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gnome-chemistry-utils-devel-0.10.8-3mdv2010.0.i586.rpm

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<h1>gcp/molecule.h</h1><a href="gcp_2molecule_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">// -*- C++ -*-</span>
<a name="l00002"></a>00002 
<a name="l00003"></a>00003 <span class="comment">/* </span>
<a name="l00004"></a>00004 <span class="comment"> * GChemPaint library</span>
<a name="l00005"></a>00005 <span class="comment"> * molecule.h </span>
<a name="l00006"></a>00006 <span class="comment"> *</span>
<a name="l00007"></a>00007 <span class="comment"> * Copyright (C) 2001-2008 Jean Bréfort &lt;jean.brefort@normalesup.org&gt;</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 </span>
<a name="l00010"></a>00010 <span class="comment"> * modify it under the terms of the GNU General Public License as </span>
<a name="l00011"></a>00011 <span class="comment"> * published by the Free Software Foundation; either version 2 of the</span>
<a name="l00012"></a>00012 <span class="comment"> * License, or (at your option) any later version.</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 <span class="comment"> * You should have received a copy of the GNU General Public License</span>
<a name="l00020"></a>00020 <span class="comment"> * along with this program; if not, write to the Free Software</span>
<a name="l00021"></a>00021 <span class="comment"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301</span>
<a name="l00022"></a>00022 <span class="comment"> * USA</span>
<a name="l00023"></a>00023 <span class="comment"> */</span>
<a name="l00024"></a>00024 
<a name="l00025"></a>00025 <span class="preprocessor">#ifndef GCHEMPAINT_MOLECULE_H</span>
<a name="l00026"></a>00026 <span class="preprocessor"></span><span class="preprocessor">#define GCHEMPAINT_MOLECULE_H</span>
<a name="l00027"></a>00027 <span class="preprocessor"></span>
<a name="l00028"></a>00028 <span class="preprocessor">#include &quot;<a class="code" href="fragment_8h.html">fragment.h</a>&quot;</span>
<a name="l00029"></a>00029 <span class="preprocessor">#include &lt;list&gt;</span>
<a name="l00030"></a>00030 <span class="preprocessor">#include &lt;<a class="code" href="gcu_2molecule_8h.html">gcu/molecule.h</a>&gt;</span>
<a name="l00031"></a>00031 <span class="preprocessor">#include &lt;openbabel/mol.h&gt;</span>
<a name="l00032"></a>00032 
<a name="l00034"></a>00034 <span class="keyword">namespace </span>gcp {
<a name="l00035"></a>00035 
<a name="l00036"></a>00036 <span class="keyword">class </span>Bond;
<a name="l00037"></a>00037 
<a name="l00041"></a><a class="code" href="classgcp_1_1Molecule.html">00041</a> <span class="keyword">class </span><a class="code" href="classgcp_1_1Molecule.html" title="GChemPaint molecule class.">Molecule</a>: <span class="keyword">public</span> gcu::<a class="code" href="classgcp_1_1Molecule.html" title="GChemPaint molecule class.">Molecule</a>
<a name="l00042"></a>00042 {
<a name="l00043"></a>00043 <span class="keyword">public</span>:
<a name="l00047"></a>00047         <a class="code" href="classgcp_1_1Molecule.html#a87a50241159cfdf8b55cd5f76280cd2a">Molecule</a> (<a class="code" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">gcu::TypeId</a> Type = gcu::MoleculeType);
<a name="l00054"></a>00054         <a class="code" href="classgcp_1_1Molecule.html#a87a50241159cfdf8b55cd5f76280cd2a">Molecule</a> (<a class="code" href="classgcp_1_1Atom.html">Atom</a>* pAtom);
<a name="l00058"></a>00058         <span class="keyword">virtual</span> <a class="code" href="classgcp_1_1Molecule.html#a617ada73c8a4f5180b895cab04debcc2">~Molecule</a> ();
