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<a href="alias_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">alias.h - OBGenericData class to hold alias information on atoms</span>
<a name="l00003"></a>00003 <span class="comment">Copyright (C) Copyright (C) 2007 by Chris Morley</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">the Free Software Foundation version 2 of the License.</span>
<a name="l00008"></a>00008 <span class="comment"></span>
<a name="l00009"></a>00009 <span class="comment">This program is distributed in the hope that it will be useful,</span>
<a name="l00010"></a>00010 <span class="comment">but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00011"></a>00011 <span class="comment">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00012"></a>00012 <span class="comment">GNU General Public License for more details.</span>
<a name="l00013"></a>00013 <span class="comment">***********************************************************************/</span>
<a name="l00014"></a>00014
<a name="l00015"></a>00015 <span class="preprocessor">#ifndef OB_ALIAS_H</span>
<a name="l00016"></a>00016 <span class="preprocessor"></span><span class="preprocessor">#define OB_ALIAS_H</span>
<a name="l00017"></a>00017 <span class="preprocessor"></span>
<a name="l00018"></a>00018 <span class="preprocessor">#include <vector></span>
<a name="l00019"></a>00019 <span class="preprocessor">#include <<a class="code" href="shared__ptr_8h.shtml" title="Shared pointer.">openbabel/shared_ptr.h</a>></span>
<a name="l00020"></a>00020 <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="l00021"></a>00021
<a name="l00022"></a><a class="code" href="namespaceOpenBabel.shtml">00022</a> <span class="keyword">namespace </span>OpenBabel
<a name="l00023"></a>00023 {
<a name="l00024"></a>00024 <span class="comment">// This macro is used in DLL builds. If it has not</span>
<a name="l00025"></a>00025 <span class="comment">// been set in babelconfig.h, define it as nothing.</span>
<a name="l00026"></a>00026 <span class="preprocessor">#ifndef OBCOMMON</span>
<a name="l00027"></a>00027 <span class="preprocessor"></span><span class="preprocessor"> #define OBCOMMON</span>
<a name="l00028"></a>00028 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
<a name="l00029"></a>00029 <span class="preprocessor"></span>
<a name="l00030"></a><a class="code" href="namespaceOpenBabel.shtml#af962a429bf8fe8b8f222ff1a6018c35e">00030</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="namespaceOpenBabel.shtml#af962a429bf8fe8b8f222ff1a6018c35e">AliasDataType</a> = 0x7883;
<a name="l00031"></a>00031
<a name="l00049"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml">00049</a> <span class="keyword">class </span>OBCOMMON <a class="code" href="classOpenBabel_1_1AliasData.shtml" title="Indicate atoms as aliases for larger functional groups.">AliasData</a> : <span class="keyword">public</span> <a class="code" href="classOpenBabel_1_1OBGenericData.shtml" title="Base class for generic data.">OBGenericData</a>
<a name="l00050"></a>00050 {
<a name="l00051"></a>00051 <span class="keyword">protected</span>:
<a name="l00052"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#a7dd8464fd3023ffafa56a134e663a4ae">00052</a> std::string <a class="code" href="classOpenBabel_1_1AliasData.shtml#a7dd8464fd3023ffafa56a134e663a4ae">_alias</a>;
<a name="l00053"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#ac8b232648a71f527f8a33b13d9562013">00053</a> std::string <a class="code" href="classOpenBabel_1_1AliasData.shtml#ac8b232648a71f527f8a33b13d9562013">_right_form</a>;
<a name="l00054"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#a08d5887a8d97196910cb41a2d551f375">00054</a> std::vector<unsigned long> <a class="code" href="classOpenBabel_1_1AliasData.shtml#a08d5887a8d97196910cb41a2d551f375">_expandedatoms</a>; <span class="comment">//atom ids (not idxs)</span>
<a name="l00055"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#a1134e770ae4315ea8bc1201e2f21da8b">00055</a> std::string <a class="code" href="classOpenBabel_1_1AliasData.shtml#a1134e770ae4315ea8bc1201e2f21da8b">_color</a>;
<a name="l00056"></a>00056 <span class="keyword">public</span>:
<a name="l00057"></a>00057
<a name="l00058"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#a55d097a56763789d4b0d070e51a580fb">00058</a> <a class="code" href="classOpenBabel_1_1AliasData.shtml#a55d097a56763789d4b0d070e51a580fb">AliasData</a>(): <a class="code" href="classOpenBabel_1_1OBGenericData.shtml" title="Base class for generic data.">OBGenericData</a>(<span class="stringliteral">"Alias"</span>, <a class="code" href="namespaceOpenBabel.shtml#af962a429bf8fe8b8f222ff1a6018c35e">AliasDataType</a>){ }
<a name="l00059"></a>00059
<a name="l00060"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#a67bda850335747e7ac5d66629bda0a67">00060</a> <span class="keyword">virtual</span> <a class="code" href="classOpenBabel_1_1OBGenericData.shtml" title="Base class for generic data.">OBGenericData</a>* <a class="code" href="classOpenBabel_1_1AliasData.shtml#a67bda850335747e7ac5d66629bda0a67">Clone</a>(<a class="code" href="classOpenBabel_1_1OBBase.shtml" title="Base Class.">OBBase</a>* <span class="comment">/*parent*/</span>)<span class="keyword"> const</span>{<span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenBabel_1_1AliasData.shtml" title="Indicate atoms as aliases for larger functional groups.">AliasData</a>(*<span class="keyword">this</span>);}
<a name="l00061"></a>00061
