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<div class="title">ring.h</div> </div>
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<a href="ring_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">ring.h - Deal with rings, find smallest set of smallest rings (SSSR).</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_RING_H</span>
<a name="l00021"></a>00021 <span class="preprocessor"></span><span class="preprocessor">#define OB_RING_H</span>
<a name="l00022"></a>00022 <span class="preprocessor"></span>
<a name="l00023"></a>00023 <span class="preprocessor">#include <deque></span>
<a name="l00024"></a>00024 <span class="preprocessor">#include <algorithm></span>
<a name="l00025"></a>00025
<a name="l00026"></a>00026 <span class="comment">// TODO: Make this work as a free-standing header</span>
<a name="l00027"></a>00027 <span class="comment">// Currently only used in ring.cpp which imports mol.h beforehand</span>
<a name="l00028"></a>00028 <span class="preprocessor">#include <<a class="code" href="bitvec_8h.shtml" title="Fast and efficient bitstring class.">openbabel/bitvec.h</a>></span>
<a name="l00029"></a>00029 <span class="preprocessor">#include <<a class="code" href="typer_8h.shtml" title="Open Babel atom and aromaticity typer.">openbabel/typer.h</a>></span>
<a name="l00030"></a>00030
<a name="l00031"></a>00031 <span class="keyword">namespace </span>OpenBabel
<a name="l00032"></a>00032 {
<a name="l00033"></a>00033
<a name="l00034"></a>00034 <span class="keyword">class </span>OBMol;
<a name="l00035"></a>00035 <span class="keyword">class </span>OBAtom;
<a name="l00036"></a>00036 <span class="keyword">class </span>OBBond;
<a name="l00037"></a>00037
<a name="l00038"></a>00038 <span class="comment">// class introduction in ring.cpp</span>
<a name="l00039"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml">00039</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBRing.shtml" title="Stores information on rings in a molecule from SSSR perception.">OBRing</a>
<a name="l00040"></a>00040 {
<a name="l00041"></a>00041 <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *_parent;
<a name="l00042"></a>00042 <span class="keyword">public</span>:
<a name="l00043"></a>00043 <span class="comment">//public data members</span>
<a name="l00044"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#ab121c8e013115dd3efb26601ad1975d0">00044</a> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBRing.shtml#ab121c8e013115dd3efb26601ad1975d0" title="a unique id to ensure a stable sort in SSSR determination">ring_id</a>;
<a name="l00045"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#a86d1b14f3c439c5be01e0f6c9dc60a1d">00045</a> std::vector<int> <a class="code" href="classOpenBabel_1_1OBRing.shtml#a86d1b14f3c439c5be01e0f6c9dc60a1d" title="the path of this ring (i.e., the atom indexes)">_path</a>;
<a name="l00046"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#ababc3e7a7e660eba9b2dfa3b2bc28782">00046</a> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> <a class="code" href="classOpenBabel_1_1OBRing.shtml#ababc3e7a7e660eba9b2dfa3b2bc28782" title="the path of this ring as a redundant bit vector">_pathset</a>;
<a name="l00047"></a>00047
<a name="l00049"></a>00049
<a name="l00050"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#aca37bf71481749f6555e916555d9e7a2">00050</a> <a class="code" href="classOpenBabel_1_1OBRing.shtml#aca37bf71481749f6555e916555d9e7a2">OBRing</a>() {}
<a name="l00052"></a>00052 <a class="code" href="classOpenBabel_1_1OBRing.shtml" title="Stores information on rings in a molecule from SSSR perception.">OBRing</a>(std::vector<int>& path, <span class="keywordtype">int</span> size);
<a name="l00053"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#a2abeced3e6e318f88abe9249833b6d25">00053</a> <a class="code" href="classOpenBabel_1_1OBRing.shtml#a2abeced3e6e318f88abe9249833b6d25">OBRing</a>(std::vector<int>& path, <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> <span class="keyword">set</span>) : _path(path), _pathset(set) {}
<a name="l00054"></a>00054 <a class="code" href="classOpenBabel_1_1OBRing.shtml" title="Stores information on rings in a molecule from SSSR perception.">OBRing</a>(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBRing.shtml" title="Stores information on rings in a molecule from SSSR perception.">OBRing</a> &src);
