<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> <meta http-equiv="X-UA-Compatible" content="IE=9"/> <title>The Gnome Chemistry Utils: chain.h Source File</title> <link href="tabs.css" rel="stylesheet" type="text/css"/> <script type="text/javascript" src="jquery.js"></script> <script type="text/javascript" src="dynsections.js"></script> <link href="doxygen.css" rel="stylesheet" type="text/css" /> </head> <body> <div id="top"><!-- do not remove this div, it is closed by doxygen! --> <div id="titlearea"> <table cellspacing="0" cellpadding="0"> <tbody> <tr style="height: 56px;"> <td style="padding-left: 0.5em;"> <div id="projectname">The Gnome Chemistry Utils  <span id="projectnumber">0.14.2</span> </div> </td> </tr> </tbody> </table> </div> <!-- end header part --> <!-- Generated by Doxygen 1.8.1.2 --> <div id="navrow1" class="tabs"> <ul class="tablist"> <li><a href="index.html"><span>Main Page</span></a></li> <li><a href="namespaces.html"><span>Namespaces</span></a></li> <li><a href="annotated.html"><span>Classes</span></a></li> <li class="current"><a href="files.html"><span>Files</span></a></li> </ul> </div> <div id="navrow2" class="tabs2"> <ul class="tablist"> <li><a href="files.html"><span>File List</span></a></li> <li><a href="globals.html"><span>File Members</span></a></li> </ul> </div> <div id="nav-path" class="navpath"> <ul> <li class="navelem"><a class="el" href="dir_6719ab1f1f7655efc2fa43f7eb574fd1.html">libs</a></li><li class="navelem"><a class="el" href="dir_a58dfd42f88c935731f32d659aed32ec.html">gcu</a></li> </ul> </div> </div><!-- top --> <div class="header"> <div class="headertitle"> <div class="title">chain.h</div> </div> </div><!--header--> <div class="contents"> <a href="chain_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/chain.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) 2001-2011 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_CHAIN_H</span></div> <div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor"></span><span class="preprocessor">#define GCU_CHAIN_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 <map></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>Molecule;</div> <div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div> <div class="line"><a name="l00043"></a><span class="lineno"><a class="code" href="structgcu_1_1ChainElt.html"> 43</a></span> <span class="keyword">typedef</span> <span class="keyword">struct</span></div> <div class="line"><a name="l00044"></a><span class="lineno"> 44</span> {</div> <div class="line"><a name="l00048"></a><span class="lineno"><a class="code" href="structgcu_1_1ChainElt.html#acc9f76940ce22b89f6526aa1ced725ca"> 48</a></span>  <a class="code" href="classgcu_1_1Bond.html">Bond</a> *<a class="code" href="structgcu_1_1ChainElt.html#acc9f76940ce22b89f6526aa1ced725ca">fwd</a>;</div> <div class="line"><a name="l00052"></a><span class="lineno"><a class="code" href="structgcu_1_1ChainElt.html#a0992741eeef0418ea8254b767e0b21c6"> 52</a></span>  <a class="code" href="classgcu_1_1Bond.html">Bond</a> *<a class="code" href="structgcu_1_1ChainElt.html#a0992741eeef0418ea8254b767e0b21c6">rev</a>;</div> <div class="line"><a name="l00053"></a><span class="lineno"> 53</span> } <a class="code" href="structgcu_1_1ChainElt.html">ChainElt</a>;</div> <div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div> <div class="line"><a name="l00059"></a><span class="lineno"><a class="code" href="classgcu_1_1Chain.html"> 59</a></span> <span class="keyword">class </span><a class="code" href="classgcu_1_1Chain.html">Chain</a>: <span class="keyword">public</span> <a class="code" href="classgcu_1_1Object.html">Object</a></div> <div class="line"><a name="l00060"></a><span class="lineno"> 60</span> {</div> <div class="line"><a name="l00061"></a><span class="lineno"> 61</span> <span class="keyword">public</span>:</div> <div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <a class="code" href="classgcu_1_1Chain.html#a8b5a4259a56f4eac2931cc9222dd41e6">Chain</a> (<a class="code" href="classgcu_1_1Bond.html">Bond</a>* pBond, <a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom = NULL, <a class="code" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Type = ChainType);</div> <div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <a class="code" href="classgcu_1_1Chain.html#a8b5a4259a56f4eac2931cc9222dd41e6">Chain</a> (<a class="code" href="classgcu_1_1Molecule.html">Molecule</a>* molecule, <a class="code" href="classgcu_1_1Bond.html">Bond</a>* pBond, <a class="code" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Type = ChainType);</div> <div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <a class="code" href="classgcu_1_1Chain.html#a8b5a4259a56f4eac2931cc9222dd41e6">Chain</a> (<a class="code" href="classgcu_1_1Molecule.html">Molecule</a>* molecule, <a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom, <a class="code" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Type = ChainType);</div> <div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keyword">virtual</span> <a class="code" href="classgcu_1_1Chain.html#a6952d1dc44218813990f6f1c19c37bf0">~Chain</a>();</div> <div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div> <div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Chain.html#ad1bc651dbdb0f6ba1968c049a87f58dc">FindCycles</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom);</div> <div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Chain.html#ac50c029851a0cca23e8b10faccb43f08">FindCycle</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom, <a