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<div class="title">align.h</div> </div>
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<a href="align_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">align.h - Align two molecules or vectors of vector3</span>
<a name="l00003"></a>00003 <span class="comment"></span>
<a name="l00004"></a>00004 <span class="comment">Copyright (C) 2010 by Noel M. O'Boyle</span>
<a name="l00005"></a>00005 <span class="comment"></span>
<a name="l00006"></a>00006 <span class="comment">This file is part of the Open Babel project.</span>
<a name="l00007"></a>00007 <span class="comment">For more information, see <http://openbabel.org/></span>
<a name="l00008"></a>00008 <span class="comment"></span>
<a name="l00009"></a>00009 <span class="comment">This program is free software; you can redistribute it and/or modify</span>
<a name="l00010"></a>00010 <span class="comment">it under the terms of the GNU General Public License as published by</span>
<a name="l00011"></a>00011 <span class="comment">the Free Software Foundation version 2 of the License.</span>
<a name="l00012"></a>00012 <span class="comment"></span>
<a name="l00013"></a>00013 <span class="comment">This program is distributed in the hope that it will be useful,</span>
<a name="l00014"></a>00014 <span class="comment">but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00015"></a>00015 <span class="comment">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00016"></a>00016 <span class="comment">GNU General Public License for more details.</span>
<a name="l00017"></a>00017 <span class="comment">***********************************************************************/</span>
<a name="l00018"></a>00018
<a name="l00019"></a>00019 <span class="preprocessor">#ifndef OB_ALIGN_H</span>
<a name="l00020"></a>00020 <span class="preprocessor"></span><span class="preprocessor">#define OB_ALIGN_H</span>
<a name="l00021"></a>00021 <span class="preprocessor"></span>
<a name="l00022"></a>00022 <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="l00023"></a>00023 <span class="preprocessor">#include <<a class="code" href="vector3_8h.shtml" title="Handle 3D coordinates.">openbabel/math/vector3.h</a>></span>
<a name="l00024"></a>00024 <span class="preprocessor">#include <<a class="code" href="matrix3x3_8h.shtml" title="Handle 3D Rotation matrix.">openbabel/math/matrix3x3.h</a>></span>
<a name="l00025"></a>00025 <span class="preprocessor">#include <<a class="code" href="isomorphism_8h.shtml" title="OBIsomorphismMapper class for finding isomorphisms.">openbabel/isomorphism.h</a>></span>
<a name="l00026"></a>00026 <span class="preprocessor">#include <Eigen/Core></span>
<a name="l00027"></a>00027
<a name="l00028"></a>00028 <span class="keyword">using namespace </span>std;
<a name="l00029"></a>00029
<a name="l00030"></a>00030 <span class="keyword">namespace </span>OpenBabel
<a name="l00031"></a>00031 {
<a name="l00066"></a><a class="code" href="classOpenBabel_1_1OBAlign.shtml">00066</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBAlign.shtml" title="Perform a least-squares alignment of two molecules or two vectors of vector3 objects.">OBAlign</a> {
<a name="l00067"></a>00067 <span class="keyword">public</span>:
<a name="l00069"></a>00069
<a name="l00070"></a>00070
<a name="l00075"></a>00075 <a class="code" href="classOpenBabel_1_1OBAlign.shtml" title="Perform a least-squares alignment of two molecules or two vectors of vector3 objects.">OBAlign</a>(<span class="keywordtype">bool</span> includeH=<span class="keyword">false</span>, <span class="keywordtype">bool</span> symmetry=<span class="keyword">true</span>);
<a name="l00079"></a>00079 <a class="code" href="classOpenBabel_1_1OBAlign.shtml" title="Perform a least-squares alignment of two molecules or two vectors of vector3 objects.">OBAlign</a>(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &refmol, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &targetmol, <span class="keywordtype">bool</span> includeH=<span class="keyword">false</span>, <span class="keywordtype">bool</span> symmetry=<span class="keyword">true</span>);