<a name="l00064"></a>00064         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#ae382280cbed9d5428b41e64c3cc7cf5e">AddChild</a> (<a class="code" href="classgcu_1_1Object.html">gcu::Object</a>* <span class="keywordtype">object</span>);
<a name="l00070"></a>00070         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#ab6d82e3990b47e5a066e0eb2f629ad92">AddAtom</a> (<a class="code" href="classgcu_1_1Atom.html">gcu::Atom</a>* pAtom);
<a name="l00076"></a>00076         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a7b8e0ddf66a62a0d149062632c08e3ce">AddFragment</a> (<a class="code" href="classgcp_1_1Fragment.html" title="Atoms groups.">Fragment</a>* pFragment);
<a name="l00082"></a>00082         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a47ebe171afdd3a3f8aed5bade9c3a5bc">AddBond</a> (<a class="code" href="classgcu_1_1Bond.html">gcu::Bond</a>* pBond);
<a name="l00089"></a>00089         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a6bd28d9624ad747709e748b447dc1b23">Add</a> (GtkWidget* w) <span class="keyword">const</span>;
<a name="l00095"></a>00095         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a2ef5c5ded47d687ab48351ac4412b599">Remove</a> (<a class="code" href="classgcu_1_1Object.html">gcu::Object</a>* pObject);
<a name="l00106"></a>00106         <span class="keywordtype">bool</span> <a class="code" href="classgcp_1_1Molecule.html#ac76c57ec603a27b43209327c4d8cce5e">Merge</a> (<a class="code" href="classgcp_1_1Molecule.html" title="GChemPaint molecule class.">Molecule</a>* pMolecule, <span class="keywordtype">bool</span> RemoveDuplicates = <span class="keyword">false</span>);
<a name="l00113"></a>00113         <span class="keywordtype">bool</span> <a class="code" href="classgcp_1_1Molecule.html#af3abe215c266c862151b4301ea30495f">Load</a> (xmlNodePtr node);
<a name="l00120"></a>00120         xmlNodePtr <a class="code" href="classgcp_1_1Molecule.html#ad4bb194b40610a85a7d5a894647dbae0">Save</a> (xmlDocPtr xml) <span class="keyword">const</span>;
<a name="l00124"></a>00124         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#af6b63bd1a55c365f22af2c69c69a41ca">Clear</a> ();
<a name="l00133"></a>00133         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a7f6eb1535a5b6ae36d8d5a7bfe1ecce5">Transform2D</a> (<a class="code" href="classgcu_1_1Matrix2D.html">gcu::Matrix2D</a>&amp; m, <span class="keywordtype">double</span> x, <span class="keywordtype">double</span> y);
<a name="l00142"></a>00142         <a class="code" href="classgcu_1_1Object.html#a6f15e766fdfb066008bd4b0779574549">Object</a>* <a class="code" href="classgcp_1_1Molecule.html#a9ec4a58d5060d29791336f54d8954d72">GetAtomAt</a> (<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> y, <span class="keywordtype">double</span> z = 0.);
<a name="l00147"></a>00147         <span class="keywordtype">double</span> <a class="code" href="classgcp_1_1Molecule.html#a141ffeeff75f342eb90fb5aec87e4e81">GetYAlign</a> ();
<a name="l00157"></a>00157         <span class="keywordtype">bool</span> <a class="code" href="classgcp_1_1Molecule.html#a246671cab3357c6ba9c0daf76f50440c">BuildContextualMenu</a> (GtkUIManager *UIManager, <a class="code" href="classgcu_1_1Object.html">gcu::Object</a> *<span class="keywordtype">object</span>, <span class="keywordtype">double</span> x, <span class="keywordtype">double</span> y);
<a name="l00166"></a>00166         <span class="keywordtype">bool</span> <a class="code" href="classgcp_1_1Molecule.html#a523bef16f9be6ff01aeb3adf5afcd0d6">OnSignal</a> (<a class="code" href="namespacegcu.html#af13348b065987fa4ca74ca0fb1ffa48e">gcu::SignalId</a> Signal, <a class="code" href="classgcu_1_1Object.html">gcu::Object</a> *Child);
<a name="l00171"></a>00171         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a3b45a9b4ee5dec6a2bda7af5df0309bc">ExportToGhemical</a> ();