<a name="l00055"></a>00055 <a class="code" href="classOpenBabel_1_1OBRing.shtml" title="Stores information on rings in a molecule from SSSR perception.">OBRing</a>& operator=(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBRing.shtml" title="Stores information on rings in a molecule from SSSR perception.">OBRing</a> &src);
<a name="l00057"></a>00057
<a name="l00058"></a>00058 <span class="comment">//member functions</span>
<a name="l00059"></a>00059
<a name="l00061"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#ab3bace7b51e6e7d78048999bc2189e27">00061</a> <span class="keywordtype">size_t</span> <a class="code" href="classOpenBabel_1_1OBRing.shtml#ab3bace7b51e6e7d78048999bc2189e27">Size</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span>(_path.size()); }
<a name="l00064"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#ab6d388ff8c4e4d4d4c37db31a36c01f4">00064</a> <span class="keywordtype">size_t</span> <a class="code" href="classOpenBabel_1_1OBRing.shtml#ab6d388ff8c4e4d4d4c37db31a36c01f4">PathSize</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span>(_path.size()); }
<a name="l00065"></a>00065
<a name="l00069"></a>00069 <span class="keywordtype">bool</span> IsAromatic();
<a name="l00070"></a>00070
<a name="l00072"></a>00072 <span class="keywordtype">void</span> SetType(<span class="keywordtype">char</span> *type);
<a name="l00074"></a>00074 <span class="keywordtype">void</span> SetType(std::string &type);
<a name="l00076"></a>00076 <span class="keywordtype">char</span> *GetType();
<a name="l00080"></a>00080 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> GetRootAtom();
<a name="l00081"></a>00081
<a name="l00083"></a>00083 <span class="keywordtype">bool</span> IsMember(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *a);
<a name="l00086"></a>00086 <span class="keywordtype">bool</span> IsMember(<a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *b);
<a name="l00088"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#a87c9cc8c92936bd191dca74f78fb84cb">00088</a> <span class="keywordtype">bool</span> IsInRing(<span class="keywordtype">int</span> i)
<a name="l00089"></a>00089 {
<a name="l00090"></a>00090 <span class="keywordflow">return</span>(_pathset.BitIsOn(i));
<a name="l00091"></a>00091 }
<a name="l00092"></a>00092
<a name="l00094"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#a82ba3a4d5db75e9f11d3ea8dd5ef32b8">00094</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBRing.shtml#a82ba3a4d5db75e9f11d3ea8dd5ef32b8" title="Set the parent of this ring to m.">SetParent</a>(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *m) { _parent = m; }
<a name="l00096"></a><a class="code" href="classOpenBabel_1_1OBRing.shtml#ad8480b61159bc6cb861b17341dc2b29a">00096</a> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *<a class="code" href="classOpenBabel_1_1OBRing.shtml#ad8480b61159bc6cb861b17341dc2b29a">GetParent</a>() { <span class="keywordflow">return</span>(_parent);}
<a name="l00097"></a>00097
<a name="l00104"></a>00104 <span class="keywordtype">bool</span> findCenterAndNormal(<a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> & center, <a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> &norm1, <a class="code" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> &norm2);
<a name="l00105"></a>00105 <span class="keyword">private</span>:
<a name="l00106"></a>00106 <span class="keywordtype">char</span> _type[30];
<a name="l00107"></a>00107 };
<a name="l00108"></a>00108
<a name="l00111"></a>00111 OBAPI <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenBabel.shtml#a8ae850aac19b7a1ff3c02b6f3c17d36f">CompareRingSize</a>(<span class="keyword">const</span> OBRing *,<span class="keyword">const</span> OBRing *);
<a name="l00112"></a>00112
<a name="l00113"></a>00113
<a name="l00117"></a><a class="code" href="classOpenBabel_1_1OBRingSearch.shtml">00117</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBRingSearch.shtml" title="Internal class to facilitate OBMol::FindSSSR()">OBRingSearch</a>
<a name="l00118"></a>00118 {
<a name="l00119"></a>00119 std::vector<OBBond*> _bonds;
<a name="l00120"></a>00120 std::vector<OBRing*> _rlist;
<a name="l00121"></a>00121 <span class="keyword">public</span>:
<a name="l00122"></a><a class="code" href="classOpenBabel_1_1OBRingSearch.shtml#af1211b4680e59ac34a16593ddcdb2761">00122</a> <a class="code" href="classOpenBabel_1_1OBRingSearch.shtml#af1211b4680e59ac34a16593ddcdb2761">OBRingSearch</a>() {}
