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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<li class="navelem"><a class="el" href="dir_4e97c0cc258ff0f7662ff874d9772b08.html">netchem</a></li><li class="navelem"><a class="el" href="dir_4a594bc01937fb65302a7a951b7d979b.html">include</a></li> </ul>
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<div class="headertitle"><div class="title">atoms.h</div></div>
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<div class="contents">
<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="comment">//</span></div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="comment">// Created by astokely on 5/4/23.</span></div>
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="comment">//</span></div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span> </div>
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="preprocessor">#ifndef NETSCI_ATOMS_H</span></div>
<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="preprocessor">#define NETSCI_ATOMS_H</span></div>
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span> </div>
<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span> </div>
<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span><span class="preprocessor">#include "atom.h"</span></div>
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span><span class="preprocessor">#include <vector></span></div>
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span><span class="preprocessor">#include <set></span></div>
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span><span class="preprocessor">#include "nlohmann/json.hpp"</span></div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span> </div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> </div>
<div class="foldopen" id="foldopen00015" data-start="{" data-end="};">
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"><a class="line" href="classAtoms.html"> 15</a></span><span class="keyword">class </span><a class="code hl_class" href="classAtoms.html">Atoms</a> {</div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="keyword">public</span>:<span class="comment"></span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="comment"> /**</span></div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="comment"> * \brief Default constructor for Atoms.</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="comment"> *</span></div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="comment"> * Constructs an empty Atoms object.</span></div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="comment"> */</span></div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"><a class="line" href="classAtoms.html#a598f94e5e4019e7e2b30dff2074135db"> 22</a></span> <a class="code hl_function" href="classAtoms.html#a598f94e5e4019e7e2b30dff2074135db">Atoms</a>();</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span><span class="comment"></span> </div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="comment"> /**</span></div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span><span class="comment"> * \brief Add an Atom to the Atoms collection.</span></div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span><span class="comment"> *</span></div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span><span class="comment"> * Adds the specified Atom to the collection of Atoms.</span></div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span><span class="comment"> *</span></div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span><span class="comment"> * \param atom Pointer to the Atom to add.</span></div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span><span class="comment"> */</span></div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"><a class="line" href="classAtoms.html#a45bbfbdc1bee07854806d39c6a316a52"> 31</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classAtoms.html#a45bbfbdc1bee07854806d39c6a316a52">addAtom</a>(<a class="code hl_class" href="classAtom.html">Atom</a>* atom);</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span><span class="comment"></span> </div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span><span class="comment"> /**</span></div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span><span class="comment"> * \brief Get the number of Atoms in the collection.</span></div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span><span class="comment"> *</span></div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span><span class="comment"> * Returns the number of Atoms in the collection.</span></div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span><span class="comment"> *</span></div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span><span class="comment"> * \return The number of Atoms.</span></div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span><span class="comment"> *</span></div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span><span class="comment"> * @PythonExample{NetChem_Atoms_numAtoms.py}</span></div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span><span class="comment"> */</span></div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"><a class="line" href="classAtoms.html#a380ae242907228f4c88f5f7777158e8a"> 42</a></span> <span class="keywordtype">int</span> <a class="code hl_function" href="classAtoms.html#a380ae242907228f4c88f5f7777158e8a">numAtoms</a>() <span class="keyword">const</span>;</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span><span class="comment"></span> </div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span><span class="comment"> /**</span></div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span><span class="comment"> * \brief Get the Atom with the specified index.</span></div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span><span class="comment"> *</span></div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span><span class="comment"> * Returns a pointer to the Atom with the specified index.</span></div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span><span class="comment"> *</span></div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span><span class="comment"> * \param atomIndex The index of the Atom.