<a name="l00179"></a>00179         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#ab0222b87475e9c9bf52a06bc1119c88e">SelectAlignmentItem</a> (<a class="code" href="classgcu_1_1Object.html">gcu::Object</a> *child);
<a name="l00183"></a><a class="code" href="classgcp_1_1Molecule.html#a3c2bd0629d723dfd530eacc571474a94">00183</a>         std::string <a class="code" href="classgcp_1_1Molecule.html#a3c2bd0629d723dfd530eacc571474a94">GetAlignmentId</a> () {<span class="keywordflow">return</span> (m_Alignment)? m_Alignment-&gt;<a class="code" href="classgcu_1_1Object.html#aa5442c94fdeb2a71e0e3e1f2250f28dc">GetId</a> (): <span class="stringliteral">&quot;&quot;</span>;}
<a name="l00191"></a>00191         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#ad4cfc1b3c10f1454296630b0b3b5d9bd">BuildOBMol</a> (OpenBabel::OBMol &amp;Mol);
<a name="l00198"></a>00198         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a1718e45650220f838c37b92c29c782cb">BuildOBMol2D</a> (OpenBabel::OBMol &amp;Mol);
<a name="l00203"></a>00203         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a1aa847bae656a7229d0f0ccad5644467">ShowInChI</a> ();
<a name="l00207"></a>00207         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a29c0359b1705958310b289c77e34d65a">BuildInChI</a> ();
<a name="l00212"></a>00212         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a2cd7d99ad18b2693bc3f4a5697494972">BuildSMILES</a> ();
<a name="l00220"></a>00220         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a875bedb82db0d14800ec16b811ca87da">ShowWebBase</a> (<span class="keywordtype">char</span> <span class="keyword">const</span> *uri_start, <span class="keywordtype">char</span> <span class="keyword">const</span> *uri_end);
<a name="l00225"></a>00225         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#ab30b793e3003aec4969b0b349ec82ac5">OpenCalc</a> ();
<a name="l00232"></a>00232         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a80e413512fc8fa7e77e805ea01bdaef3">CheckCrossings</a> (<a class="code" href="classgcp_1_1Bond.html">Bond</a> *pBond);
<a name="l00237"></a>00237         <span class="keywordtype">char</span> <span class="keyword">const</span> *<a class="code" href="classgcp_1_1Molecule.html#a43d905bf39d2e97f943d7594a7795515">GetInChI</a> ();
<a name="l00242"></a>00242         std::string <a class="code" href="classgcp_1_1Molecule.html#a99411028335058377bda5ac80483c50e">GetRawFormula</a> () <span class="keyword">const</span>;
<a name="l00246"></a>00246         <span class="keywordtype">void</span> <a class="code" href="classgcp_1_1Molecule.html#a37c6ce6b2910d96e6afa5bcdf42c1de3">OnLoaded</a> ();
<a name="l00251"></a>00251         <span class="keywordtype">unsigned</span> <a class="code" href="classgcp_1_1Molecule.html#ae6df1b3fd7f5068a82f1c9f33d0c2542">GetAtomsNumber</a> () <span class="keyword">const</span>;
<a name="l00252"></a>00252 
<a name="l00253"></a>00253 <span class="keyword">private</span>:
<a name="l00254"></a>00254         std::list&lt;Fragment*&gt; m_Fragments;
<a name="l00255"></a>00255         <a class="code" href="classgcu_1_1Object.html">gcu::Object</a> *m_Alignment;
<a name="l00256"></a>00256         std::string m_InChI;
<a name="l00257"></a>00257         <span class="keywordtype">bool</span> m_Changed;
<a name="l00258"></a>00258         <span class="keywordtype">bool</span> m_IsResidue;
<a name="l00259"></a>00259 };
<a name="l00260"></a>00260 
<a name="l00261"></a>00261 }       <span class="comment">//      namespace gcp</span>
<a name="l00262"></a>00262 
<a name="l00263"></a>00263 <span class="preprocessor">#endif // GCHEMPAINT_MOLECULE_H</span>
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