<a name="l00083"></a>00083 <a class="code" href="classOpenBabel_1_1OBAlign.shtml" title="Perform a least-squares alignment of two molecules or two vectors of vector3 objects.">OBAlign</a>(<span class="keyword">const</span> vector<vector3> &ref, <span class="keyword">const</span> vector<vector3> &target);
<a name="l00085"></a>00085
<a name="l00087"></a>00087
<a name="l00088"></a>00088
<a name="l00094"></a>00094 <span class="keywordtype">void</span> SetRef(<span class="keyword">const</span> vector<vector3> &ref);
<a name="l00099"></a>00099 <span class="keywordtype">void</span> SetTarget(<span class="keyword">const</span> vector<vector3> &target);
<a name="l00106"></a>00106 <span class="keywordtype">void</span> SetRefMol(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &refmol);
<a name="l00111"></a>00111 <span class="keywordtype">void</span> SetTargetMol(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &targetmol);
<a name="l00113"></a>00113
<a name="l00115"></a>00115
<a name="l00116"></a>00116
<a name="l00119"></a>00119 <span class="keywordtype">bool</span> Align();
<a name="l00121"></a>00121
<a name="l00123"></a>00123
<a name="l00124"></a>00124
<a name="l00129"></a>00129 <span class="keywordtype">double</span> GetRMSD();
<a name="l00151"></a>00151 <a class="code" href="classOpenBabel_1_1matrix3x3.shtml" title="Represents a real 3x3 matrix.">matrix3x3</a> GetRotMatrix();
<a name="l00159"></a>00159 vector<vector3> GetAlignment();
<a name="l00165"></a>00165 <span class="keywordtype">bool</span> UpdateCoords(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>* target);
<a name="l00167"></a>00167
<a name="l00168"></a>00168 <span class="keyword">private</span>:
<a name="l00169"></a>00169 <span class="keywordtype">bool</span> _ready;
<a name="l00170"></a>00170 <span class="keywordtype">bool</span> _symmetry;
<a name="l00171"></a>00171 <span class="keywordtype">bool</span> _includeH;
<a name="l00172"></a>00172 <span class="keywordtype">double</span> _rmsd;
<a name="l00173"></a>00173 <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> _frag_atoms;
<a name="l00174"></a>00174 <a class="code" href="group__substructure.shtml#ga6179e6c11d4f797e8d0ef6ac5c9f25a8" title="A group of automorphic permutations.">Automorphisms</a> _aut;
<a name="l00175"></a>00175 <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>* _prefmol;
<a name="l00176"></a>00176 <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>* _ptargetmol;
<a name="l00177"></a>00177 Eigen::MatrixXd _rotMatrix;
<a name="l00178"></a>00178 Eigen::Vector3d _ref_centr, _target_centr;
<a name="l00179"></a>00179 <span class="keyword">const</span> vector<vector3> *_pref;
<a name="l00180"></a>00180 <span class="keyword">const</span> vector<vector3> *_ptarget;
<a name="l00181"></a>00181 vector<vector3> _refmol_coords;
<a name="l00182"></a>00182 vector<vector3> _targetmol_coords;
<a name="l00183"></a>00183 Eigen::MatrixXd _result;
<a name="l00184"></a>00184 Eigen::MatrixXd _mref, _mtarget;
<a name="l00185"></a>00185 <span class="keywordtype">void</span> VectorsToMatrix(<span class="keyword">const</span> vector<vector3> *pcoords, Eigen::MatrixXd &coords);
<a name="l00186"></a>00186 Eigen::Vector3d MoveToOrigin(Eigen::MatrixXd &coords);
<a name="l00187"></a>00187 <span class="keywordtype">void</span> SimpleAlign(<span class="keyword">const</span> Eigen::MatrixXd &mtarget);
<a name="l00188"></a>00188 <span class="comment">// Generate a mapping from the permutation map to the index of</span>
<a name="l00189"></a>00189 <span class="comment">// correct column in _mtarget. Need to handle the fact that the</span>
<a name="l00190"></a>00190 <span class="comment">// permutation group contains non-fragment atoms.</span>
<a name="l00191"></a>00191 <span class="comment">// For example, map(213465) will be converted to newidx(102354).</span>
<a name="l00192"></a>00192 <span class="comment">// If the atom with Idx=3 is not in the fragment, it will be</span>
<a name="l00193"></a>00193 <span class="comment">// converted to newidx(10X243) instead.</span>
<a name="l00194"></a>00194 vector<unsigned int> _newidx;
<a name="l00195"></a>00195 };
<a name="l00196"></a>00196 }
<a name="l00197"></a>00197
<a name="l00198"></a>00198 <span class="preprocessor">#endif // OB_ALIGN_H</span>
<a name="l00199"></a>00199 <span class="preprocessor"></span>
</pre></div></div>
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