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<div class="title">rotamer.h</div> </div>
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<a href="rotamer_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">rotamer.h - Handle rotamer list data.</span>
<a name="l00003"></a>00003 <span class="comment"></span>
<a name="l00004"></a>00004 <span class="comment">Copyright (C) 1998-2000 by OpenEye Scientific Software, Inc.</span>
<a name="l00005"></a>00005 <span class="comment">Some portions Copyright (C) 2001-2006 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_ROTAMER_H</span>
<a name="l00021"></a>00021 <span class="preprocessor"></span><span class="preprocessor">#define OB_ROTAMER_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 <map></span>
<a name="l00025"></a>00025
<a name="l00026"></a>00026 <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="l00027"></a>00027 <span class="preprocessor">#include <<a class="code" href="rotor_8h.shtml" title="Rotate torsional according to rotor rules.">openbabel/rotor.h</a>></span>
<a name="l00028"></a>00028 <span class="preprocessor">#include <<a class="code" href="generic_8h.shtml" title="Handle generic data classes. Custom data for atoms, bonds, etc.">openbabel/generic.h</a>></span>
<a name="l00029"></a>00029
<a name="l00030"></a>00030 <span class="keyword">namespace </span>OpenBabel
<a name="l00031"></a>00031 {
<a name="l00032"></a>00032
<a name="l00034"></a>00034 <span class="comment">// Further class introduction in rotamer.cpp</span>
<a name="l00035"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml">00035</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBRotamerList.shtml" title="Supports a set of rotamer coordinate sets for some number of potentially rotatable bonds...">OBRotamerList</a> : <span class="keyword">public</span> <a class="code" href="classOpenBabel_1_1OBGenericData.shtml" title="Base class for generic data.">OBGenericData</a>
<a name="l00036"></a>00036 {
<a name="l00038"></a>00038 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> _NBaseCoords;
<a name="l00040"></a>00040 std::vector<double*> _c;
<a name="l00042"></a>00042 std::vector<std::pair<OBAtom**,std::vector<int> > > _vrotor;
<a name="l00045"></a>00045 std::vector<std::vector<double> > _vres;
<a name="l00047"></a>00047 std::vector<unsigned char*> _vrotamer;
<a name="l00048"></a>00048
<a name="l00049"></a>00049 <span class="comment">/*Because contains OBAtom*, these aren't meaningful without knowing the parent molecule</span>
<a name="l00050"></a>00050 <span class="comment"> OBRotamerList(const OBRotamerList &cpy) : OBGenericData(cpy)</span>
<a name="l00051"></a>00051 <span class="comment"> {}</span>
<a name="l00052"></a>00052 <span class="comment"> OBRotamerList& operator =(const OBRotamerList &)</span>
<a name="l00053"></a>00053 <span class="comment"> {</span>
<a name="l00054"></a>00054 <span class="comment"> return *this;</span>
<a name="l00055"></a>00055 <span class="comment"> }</span>
<a name="l00056"></a>00056 <span class="comment"> */</span>
<a name="l00057"></a>00057
<a name="l00058"></a>00058 <span class="keyword">public</span>:
<a name="l00059"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml#aa1cef5a8affd0b0f75891495f1674805">00059</a> <a class="code" href="classOpenBabel_1_1OBRotamerList.shtml" title="Supports a set of rotamer coordinate sets for some number of potentially rotatable bonds...">OBRotamerList</a>()
<a name="l00060"></a>00060 {
<a name="l00061"></a>00061 _NBaseCoords=0;
<a name="l00062"></a>00062 _type= <a class="code" href="namespaceOpenBabel_1_1OBGenericDataType.shtml#a06fc87d81c62e9abb8790b6e5713c55ba6792a664f1614a75f33128e139392ef1" title="Information for generating & manipulating rotamers, i.e. OBRotamerList.">OBGenericDataType::RotamerList</a>;
<a name="l00063"></a>00063 _attr=<span class="stringliteral">"RotamerList"</span>;
<a name="l00064"></a>00064 }
<a name="l00065"></a>00065 <span class="keyword">virtual</span> <a class="code" href="classOpenBabel_1_1OBGenericData.shtml" title="Base class for generic data.">OBGenericData</a>* Clone(<a class="code" href="classOpenBabel_1_1OBBase.shtml" title="Base Class.">OBBase</a>* parent) <span class="keyword">const</span>;
<a name="l00066"></a>00066
<a name="l00067"></a>00067 ~<a class="code" href="classOpenBabel_1_1OBRotamerList.shtml" title="Supports a set of rotamer coordinate sets for some number of potentially rotatable bonds...">OBRotamerList</a>();
<a name="l00069"></a>00069 <span class="keywordtype">void</span> Setup(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>&,<a class="code" href="classOpenBabel_1_1OBRotorList.shtml" title="Given an OBMol, set up a list of possibly rotatable torsions,.">OBRotorList</a>&);
<a name="l00074"></a>00074 <span class="keywordtype">void</span> Setup(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol,<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>*ref,<span class="keywordtype">int</span> nrotors);
<a name="l00076"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml#abccb611f60719e4ec9acf271a5aa934d">00076</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> NumRotors()<span class="keyword"> const</span>
<a name="l00077"></a>00077 <span class="keyword"> </span>{
<a name="l00078"></a>00078 <span class="keywordflow">return</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>)_vrotor.size();
<a name="l00079"></a>00079 }