<a name="l00123"></a>00123 ~<a class="code" href="classOpenBabel_1_1OBRingSearch.shtml" title="Internal class to facilitate OBMol::FindSSSR()">OBRingSearch</a>();
<a name="l00124"></a>00124
<a name="l00126"></a><a class="code" href="classOpenBabel_1_1OBRingSearch.shtml#acd7836d1e4e1ab6fbd3faa49403e5503">00126</a> <span class="keywordtype">void</span> SortRings()
<a name="l00127"></a>00127 {
<a name="l00128"></a>00128 std::vector<OBRing*>::iterator j;
<a name="l00129"></a>00129 <span class="keywordtype">int</span> ring_id; <span class="comment">// for each ring, assign a unique id to ensure a stable sort</span>
<a name="l00130"></a>00130
<a name="l00131"></a>00131 <span class="keywordflow">for</span> (j = _rlist.begin(), ring_id = 0; j != _rlist.end(); ++j, ++ring_id)
<a name="l00132"></a>00132 (*j)->ring_id = ring_id;
<a name="l00133"></a>00133 std::sort(_rlist.begin(),_rlist.end(),<a class="code" href="namespaceOpenBabel.shtml#a8ae850aac19b7a1ff3c02b6f3c17d36f">CompareRingSize</a>);
<a name="l00134"></a>00134 }
<a name="l00136"></a>00136 <span class="keywordtype">void</span> RemoveRedundant(<span class="keywordtype">int</span>);
<a name="l00138"></a>00138 <span class="keywordtype">void</span> AddRingFromClosure(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> &,<a class="code" href="classOpenBabel_1_1OBBond.shtml" title="Bond class.">OBBond</a> *);
<a name="l00139"></a>00139
<a name="l00140"></a>00140 <span class="keywordtype">bool</span> SaveUniqueRing(std::deque<int>&,std::deque<int>&);
<a name="l00141"></a>00141
<a name="l00143"></a>00143 <span class="keywordtype">void</span> WriteRings();
<a name="l00144"></a>00144
<a name="l00146"></a>00146
<a name="l00147"></a>00147
<a name="l00148"></a><a class="code" href="classOpenBabel_1_1OBRingSearch.shtml#aa1a05257821a8156625beabb7dd58e0b">00148</a> std::vector<OBRing*>::iterator BeginRings()
<a name="l00149"></a>00149 {
<a name="l00150"></a>00150 <span class="keywordflow">return</span>(_rlist.begin());
<a name="l00151"></a>00151 }
<a name="l00153"></a><a class="code" href="classOpenBabel_1_1OBRingSearch.shtml#a07ad405727c652a6a280d821b9d1ac47">00153</a> std::vector<OBRing*>::iterator EndRings()
<a name="l00154"></a>00154 {
<a name="l00155"></a>00155 <span class="keywordflow">return</span>(_rlist.end());
<a name="l00156"></a>00156 }
<a name="l00158"></a>00158 };
<a name="l00159"></a>00159
<a name="l00164"></a><a class="code" href="classOpenBabel_1_1OBRTree.shtml">00164</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBRTree.shtml" title="Internal class for OBRing search algorithms to create a search tree of OBAtom objects.">OBRTree</a>
<a name="l00165"></a>00165 {
<a name="l00166"></a>00166 <a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a> *_atom;
<a name="l00167"></a>00167 <a class="code" href="classOpenBabel_1_1OBRTree.shtml" title="Internal class for OBRing search algorithms to create a search tree of OBAtom objects.">OBRTree</a> *_prv;
<a name="l00168"></a>00168 <span class="keyword">public</span>:
<a name="l00170"></a>00170 <a class="code" href="classOpenBabel_1_1OBRTree.shtml" title="Internal class for OBRing search algorithms to create a search tree of OBAtom objects.">OBRTree</a>(<a class="code" href="classOpenBabel_1_1OBAtom.shtml" title="Atom class.">OBAtom</a>*,<a class="code" href="classOpenBabel_1_1OBRTree.shtml" title="Internal class for OBRing search algorithms to create a search tree of OBAtom objects.">OBRTree</a>*);
<a name="l00171"></a><a class="code" href="classOpenBabel_1_1OBRTree.shtml#a552ea16c4bb845b80b7cd56c2bd5c87d">00171</a> <a class="code" href="classOpenBabel_1_1OBRTree.shtml#a552ea16c4bb845b80b7cd56c2bd5c87d">~OBRTree</a>() {}
<a name="l00172"></a>00172
<a name="l00174"></a>00174 <span class="keywordtype">int</span> GetAtomIdx();
<a name="l00176"></a>00176 <span class="keywordtype">void</span> PathToRoot(std::vector<OBAtom*>&);
<a name="l00177"></a>00177 };
<a name="l00178"></a>00178
<a name="l00179"></a>00179 } <span class="comment">// end namespace OpenBabel</span>
<a name="l00180"></a>00180
<a name="l00181"></a>00181 <span class="preprocessor">#endif // OB_RING_H</span>
<a name="l00182"></a>00182 <span class="preprocessor"></span>
</pre></div></div>
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