</span></div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span><span class="comment"> * \return A pointer to the Atom with the specified index.</span></div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span><span class="comment"> *</span></div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span><span class="comment"> * @PythonExample{NetChem_Atoms_at.py}</span></div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span><span class="comment"> */</span></div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"><a class="line" href="classAtoms.html#a6fda32c824a6c5cf0c79824387c1aa6d"> 54</a></span> <a class="code hl_class" href="classAtom.html">Atom</a>* <a class="code hl_function" href="classAtoms.html#a6fda32c824a6c5cf0c79824387c1aa6d">at</a>(<span class="keywordtype">int</span> atomIndex);</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span><span class="comment"></span> </div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span><span class="comment"> /**</span></div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span><span class="comment"> * \brief Get the number of unique Atom tags.</span></div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span><span class="comment"> *</span></div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span><span class="comment"> * Returns the number of unique Atom tags.</span></div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span><span class="comment"> * Atoms with the same tag belong to the same Node.</span></div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span><span class="comment"> *</span></div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span><span class="comment"> * \return The number of unique Atom tags.</span></div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span><span class="comment"> */</span></div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"><a class="line" href="classAtoms.html#ad8e79d107094e3cbe88c045e99b8657c"> 64</a></span> <span class="keywordtype">int</span> <a class="code hl_function" href="classAtoms.html#ad8e79d107094e3cbe88c045e99b8657c">numUniqueTags</a>() <span class="keyword">const</span>;</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span><span class="comment"></span> </div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span><span class="comment"> /**</span></div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span><span class="comment"> * \brief Get a reference to the vector of Atoms.</span></div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span><span class="comment"> *</span></div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span><span class="comment"> * Returns a reference to the vector of Atoms.</span></div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span><span class="comment"> *</span></div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span><span class="comment"> * \return A reference to the vector of Atoms.</span></div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span><span class="comment"> *</span></div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span><span class="comment"> * @PythonExample{NetChem_Atoms_atoms.py}</span></div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span><span class="comment"> */</span></div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"><a class="line" href="classAtoms.html#af9f5ca488ebdfbbf0c68fc82090d13aa"> 75</a></span> std::vector<Atom*>& <a class="code hl_function" href="classAtoms.html#af9f5ca488ebdfbbf0c68fc82090d13aa">atoms</a>();</div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span><span class="keyword">private</span>:</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> <span class="keyword">friend</span> nlohmann::adl_serializer<Atoms*>;</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> std::vector<Atom*> atoms_;</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> std::set<std::string> uniqueTags_;</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span>};</div>
</div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> </div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span><span class="preprocessor">#endif </span><span class="comment">//NETSCI_ATOMS_H</span></div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="ttc" id="aclassAtom_html"><div class="ttname"><a href="classAtom.html">Atom</a></div><div class="ttdef"><b>Definition</b> atom.h:12</div></div>
<div class="ttc" id="aclassAtoms_html"><div class="ttname"><a href="classAtoms.html">Atoms</a></div><div class="ttdef"><b>Definition</b> atoms.h:15</div></div>
<div class="ttc" id="aclassAtoms_html_a380ae242907228f4c88f5f7777158e8a"><div class="ttname"><a href="classAtoms.html#a380ae242907228f4c88f5f7777158e8a">Atoms::numAtoms</a></div><div class="ttdeci">int numAtoms() const</div><div class="ttdoc">Get the number of Atoms in the collection.</div></div>
<div class="ttc" id="aclassAtoms_html_a45bbfbdc1bee07854806d39c6a316a52"><div class="ttname"><a href="classAtoms.html#a45bbfbdc1bee07854806d39c6a316a52">Atoms::addAtom</a></div><div class="ttdeci">void addAtom(Atom *atom)</div><div class="ttdoc">Add an Atom to the Atoms collection.</div></div>
<div class="ttc" id="aclassAtoms_html_a598f94e5e4019e7e2b30dff2074135db"><div class="ttname"><a href="classAtoms.html#a598f94e5e4019e7e2b30dff2074135db">Atoms::Atoms</a></div><div class="ttdeci">Atoms()</div><div class="ttdoc">Default constructor for Atoms.</div></div>
<div class="ttc" id="aclassAtoms_html_a6fda32c824a6c5cf0c79824387c1aa6d"><div class="ttname"><a href="classAtoms.html#a6fda32c824a6c5cf0c79824387c1aa6d">Atoms::at</a></div><div class="ttdeci">Atom * at(int atomIndex)</div><div class="ttdoc">Get the Atom with the specified index.</div></div>
<div class="ttc" id="aclassAtoms_html_ad8e79d107094e3cbe88c045e99b8657c"><div class="ttname"><a href="classAtoms.html#ad8e79d107094e3cbe88c045e99b8657c">Atoms::numUniqueTags</a></div><div class="ttdeci">int numUniqueTags() const</div><div class="ttdoc">Get the number of unique Atom tags.</div></div>
<div class="ttc" id="aclassAtoms_html_af9f5ca488ebdfbbf0c68fc82090d13aa"><div class="ttname"><a href="classAtoms.html#af9f5ca488ebdfbbf0c68fc82090d13aa">Atoms::atoms</a></div><div class="ttdeci">std::vector< Atom * > & atoms()</div><div class="ttdoc">Get a reference to the vector of Atoms.</div></div>
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