class="code" href="classgcu_1_1Bond.html">Bond</a>* pBond);</div> <div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Chain.html#a3449a637c0e60112b22f90b6fa95b4b9">Erase</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom1, <a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom2);</div> <div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Chain.html#a3e0a4ab81a6d78688b6ee146a22fad72">Insert</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom1, <a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom2, <a class="code" href="classgcu_1_1Chain.html">Chain</a>& chain);</div> <div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Chain.html#a9ba123c66cf0f663e90f2967a263dda2">Extract</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom1, <a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom2, <a class="code" href="classgcu_1_1Chain.html">Chain</a>& chain);</div> <div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Chain.html#a4212d690960806d4211d28076bc95956">Reverse</a> ();</div> <div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordtype">void</span> Append (<a class="code" href="classgcu_1_1Chain.html">Chain</a>& chain);</div> <div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordtype">void</span> <a class="code" href="classgcu_1_1Chain.html#a37a98dd53d5d52868e6e6db39f21a72e">AddBond</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* start, <a class="code" href="classgcu_1_1Atom.html">Atom</a>* end);</div> <div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="keywordtype">unsigned</span> <a class="code" href="classgcu_1_1Chain.html#a817e6e3e481dff040192ca0f237563ae">GetUnsaturations</a> ();</div> <div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">unsigned</span> <a class="code" href="classgcu_1_1Chain.html#ad47d041d0e908602ec35453ce46833a3">GetHeteroatoms</a> ();</div> <div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Chain.html#ae54189912eaaf4f02d7a03b3658fc671">Contains</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom);</div> <div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordtype">bool</span> <a class="code" href="classgcu_1_1Chain.html#ae54189912eaaf4f02d7a03b3658fc671">Contains</a> (<a class="code" href="classgcu_1_1Bond.html">Bond</a>* pBond);</div> <div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="keywordtype">unsigned</span> <a class="code" href="classgcu_1_1Chain.html#a41c88d5be7504a416e5d1da2cd088302">GetLength</a> ();</div> <div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keywordtype">double</span> <a class="code" href="classgcu_1_1Chain.html#a8673fd54a49ad9beb99b641fc770b97e">GetMeanBondLength</a> ();</div> <div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <a class="code" href="classgcu_1_1Atom.html">Atom</a>* <a class="code" href="classgcu_1_1Chain.html#a562f70d1331071b5f4d4819644f64592">GetFirstAtom</a> ();</div> <div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <a class="code" href="classgcu_1_1Atom.html">Atom</a>* <a class="code" href="classgcu_1_1Chain.html#a4e43fccf28cbef4304bebae341b5453b">GetNextAtom</a> (<a class="code" href="classgcu_1_1Atom.html">Atom</a>* pAtom);</div> <div class="line"><a name="l00185"></a><span class="lineno"> 185</span> </div> <div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  std::string <a class="code" href="classgcu_1_1Chain.html#a1644982524595342b02a318143a3322d">Name</a> ();</div> <div class="line"><a name="l00190"></a><span class="lineno"> 190</span> </div> <div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="keywordtype">unsigned</span> <a class="code" href="classgcu_1_1Chain.html#a87aad41d5d5b560df9038d7c917844a5">BuildLength</a> (<span class="keywordtype">unsigned</span> *cycle_size = NULL, <span class="keywordtype">unsigned</span> *cycle_pos = NULL);</div> <div class="line"><a name="l00200"></a><span class="lineno"> 200</span> </div> <div class="line"><a name="l00201"></a><span class="lineno"> 201</span> <span class="keyword">protected</span>:</div> <div class="line"><a name="l00205"></a><span class="lineno"><a class="code" href="classgcu_1_1Chain.html#acb5f7fb52cf019721daf6e761cdea6ae"> 205</a></span>  std::map<Atom*, ChainElt> <a class="code" href="classgcu_1_1Chain.html#acb5f7fb52cf019721daf6e761cdea6ae">m_Bonds</a>;</div> <div class="line"><a name="l00209"></a><span class="lineno"><a class="code" href="classgcu_1_1Chain.html#a335946bc030113d283a351caac1ecae0"> 209</a></span>  <a class="code" href="classgcu_1_1Molecule.html">Molecule</a>* <a class="code" href="classgcu_1_1Chain.html#a335946bc030113d283a351caac1ecae0">m_Molecule</a>;</div> <div class="line"><a name="l00210"></a><span class="lineno"> 210</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="comment">// namespace gcu</span></div> <div class="line"><a name="l00213"></a><span class="lineno"> 213</span> </div> <div class="line"><a name="l00214"></a><span class="lineno"> 214</span> <span class="preprocessor">#endif // GCHEMPAINT_CHAIN_H</span></div> </div><!-- fragment --></div><!-- contents --> <!-- start footer part --> <hr class="footer"/><address class="footer"><small> Generated on Thu Mar 14 2013 17:34:28 for The Gnome Chemistry Utils by  <a href="http://www.doxygen.org/index.html"> <img class="footer" src="doxygen.png" alt="doxygen"/> </a> 1.8.1.2 </small></address> </body> </html>