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<div id="projectname">The Gnome Chemistry Utils
 <span id="projectnumber">0.14.2</span>
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<div class="title">gcr/bond.h</div> </div>
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<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"> * gcr/bond.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) 2002-2010 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 GCR_BOND_H</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor"></span><span class="preprocessor">#define GCR_BOND_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 <libxml/parser.h></span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor">#include <list></span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor">#include <<a class="code" href="gcu_2bond_8h.html">gcu/bond.h</a>></span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="keyword">namespace </span>gcr</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> </div>
<div class="line"><a name="l00038"></a><span class="lineno"><a class="code" href="classgcr_1_1Bond.html"> 38</a></span> <span class="keyword">class </span><a class="code" href="classgcr_1_1Bond.html">Bond</a>: <span class="keyword">public</span> <a class="code" href="classgcu_1_1Bond.html">gcu::Bond</a></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> {</div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <a class="code" href="classgcr_1_1Bond.html#a1dac8cb316c26512ee2390d5345ac3cd">Bond</a> ();</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keyword">virtual</span> <a class="code" href="classgcr_1_1Bond.html#a76d7374bcc8a57f6bc2e235615191c44">~Bond</a> ();</div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="keyword">public</span> :</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <a class="code" href="classgcr_1_1Bond.html#a1dac8cb316c26512ee2390d5345ac3cd">Bond</a> (<span class="keywordtype">double</span> X1, <span class="keywordtype">double</span> Y1, <span class="keywordtype">double</span> Z1, <span class="keywordtype">double</span> X2, <span class="keywordtype">double</span> Y2, <span class="keywordtype">double</span> Z2, <span class="keywordtype">double</span> r, <span class="keywordtype">float</span> red, <span class="keywordtype">float</span> green, <span class="keywordtype">float</span> blue, <span class="keywordtype">float</span> alpha);</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <a class="code" href="classgcr_1_1Bond.html#a1dac8cb316c26512ee2390d5345ac3cd">Bond</a> (<a class="code" href="classgcr_1_1Bond.html">Bond</a>& cbBond);</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <a class="code" href="classgcr_1_1Bond.html">Bond</a>& operator= (<a class="code" href="classgcr_1_1Bond.html">Bond</a>&);</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordtype">void</span> Draw ();</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordtype">double</span> X1 (<span class="keywordtype">void</span>) {<span class="keywordflow">return</span> m_dx;}</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keywordtype">double</span> Y1 (<span class="keywordtype">void</span>) {<span class="keywordflow">return</span> m_dy;}</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordtype">double</span> Z1 (<span class="keywordtype">void</span>) {<span class="keywordflow">return</span> m_dz;}</div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keywordtype">double</span> X2 (<span class="keywordtype">void</span>) {<span class="keywordflow">return</span> m_dx2;}</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keywordtype">double</span> Y2 (<span class="keywordtype">void</span>) {<span class="keywordflow">return</span> m_dy2;}</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordtype">double</span> Z2 (<span class="keywordtype">void</span>) {<span class="keywordflow">return</span> m_dz2;}</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordtype">double</span> Xmax ();</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keywordtype">double</span> Ymax ();</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordtype">double</span> Zmax ();</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordtype">double</span> Xmin ();</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordtype">double</span> Ymin ();</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordtype">double</span> Zmin ();</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keywordtype">double</span> Long () {<span class="keywordflow">return</span> m_dl;}</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordtype">void</span> SetPosition (<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> y, <span class="keywordtype">double</span> z, <span class="keywordtype">double</span> x1, <span class="keywordtype">double</span> y1, <span class="keywordtype">double</span> z1);</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordtype">void</span> SetColor (<span class="keywordtype">float</span> red, <span class="keywordtype">float</span> green, <span class="keywordtype">float</span> blue, <span class="keywordtype">float</span> alpha);</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordtype">void</span> GetColor (<span class="keywordtype">double</span> *red, <span class="keywordtype">double</span> *green, <span class="keywordtype">double</span> *blue, <span class="keywordtype">double</span> *alpha);</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordtype">void</span> SetRadius (<span class="keywordtype">double</span> r);</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordtype">double</span> GetRadius () {<span class="keywordflow">return</span> m_dr;};</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordtype">bool</span> operator== (<a class="code" href="classgcr_1_1Bond.html">Bond</a>&);</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classgcr_1_1Bond.html#a87c0e522a15f29e92db40c7f29d48c0b">Move</a> (<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> y, <span class="keywordtype">double</span> z);</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordtype">double</span> ScalProd (<span class="keywordtype">int</span> h, <span class="keywordtype">int</span> k, <span class="keywordtype">int</span> l);</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keywordtype">void</span> Cleave () {m_nCleave++;}</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordtype">void</span> NetToCartesian (<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="l00073"></a><span class="lineno"> 73</span>  <span class="keywordtype">double</span> Distance (<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> y, <span class="keywordtype">double</span> z, <span class="keywordtype">bool</span> bFixed);</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordtype">bool</span> IsCleaved () {<span class="keywordflow">return</span> m_nCleave != 0;}</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordtype">void</span> GetRotation (<span class="keywordtype">double</span>& x, <span class="keywordtype">double</span>& y, <span class="keywordtype">double</span>& z, <span class="keywordtype">double</span>& th);</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keyword">virtual</span> xmlNodePtr Save (xmlDocPtr xml);</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classgcr_1_1Bond.html#ac188dd995ef9ad60c3b4734a5cbeca91">Load</a> (xmlNodePtr node);</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">private</span> :</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordtype">float</span> m_fBlue, m_fRed, m_fGreen, m_fAlpha;</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordtype">double</span> m_dx, m_dy, m_dz, m_dx2, m_dy2, m_dz2, m_dr, m_dl;</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordtype">double</span> m_dxrot, m_dyrot, m_darot;<span class="comment">//rotation axis coordinates (z = 0) and angle</span></div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keywordtype">int</span> m_nCleave; <span class="comment">//0 if not cleaved</span></div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> };</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> <span class="keyword">typedef</span> std::list<Bond*> BondList;</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> }<span class="comment">// namespace gcr</span></div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> <span class="preprocessor">#endif // GCR_BOND_H</span></div>
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