<a name="l00063"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#ad3cc04112e0d8320faff12cd8e70bcd4">00063</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1AliasData.shtml#ad3cc04112e0d8320faff12cd8e70bcd4" title="Add an alias.">SetAlias</a>(<span class="keyword">const</span> std::string& alias) {_alias = alias;}
<a name="l00064"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#aff1fad2cef60a4d52443058c69ec835d">00064</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1AliasData.shtml#aff1fad2cef60a4d52443058c69ec835d">SetAlias</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* alias) {_alias = alias;}
<a name="l00065"></a>00065
<a name="l00067"></a>00067 std::string GetAlias(<span class="keywordtype">bool</span> rightAligned = <span class="keyword">false</span>) <span class="keyword">const</span>;
<a name="l00068"></a>00068
<a name="l00070"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#afe19945cf89192f929d6f0931ef66a63">00070</a> std::string <a class="code" href="classOpenBabel_1_1AliasData.shtml#afe19945cf89192f929d6f0931ef66a63" title="Return the color which has been assigned to this alias.">GetColor</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> _color; }
<a name="l00071"></a>00071
<a name="l00073"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#adae56afc36beb65bb8fb4cc32afd7d19">00073</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1AliasData.shtml#adae56afc36beb65bb8fb4cc32afd7d19" title="Assign a color to this alias.">SetColor</a>(std::string color){ _color = color; }
<a name="l00074"></a>00074
<a name="l00075"></a><a class="code" href="classOpenBabel_1_1AliasData.shtml#a01c2d9efc5bbab7c9f080f3eec0b94b7">00075</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1AliasData.shtml#a01c2d9efc5bbab7c9f080f3eec0b94b7">IsExpanded</a>()<span class="keyword">const </span>{ <span class="keywordflow">return</span> !_expandedatoms.empty(); }
<a name="l00076"></a>00076
<a name="l00079"></a>00079 <span class="keyword">static</span> <span class="keywordtype">void</span> RevertToAliasForm(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>& mol);
<a name="l00080"></a>00080
<a name="l00082"></a>00082 <span class="keywordtype">bool</span> Expand(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>& mol, <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> atomindex);
<a name="l00083"></a>00083
<a name="l00084"></a>00084 <span class="preprocessor"> #ifdef HAVE_SHARED_POINTER</span>
<a name="l00085"></a>00085 <span class="preprocessor"></span>
<a name="l00086"></a>00086
<a name="l00087"></a>00087 <span class="keyword">static</span> <span class="keywordtype">bool</span> AddAliases(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>* pmol);
<a name="l00088"></a>00088 <span class="preprocessor"> #endif</span>
<a name="l00089"></a>00089 <span class="preprocessor"></span>
<a name="l00090"></a>00090 <span class="keyword">private</span>:
<a name="l00092"></a>00092 <span class="keywordtype">bool</span> FormulaParse(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>& mol, <span class="keyword">const</span> <span class="keywordtype">unsigned</span> atomindex);
<a name="l00093"></a>00093
<a name="l00095"></a>00095 <span class="keywordtype">void</span> AddExpandedAtom(<span class="keywordtype">int</span> <span class="keywordtype">id</span>);
<a name="l00096"></a>00096
<a name="l00098"></a>00098 <span class="keywordtype">void</span> DeleteExpandedAtoms(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>& mol);
<a name="l00099"></a>00099
<a name="l00100"></a>00100 <span class="keyword">struct </span>AliasItem
<a name="l00101"></a>00101 {
<a name="l00102"></a>00102 std::string right_form;
<a name="l00103"></a>00103 std::string smiles;
<a name="l00104"></a>00104 std::string color;
<a name="l00105"></a>00105 };
<a name="l00106"></a>00106 <span class="keyword">typedef</span> std::map<std::string, AliasItem> SuperAtomTable; <span class="comment">//key=alias left-form</span>
<a name="l00107"></a>00107
<a name="l00108"></a>00108 <span class="keyword">static</span> <span class="keywordtype">bool</span> LoadFile(SuperAtomTable& table);
<a name="l00109"></a>00109 <span class="keyword">static</span> SuperAtomTable& table()
<a name="l00110"></a>00110 {
<a name="l00111"></a>00111 <span class="keyword">static</span> SuperAtomTable t;
<a name="l00112"></a>00112 <span class="keywordflow">if</span>(t.empty())
<a name="l00113"></a>00113 LoadFile(t);
<a name="l00114"></a>00114 <span class="keywordflow">return</span> t;
<a name="l00115"></a>00115 }
<a name="l00116"></a>00116 <span class="keywordtype">bool</span> FromNameLookup(OBMol& mol, <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> atomindex);
<a name="l00117"></a>00117 <span class="preprocessor">#ifdef HAVE_SHARED_POINTER</span>
<a name="l00118"></a>00118 <span class="preprocessor"></span> <span class="keyword">typedef</span> std::vector< std::pair<std::string, shared_ptr<OBSmartsPattern> > > SmartsTable;
<a name="l00119"></a>00119 <span class="keyword">static</span> <span class="keywordtype">bool</span> LoadFile(SmartsTable& smtable);
<a name="l00120"></a>00120 <span class="preprocessor">#endif</span>
<a name="l00121"></a>00121 <span class="preprocessor"></span>};
<a name="l00122"></a>00122 } <span class="comment">//namespace</span>
<a name="l00123"></a>00123
<a name="l00124"></a>00124 <span class="preprocessor">#endif // OB_ALIAS_H</span>
<a name="l00125"></a>00125 <span class="preprocessor"></span>
</pre></div></div>
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