="structgcu_1_1SymbolResidue.html#a2016ca0bea9f9acb6a5fe9726e38515d">00054</a>         <span class="keywordtype">bool</span> ambiguous;
<a name="l00055"></a>00055 } <a class="code" href="structgcu_1_1SymbolResidue.html">SymbolResidue</a>;
<a name="l00056"></a>00056 
<a name="l00057"></a>00057 <span class="keyword">typedef</span> std::map&lt;std::string, SymbolResidue&gt;::iterator ResidueIterator;
<a name="l00058"></a>00058 
<a name="l00066"></a><a class="code" href="classgcu_1_1Residue.html">00066</a> <span class="keyword">class </span><a class="code" href="classgcu_1_1Residue.html">Residue</a>
<a name="l00067"></a>00067 {
<a name="l00068"></a>00068 <span class="keyword">public</span>:
<a name="l00072"></a>00072         <a class="code" href="classgcu_1_1Residue.html#a72f5130fa5fd589db8a28aca5f90524e">Residue</a> ();
<a name="l00079"></a>00079         <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);
<a name="l00083"></a>00083         <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1Residue.html#a62b6b69527e5db5bbb70b9fefa64cba8">~Residue</a> ();
<a name="l00084"></a>00084 
<a name="l00098"></a><a class="code" href="classgcu_1_1Residue.html#a1a861fa8e57112b8025fc640b6f885ae">00098</a>         std::map&lt;int,int&gt; <span class="keyword">const</span> &amp;<a class="code" href="classgcu_1_1Residue.html#a1a861fa8e57112b8025fc640b6f885ae">GetRawFormula</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> m_Raw;}
<a name="l00105"></a><a class="code" href="classgcu_1_1Residue.html#ad4d8a7d85d659bf901c597fea3793683">00105</a>         std::map&lt;std::string, bool&gt; <span class="keyword">const</span> &amp;<a class="code" href="classgcu_1_1Residue.html#ad4d8a7d85d659bf901c597fea3793683">GetSymbols</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> m_Symbols;}
<a name="l00110"></a><a class="code" href="classgcu_1_1Residue.html#a1871b94a8f5bcec18e4ffa38c6f36c1f">00110</a>         std::map&lt;std::string, std::string&gt; <span class="keyword">const</span> &amp;<a class="code" href="classgcu_1_1Residue.html#a1871b94a8f5bcec18e4ffa38c6f36c1f">GetNames</a> ()<span class="keyword"> const </span>{<span class="keywordflow">return</span> m_Names;}
<a name="l00114"></a>00114         <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);
<a name="l00120"></a>00120         <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);
<a name="l00126"></a>00126         <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);
<a name="l00132"></a>00132         <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Residue.html#a6e15c7aa2b9889faaf76ad58ba19fa2e">Load</a> (xmlNodePtr node);
<a name="l00140"></a>00140         <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);
<a name="l00146"></a>00146         <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);
<a name="l00155"></a>00155         <span class="keyword">static</span> std::string <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Residue.html#afa1a0b80886c8d255deb7d7b10524a7f">GetFirstResidueSymbol</a> (ResidueIterator &amp;i);
<a name="l00165"></a>00165         <span class="keyword">static</span> std::string <span class="keyword">const</span> *<a class="code" href="classgcu_1_1Residue.html#aaf275bb0e7b7d6afdda06d2d617c0730">GetNextResidueSymbol</a> (ResidueIterator &amp;i);
<a name="l00170"></a><a class="code" href="classgcu_1_1Residue.html#a57c96641d1c58fcc6f343188fbe93c77">00170</a>         <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Residue.html#a57c96641d1c58fcc6f343188fbe93c77">operator== </a>(<a class="code" href="classgcu_1_1Molecule.html">Molecule</a> <span class="keyword">const</span> &amp;mol)<span class="keyword"> const </span>{<span class="keywordflow">return</span> <span class="keyword">false</span>;}
<a name="l00171"></a>00171 
<a name="l00172"></a>00172 <span class="keyword">public</span>:
<a name="l00177"></a><a class="code" href="classgcu_1_1Residue.html#a052795f0ebd6cd932e42bd50c6f2c412">00177</a>         <span class="keyword">static</span> <span class="keywordtype">unsigned</span> <a class="code" href="classgcu_1_1Residue.html#a052795f0ebd6cd932e42bd50c6f2c412">MaxSymbolLength</a>;
<a name="l00178"></a>00178 
<a name="l00179"></a>00179 <span class="keyword">private</span>:
<a name="l00180"></a>00180         std::map&lt;int,int&gt; m_Raw;
<a name="l00181"></a>00181         std::map&lt;std::string, bool&gt; m_Symbols; <span class="comment">// boolean is true if the symbol is ambiguous</span>
<a name="l00182"></a>00182         std::map&lt;std::string, std::string&gt; m_Names;
<a name="l00183"></a>00183 
<a name="l00187"></a><a class="code" href="classgcu_1_1Residue.html#ae827a589804c5124ea07443c87f77058">00187</a> <a class="code" href="macros_8h.html#ae59df402113b58e8e28a7898e09a19a2">GCU_RO_PROP</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *, Name)
<a name="l00202"></a><a class="code" href="classgcu_1_1Residue.html#a3a75e74ef6c8f6816a6d2dd22961c965">00202</a> <a class="code" href="macros_8h.html#a2e6e8322502a538f4583d41206cea297">GCU_PROP</a> (<span class="keywordtype">bool</span>, Generic)
<a name="l00207"></a><a class="code" href="classgcu_1_1Residue.html#acc4b9089357090d0cc1c484e5874f775">00207</a> <a class="code" href="macros_8h.html#ad52419f8ee19ed3a6e49ca7db37e6a47">GCU_PROT_POINTER_PROP</a> (<a class="code" href="classgcu_1_1Document.html">Document</a>, Document);
<a name="l00212"></a><a class="code" href="classgcu_1_1Residue.html#adfd41c037e534060849b2332464a2fdb">00212</a> <a class="code" href="macros_8h.html#ad52419f8ee19ed3a6e49ca7db37e6a47">GCU_PROT_POINTER_PROP</a> (<a class="code" href="classgcu_1_1Molecule.html">Molecule</a>, Molecule);
<a name="l00217"></a><a class="code" href="classgcu_1_1Residue.html#afd7c1c902c91a7b193caf4c332ee4686">00217</a> <a class="code" href="macros_8h.html#ae59df402113b58e8e28a7898e09a19a2">GCU_RO_PROP</a> (Document *, Owner)
<a name="l00218"></a>00218 };
<a name="l00219"></a>00219 
<a name="l00220"></a>00220 }       <span class="comment">//      namespace gcu</span>
<a name="l00221"></a>00221 
<a name="l00222"></a>00222 <span class="preprocessor">#endif  //      GCU_RESIDUE_H</span>
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