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<div class="title">phmodel.h</div> </div>
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<a href="phmodel_8h.shtml">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/**********************************************************************</span>
<a name="l00002"></a>00002 <span class="comment">phmodel.h - Read pH rules and assign charges.</span>
<a name="l00003"></a>00003 <span class="comment"></span>
<a name="l00004"></a>00004 <span class="comment">Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.</span>
<a name="l00005"></a>00005 <span class="comment">Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison</span>
<a name="l00006"></a>00006 <span class="comment"></span>
<a name="l00007"></a>00007 <span class="comment">This file is part of the Open Babel project.</span>
<a name="l00008"></a>00008 <span class="comment">For more information, see <http://openbabel.org/></span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">This program is free software; you can redistribute it and/or modify</span>
<a name="l00011"></a>00011 <span class="comment">it under the terms of the GNU General Public License as published by</span>
<a name="l00012"></a>00012 <span class="comment">the Free Software Foundation version 2 of the License.</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
<a name="l00020"></a>00020 <span class="preprocessor">#ifndef OB_PHMODEL_H</span>
<a name="l00021"></a>00021 <span class="preprocessor"></span><span class="preprocessor">#define OB_PHMODEL_H</span>
<a name="l00022"></a>00022 <span class="preprocessor"></span>
<a name="l00023"></a>00023 <span class="preprocessor">#include <<a class="code" href="parsmart_8h.shtml" title="Daylight SMARTS parser.">openbabel/parsmart.h</a>></span>
<a name="l00024"></a>00024 <span class="preprocessor">#include <<a class="code" href="data_8h.shtml" title="Global data and resource file parsers.">openbabel/data.h</a>></span>
<a name="l00025"></a>00025
<a name="l00026"></a>00026 <span class="keyword">namespace </span>OpenBabel
<a name="l00027"></a>00027 {
<a name="l00028"></a>00028
<a name="l00029"></a>00029 <span class="comment">// class introduction in phmodel.cpp</span>
<a name="l00030"></a><a class="code" href="classOpenBabel_1_1OBChemTsfm.shtml">00030</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBChemTsfm.shtml" title="SMARTS based structural modification (chemical transformation)">OBChemTsfm</a>
<a name="l00031"></a>00031 {
<a name="l00032"></a>00032 std::vector<int> _vadel;
<a name="l00033"></a>00033 std::vector<std::pair<int,int> > _vele;
<a name="l00034"></a>00034 std::vector<std::pair<int,int> > _vchrg;
<a name="l00035"></a>00035 std::vector<std::pair<int,int> > _vbdel;
<a name="l00036"></a>00036 std::vector<std::pair<std::pair<int,int>,<span class="keywordtype">int</span>> > _vbond;
<a name="l00037"></a>00037 <a class="code" href="classOpenBabel_1_1OBSmartsPattern.shtml" title="SMARTS (SMiles ARbitrary Target Specification) substructure searching.">OBSmartsPattern</a> _bgn,_end;
<a name="l00038"></a>00038 <span class="keyword">public</span>:
<a name="l00039"></a><a class="code" href="classOpenBabel_1_1OBChemTsfm.shtml#ab934cf70bc4829c0ce0691620a472306">00039</a> <a class="code" href="classOpenBabel_1_1OBChemTsfm.shtml#ab934cf70bc4829c0ce0691620a472306">OBChemTsfm</a>() {}
<a name="l00040"></a><a class="code" href="classOpenBabel_1_1OBChemTsfm.shtml#aaa824092d9dc953474727b7a328d68ad">00040</a> <a class="code" href="classOpenBabel_1_1OBChemTsfm.shtml#aaa824092d9dc953474727b7a328d68ad">~OBChemTsfm</a>() {}
<a name="l00042"></a>00042 <span class="keywordtype">bool</span> Init(std::string&start, std::string &end);
<a name="l00044"></a>00044 <span class="keywordtype">bool</span> Apply(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>&);
<a name="l00054"></a>00054 <span class="keywordtype">bool</span> IsAcid();
<a name="l00064"></a>00064 <span class="keywordtype">bool</span> IsBase();
<a name="l00065"></a>00065 };
<a name="l00066"></a>00066
<a name="l00107"></a><a class="code" href="classOpenBabel_1_1OBPhModel.shtml">00107</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBPhModel.shtml" title="Corrections for pH used by OBMol::CorrectForPH()">OBPhModel</a> : <span class="keyword">public</span> <a class="code" href="classOpenBabel_1_1OBGlobalDataBase.shtml" title="Base data table class, handles reading data files.">OBGlobalDataBase</a>
<a name="l00108"></a>00108 {
<a name="l00109"></a>00109 std::vector<std::vector<int> > _mlist;
<a name="l00110"></a>00110 std::vector<OBChemTsfm*> _vtsfm;
<a name="l00111"></a>00111 std::vector<double> _vpKa;
<a name="l00112"></a>00112 std::vector<std::pair<OBSmartsPattern*,std::vector<double> > > _vschrg;
<a name="l00113"></a>00113 <span class="keyword">public</span>:
<a name="l00114"></a>00114 <a class="code" href="classOpenBabel_1_1OBPhModel.shtml" title="Corrections for pH used by OBMol::CorrectForPH()">OBPhModel</a>();
<a name="l00115"></a>00115 ~<a class="code" href="classOpenBabel_1_1OBPhModel.shtml" title="Corrections for pH used by OBMol::CorrectForPH()">OBPhModel</a>();
<a name="l00116"></a>00116
<a name="l00117"></a>00117 <span class="keywordtype">void</span> ParseLine(<span class="keyword">const</span> <span class="keywordtype">char</span>*);
<a name="l00119"></a><a class="code" href="classOpenBabel_1_1OBPhModel.shtml#aab7c531e5ffc5174e57a85e853931534">00119</a> <span class="keywordtype">size_t</span> <a class="code" href="classOpenBabel_1_1OBPhModel.shtml#aab7c531e5ffc5174e57a85e853931534">GetSize</a>() { <span class="keywordflow">return</span> _vtsfm.size();}
<a name="l00120"></a>00120 <span class="keywordtype">void</span> AssignSeedPartialCharge(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>&);
<a name="l00121"></a>00121 <span class="comment">//void CorrectForPH(OBMol&);</span>
<a name="l00122"></a>00122 <span class="keywordtype">void</span> CorrectForPH(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>&, <span class="keywordtype">double</span> pH = 7.4 );
<a name="l00123"></a>00123 };
<a name="l00124"></a>00124
<a name="l00125"></a>00125
<a name="l00126"></a>00126
<a name="l00127"></a>00127 } <span class="comment">//namespace OpenBabel</span>
<a name="l00128"></a>00128
<a name="l00129"></a>00129 <span class="preprocessor">#endif // OB_PHMODEL_H</span>
<a name="l00130"></a>00130 <span class="preprocessor"></span>
<a name="l00133"></a>00133
</pre></div></div>
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