<a name="l00081"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml#a747209e491f2149ac86230cf6c3bd146">00081</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> NumRotamers()<span class="keyword"> const</span>
<a name="l00082"></a>00082 <span class="keyword"> </span>{
<a name="l00083"></a>00083 <span class="keywordflow">return</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>)_vrotamer.size();
<a name="l00084"></a>00084 }
<a name="l00086"></a>00086 <span class="keywordtype">void</span> AddRotamer(<span class="keywordtype">double</span>*);
<a name="l00088"></a>00088 <span class="keywordtype">void</span> AddRotamer(<span class="keywordtype">int</span> *key);
<a name="l00090"></a>00090 <span class="keywordtype">void</span> AddRotamer(std::vector<int> key);
<a name="l00092"></a>00092 <span class="keywordtype">void</span> AddRotamer(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> *key);
<a name="l00094"></a>00094 <span class="keywordtype">void</span> AddRotamers(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> *arr,<span class="keywordtype">int</span> nconf);
<a name="l00096"></a>00096 <span class="keywordtype">void</span> GetReferenceArray(<span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>*) <span class="keyword">const</span>;
<a name="l00097"></a>00097
<a name="l00099"></a>00099
<a name="l00100"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml#a2948e1a74f2c22c575d6ddc6643f6ef1">00100</a> std::vector<unsigned char*>::iterator BeginRotamer()
<a name="l00101"></a>00101 {
<a name="l00102"></a>00102 <span class="keywordflow">return</span> _vrotamer.begin();
<a name="l00103"></a>00103 }
<a name="l00104"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml#a589d2df01c6f3e1cb1bf95b25e804409">00104</a> std::vector<unsigned char*>::iterator EndRotamer()
<a name="l00105"></a>00105 {
<a name="l00106"></a>00106 <span class="keywordflow">return</span> _vrotamer.end();
<a name="l00107"></a>00107 }
<a name="l00109"></a>00109
<a name="l00112"></a>00112 std::vector<double*> CreateConformerList(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>& mol);
<a name="l00113"></a>00113
<a name="l00116"></a>00116 <span class="keywordtype">void</span> ExpandConformerList(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>&mol,std::vector<double*>& confs);
<a name="l00117"></a>00117
<a name="l00118"></a>00118 <span class="keywordtype">void</span> SetCurrentCoordinates(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &mol, std::vector<int> arr);
<a name="l00119"></a>00119
<a name="l00122"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml#a91c3efe37db1542a2f553440143915f9">00122</a> <span class="keywordtype">void</span> SetBaseCoordinateSets(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>& mol)
<a name="l00123"></a>00123 {
<a name="l00124"></a>00124 SetBaseCoordinateSets(mol.<a class="code" href="classOpenBabel_1_1OBMol.shtml#a5246a44bf82aa31c2f428665db94bfb8">GetConformers</a>(), mol.<a class="code" href="classOpenBabel_1_1OBMol.shtml#a0c317a10161689c407f29a6fcacdb852">NumAtoms</a>());
<a name="l00125"></a>00125 }
<a name="l00126"></a>00126
<a name="l00128"></a>00128
<a name="l00131"></a>00131 <span class="keywordtype">void</span> SetBaseCoordinateSets(std::vector<double*> bc, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> N);
<a name="l00132"></a>00132
<a name="l00134"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml#a11ab9cdfece6567dfc4db629cddd0a93">00134</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> NumBaseCoordinateSets()<span class="keyword"> const</span>
<a name="l00135"></a>00135 <span class="keyword"> </span>{
<a name="l00136"></a>00136 <span class="keywordflow">return</span> <span class="keyword">static_cast<</span><span class="keywordtype">unsigned</span> <span class="keywordtype">int</span><span class="keyword">></span> (_c.size());
<a name="l00137"></a>00137 }
<a name="l00138"></a>00138
<a name="l00140"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml#adbaf9eeafb825763acadfc785220412a">00140</a> <span class="keywordtype">double</span> *GetBaseCoordinateSet(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i)<span class="keyword"> const</span>
<a name="l00141"></a>00141 <span class="keyword"> </span>{
<a name="l00142"></a>00142 <span class="keywordflow">return</span> (i<_c.size()) ? _c[i] : NULL;
<a name="l00143"></a>00143 }
<a name="l00144"></a>00144
<a name="l00146"></a><a class="code" href="classOpenBabel_1_1OBRotamerList.shtml#a0c317a10161689c407f29a6fcacdb852">00146</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> NumAtoms()<span class="keyword"> const</span>
<a name="l00147"></a>00147 <span class="keyword"> </span>{
<a name="l00148"></a>00148 <span class="keywordflow">return</span> _NBaseCoords;
<a name="l00149"></a>00149 }
<a name="l00150"></a>00150 };
<a name="l00151"></a>00151
<a name="l00153"></a>00153 <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#a8b1ba3c73d4038fd69729fbeb588008a" title="Swap Byte instruction (i.e., handle transfers between endian forms)">Swab</a>(<span class="keywordtype">int</span>);
<a name="l00154"></a>00154
<a name="l00155"></a>00155 }
<a name="l00156"></a>00156
<a name="l00157"></a>00157 <span class="preprocessor">#endif // OB_ROTAMER_H</span>
<a name="l00158"></a>00158 <span class="preprocessor"></span>
</pre></div></div>
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