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<a href="builder_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">builder.h - OBBuilder class.</span>
<a name="l00003"></a>00003 <span class="comment"></span>
<a name="l00004"></a>00004 <span class="comment">Copyright (C) 2007-2008 by Tim Vandermeersch</span>
<a name="l00005"></a>00005 <span class="comment"> <tim.vandermeersch@gmail.com></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_BUILDER_H</span>
<a name="l00021"></a>00021 <span class="preprocessor"></span><span class="preprocessor">#define OB_BUILDER_H</span>
<a name="l00022"></a>00022 <span class="preprocessor"></span>
<a name="l00023"></a>00023 <span class="preprocessor">#include <vector></span>
<a name="l00024"></a>00024 <span class="preprocessor">#include <string></span>
<a name="l00025"></a>00025 <span class="preprocessor">#include <map></span>
<a name="l00026"></a>00026
<a name="l00027"></a>00027 <span class="preprocessor">#include <list></span>
<a name="l00028"></a>00028 <span class="preprocessor">#include <set></span>
<a name="l00029"></a>00029 <span class="preprocessor">#include <<a class="code" href="base_8h.shtml" title="Base classes to build a graph.">openbabel/base.h</a>></span>
<a name="l00030"></a>00030 <span class="preprocessor">#include <<a class="code" href="mol_8h.shtml" title="Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue. (the main header for Open Babel)...">openbabel/mol.h</a>></span>
<a name="l00031"></a>00031 <span class="preprocessor">#include <<a class="code" href="stereo_8h.shtml" title="Process molecular stereochemistry information.">openbabel/stereo/stereo.h</a>></span>
<a name="l00032"></a>00032
<a name="l00033"></a>00033 <span class="keyword">namespace </span>OpenBabel
<a name="l00034"></a>00034 {
<a name="l00037"></a><a class="code" href="classOpenBabel_1_1OBBuilder.shtml">00037</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBBuilder.shtml" title="Class to build 3D structures.">OBBuilder</a> {
<a name="l00038"></a>00038 <span class="keyword">public</span>:
<a name="l00039"></a>00039
<a name="l00040"></a><a class="code" href="classOpenBabel_1_1OBBuilder.shtml#a7bb41c313c47405a2040198e671caad5">00040</a> <a class="code" href="classOpenBabel_1_1OBBuilder.shtml#a7bb41c313c47405a2040198e671caad5">OBBuilder</a>(): _keeprings(false) {}
<a name="l00041"></a>00041
<a name="l00043"></a>00043
<a name="l00044"></a>00044
<a name="l00049"></a>00049 <span class="keywordtype">bool</span> Build(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol);
<a name="l00051"></a>00051
<a name="l00053"></a>00053
<a name="l00054"></a>00054
<a name="l00062"></a><a class="code" href="classOpenBabel_1_1OBBuilder.shtml#acf9a71f4ec162379069afdcae3088beb">00062</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBBuilder.shtml#acf9a71f4ec162379069afdcae3088beb">SetKeepRings</a>() { _keeprings = <span class="keyword">true</span>; }
<a name="l00063"></a><a class="code" href="classOpenBabel_1_1OBBuilder.shtml#aa981684e16a4cc7f7acf0cb9df1ce55b">00063</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBBuilder.shtml#aa981684e16a4cc7f7acf0cb9df1ce55b">UnsetKeepRings</a>() { _keeprings = <span class="keyword">false</span>; }
<a name="l00065"></a>00065
<a name="l00066"></a>00066
<a name="l00068"></a>00068 <span class="keywordtype">void</span> LoadFragments();
<a name="l00069"></a>00069
<a name="l00074"></a>00074 <span class="keyword">static</span> <a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> GetNewBondVector(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *atom);
<a name="l00075"></a>00075 <span class="keyword">static</span> <a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> GetNewBondVector(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *atom, <span class="keywordtype">double</span> length);
<a name="l00076"></a>00076
<a name="l00088"></a>00088 <span class="keyword">static</span> <span class="keywordtype">bool</span> Connect(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">int</span> a, <span class="keywordtype">int</span> b, <a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> &newpos, <span class="keywordtype">int</span> bondOrder = 1);
<a name="l00099"></a>00099 <span class="keyword">static</span> <span class="keywordtype">bool</span> Connect(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">int</span> a, <span class="keywordtype">int</span> b, <span class="keywordtype">int</span> bondOrder = 1);
<a name="l00127"></a>00127 <span class="keyword">static</span> <span class="keywordtype">bool</span> Swap(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">int</span> a, <span class="keywordtype">int</span> b, <span class="keywordtype">int</span> c, <span class="keywordtype">int</span> d);
<a name="l00134"></a>00134 <span class="comment">//bool Insert(OBMol &mol, int a, int b, std::string smiles, int c, int d);</span>
<a name="l00137"></a>00137 <span class="comment"></span> <span class="keyword">static</span> <span class="keywordtype">void</span> CorrectStereoBonds(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol);
<a name="l00141"></a>00141 <span class="keyword">static</span> <span class="keywordtype">void</span> CorrectStereoAtoms(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol);
<a name="l00144"></a>00144 <span class="keyword">static</span> <span class="keywordtype">bool</span> IsSpiroAtom(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> atomId, <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol);
<a name="l00149"></a>00149 <span class="keyword">static</span> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> GetFragment(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *atom);
<a name="l00150"></a>00150 <span class="keyword">static</span> <span class="keywordtype">void</span> AddNbrs(<a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &fragment, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *atom);
<a name="l00151"></a>00151
<a name="l00152"></a>00152 <span class="keyword">private</span>:
<a name="l00154"></a>00154 <span class="keyword">static</span> std::vector<std::pair<OBSmartsPattern*, std::vector<vector3> > > _fragments;
<a name="l00156"></a>00156 <span class="comment">// supports the case where the fragments overlap at a spiro atom only.</span>
<a name="l00157"></a>00157 <span class="keyword">static</span> <span class="keywordtype">void</span> ConnectFrags(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &workmol, std::vector<int> match, std::vector<vector3> coords,
<a name="l00158"></a>00158 std::vector<int> pivot);
<a name="l00160"></a>00160 <span class="keyword">static</span> <span class="keywordtype">void</span> FlipSpiro(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">int</span> idx);
<a name="l00161"></a>00161 <span class="keyword">static</span> <span class="keywordtype">bool</span> FixRingStereo(std::vector<std::pair<OBStereo::Ref, bool> > atomIds,
<a name="l00162"></a>00162 <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <a class="code" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> &unfixedcenters);
<a name="l00163"></a>00163 <span class="keyword">static</span> <span class="keywordtype">void</span> AddRingNbrs(<a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &fragment, <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *atom, <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol);
<a name="l00164"></a>00164 <span class="keyword">static</span> <span class="keywordtype">bool</span> SwapWithVector(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, <span class="keywordtype">int</span> a, <span class="keywordtype">int</span> b, <span class="keywordtype">int</span> c, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> &newlocation);
<a name="l00165"></a>00165 <span class="keywordtype">bool</span> _keeprings;
<a name="l00166"></a>00166 }; <span class="comment">// class OBBuilder</span>
<a name="l00167"></a>00167
<a name="l00168"></a>00168 }<span class="comment">// namespace OpenBabel</span>
<a name="l00169"></a>00169
<a name="l00170"></a>00170 <span class="preprocessor">#endif // OB_BUILDER_H</span>
<a name="l00171"></a>00171 <span class="preprocessor"></span>
</pre></div></div>
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