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<title>The Gnome Chemistry Utils: gcp::Molecule Class Reference</title>
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<h1>gcp::Molecule Class Reference</h1><!-- doxytag: class="gcp::Molecule" --><!-- doxytag: inherits="gcu::Molecule" -->
<p>GChemPaint molecule class.
<a href="#_details">More...</a></p>
<p><code>#include <<a class="el" href="gcp_2molecule_8h_source.html">gcp/molecule.h</a>></code></p>
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Inheritance diagram for gcp::Molecule:</div>
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<img src="classgcp_1_1Molecule.gif" usemap="#gcp::Molecule_map" alt=""/>
<map id="gcp::Molecule_map" name="gcp::Molecule_map">
<area href="classgcu_1_1Molecule.html" alt="gcu::Molecule" shape="rect" coords="0,56,91,80"/>
<area href="classgcu_1_1Object.html" alt="gcu::Object" shape="rect" coords="0,0,91,24"/>
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<p><a href="classgcp_1_1Molecule-members.html">List of all members.</a></p>
<table border="0" cellpadding="0" cellspacing="0">
<tr><td colspan="2"><h2>Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a87a50241159cfdf8b55cd5f76280cd2a">Molecule</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">gcu::TypeId</a> Type=gcu::MoleculeType)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#af00b30e1024eae871bf9e3a27f193dc8">Molecule</a> (<a class="el" href="classgcp_1_1Atom.html">Atom</a> *pAtom)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a617ada73c8a4f5180b895cab04debcc2">~Molecule</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#ae382280cbed9d5428b41e64c3cc7cf5e">AddChild</a> (<a class="el" href="classgcu_1_1Object.html">gcu::Object</a> *object)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#ab6d82e3990b47e5a066e0eb2f629ad92">AddAtom</a> (<a class="el" href="classgcu_1_1Atom.html">gcu::Atom</a> *pAtom)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a7b8e0ddf66a62a0d149062632c08e3ce">AddFragment</a> (<a class="el" href="classgcp_1_1Fragment.html">Fragment</a> *pFragment)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a47ebe171afdd3a3f8aed5bade9c3a5bc">AddBond</a> (<a class="el" href="classgcu_1_1Bond.html">gcu::Bond</a> *pBond)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a6bd28d9624ad747709e748b447dc1b23">Add</a> (GtkWidget *w) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a2ef5c5ded47d687ab48351ac4412b599">Remove</a> (<a class="el" href="classgcu_1_1Object.html">gcu::Object</a> *pObject)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#ac76c57ec603a27b43209327c4d8cce5e">Merge</a> (<a class="el" href="classgcp_1_1Molecule.html">Molecule</a> *pMolecule, bool RemoveDuplicates=false)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#af3abe215c266c862151b4301ea30495f">Load</a> (xmlNodePtr node)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#ad4bb194b40610a85a7d5a894647dbae0">Save</a> (xmlDocPtr xml) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#af6b63bd1a55c365f22af2c69c69a41ca">Clear</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a7f6eb1535a5b6ae36d8d5a7bfe1ecce5">Transform2D</a> (<a class="el" href="classgcu_1_1Matrix2D.html">gcu::Matrix2D</a> &m, double x, double y)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">Object * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a9ec4a58d5060d29791336f54d8954d72">GetAtomAt</a> (double x, double y, double z=0.)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a141ffeeff75f342eb90fb5aec87e4e81">GetYAlign</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a246671cab3357c6ba9c0daf76f50440c">BuildContextualMenu</a> (GtkUIManager *UIManager, <a class="el" href="classgcu_1_1Object.html">gcu::Object</a> *object, double x, double y)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a523bef16f9be6ff01aeb3adf5afcd0d6">OnSignal</a> (<a class="el" href="namespacegcu.html#af13348b065987fa4ca74ca0fb1ffa48e">gcu::SignalId</a> Signal, <a class="el" href="classgcu_1_1Object.html">gcu::Object</a> *Child)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a3b45a9b4ee5dec6a2bda7af5df0309bc">ExportToGhemical</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#ab0222b87475e9c9bf52a06bc1119c88e">SelectAlignmentItem</a> (<a class="el" href="classgcu_1_1Object.html">gcu::Object</a> *child)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a3c2bd0629d723dfd530eacc571474a94">GetAlignmentId</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#ad4cfc1b3c10f1454296630b0b3b5d9bd">BuildOBMol</a> (OpenBabel::OBMol &Mol)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a1718e45650220f838c37b92c29c782cb">BuildOBMol2D</a> (OpenBabel::OBMol &Mol)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a1aa847bae656a7229d0f0ccad5644467">ShowInChI</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a29c0359b1705958310b289c77e34d65a">BuildInChI</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a2cd7d99ad18b2693bc3f4a5697494972">BuildSMILES</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a875bedb82db0d14800ec16b811ca87da">ShowWebBase</a> (char const *uri_start, char const *uri_end)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#ab30b793e3003aec4969b0b349ec82ac5">OpenCalc</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a80e413512fc8fa7e77e805ea01bdaef3">CheckCrossings</a> (<a class="el" href="classgcp_1_1Bond.html">Bond</a> *pBond)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">char const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a43d905bf39d2e97f943d7594a7795515">GetInChI</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a99411028335058377bda5ac80483c50e">GetRawFormula</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#a37c6ce6b2910d96e6afa5bcdf42c1de3">OnLoaded</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcp_1_1Molecule.html#ae6df1b3fd7f5068a82f1c9f33d0c2542">GetAtomsNumber</a> () const </td></tr>
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<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>GChemPaint molecule class. </p>
<p>Definition at line <a class="el" href="gcp_2molecule_8h_source.html#l00041">41</a> of file <a class="el" href="gcp_2molecule_8h_source.html">gcp/molecule.h</a>.</p>
<hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="a87a50241159cfdf8b55cd5f76280cd2a"></a><!-- doxytag: member="gcp::Molecule::Molecule" ref="a87a50241159cfdf8b55cd5f76280cd2a" args="(gcu::TypeId Type=gcu::MoleculeType)" -->
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<td class="memname">gcp::Molecule::Molecule </td>
<td>(</td>
<td class="paramtype"><a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">gcu::TypeId</a> </td>
<td class="paramname"> <em>Type</em> = <code>gcu::MoleculeType</code></td>
<td> ) </td>
<td></td>
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<p>The default constructor. Builds a new empty molecule. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Molecule.html#ab8ac57bf99fc726a3605809ed436cadf">gcu::Molecule</a>.</p>
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</div>
<a class="anchor" id="af00b30e1024eae871bf9e3a27f193dc8"></a><!-- doxytag: member="gcp::Molecule::Molecule" ref="af00b30e1024eae871bf9e3a27f193dc8" args="(Atom *pAtom)" -->
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<td class="memname">gcp::Molecule::Molecule </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcp_1_1Atom.html">Atom</a> * </td>
<td class="paramname"> <em>pAtom</em></td>
<td> ) </td>
<td></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pAtom</em> </td><td>an atom.</td></tr>
</table>
</dd>
</dl>
<p>Constructs a new molecule containing <em>pAtom</em> and all atoms which might be bonded to it, and the corresponding bonds. </p>
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<a class="anchor" id="a617ada73c8a4f5180b895cab04debcc2"></a><!-- doxytag: member="gcp::Molecule::~Molecule" ref="a617ada73c8a4f5180b895cab04debcc2" args="()" -->
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<td class="memname">virtual gcp::Molecule::~Molecule </td>
<td>(</td>
<td class="paramname"></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<div class="memdoc">
<p>The destructor. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Molecule.html#a27d96d88547230d32ea7f8bfc6601742">gcu::Molecule</a>.</p>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a6bd28d9624ad747709e748b447dc1b23"></a><!-- doxytag: member="gcp::Molecule::Add" ref="a6bd28d9624ad747709e748b447dc1b23" args="(GtkWidget *w) const " -->
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<td class="memname">void gcp::Molecule::Add </td>
<td>(</td>
<td class="paramtype">GtkWidget * </td>
<td class="paramname"> <em>w</em></td>
<td> ) </td>
<td> const<code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>w</em> </td><td>the GtkWidget inside which the molecule will be displayed.</td></tr>
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</dd>
</dl>
<p>Used to add a representation of the molecule in the widget. It just calls the method for all its children. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#afcd1e6f8bc15be563bd33429757d9d21">gcu::Object</a>.</p>
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<a class="anchor" id="ab6d82e3990b47e5a066e0eb2f629ad92"></a><!-- doxytag: member="gcp::Molecule::AddAtom" ref="ab6d82e3990b47e5a066e0eb2f629ad92" args="(gcu::Atom *pAtom)" -->
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<td class="memname">void gcp::Molecule::AddAtom </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">gcu::Atom</a> * </td>
<td class="paramname"> <em>pAtom</em></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pAtom</em> </td><td>an atom.</td></tr>
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</dd>
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<p>Adds an atom to the molecule. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Molecule.html#a2f277cc2b9f40b2ece88df56c1fe5c95">gcu::Molecule</a>.</p>
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<a class="anchor" id="a47ebe171afdd3a3f8aed5bade9c3a5bc"></a><!-- doxytag: member="gcp::Molecule::AddBond" ref="a47ebe171afdd3a3f8aed5bade9c3a5bc" args="(gcu::Bond *pBond)" -->
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<td class="memname">void gcp::Molecule::AddBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">gcu::Bond</a> * </td>
<td class="paramname"> <em>pBond</em></td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pBond</em> </td><td>a bond.</td></tr>
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</dd>
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<p>Adds a bond to the molecule. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Molecule.html#a30a68fe89c3c1f81497ec1498acc1012">gcu::Molecule</a>.</p>
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<a class="anchor" id="ae382280cbed9d5428b41e64c3cc7cf5e"></a><!-- doxytag: member="gcp::Molecule::AddChild" ref="ae382280cbed9d5428b41e64c3cc7cf5e" args="(gcu::Object *object)" -->
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<td class="memname">void gcp::Molecule::AddChild </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Object.html">gcu::Object</a> * </td>
<td class="paramname"> <em>object</em></td>
<td> ) </td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>object</em> </td><td>the object to add to the molecule.</td></tr>
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</dd>
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<p>Adds an object (atom, bond, or fragment) to the molecule. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Molecule.html#ab9ec078566194173ab67d60074b6b245">gcu::Molecule</a>.</p>
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<a class="anchor" id="a7b8e0ddf66a62a0d149062632c08e3ce"></a><!-- doxytag: member="gcp::Molecule::AddFragment" ref="a7b8e0ddf66a62a0d149062632c08e3ce" args="(Fragment *pFragment)" -->
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<td class="memname">void gcp::Molecule::AddFragment </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcp_1_1Fragment.html">Fragment</a> * </td>
<td class="paramname"> <em>pFragment</em></td>
<td> ) </td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pFragment</em> </td><td>an atoms group.</td></tr>
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</dd>
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<p>Adds a fragment to the molecule. </p>
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<a class="anchor" id="a246671cab3357c6ba9c0daf76f50440c"></a><!-- doxytag: member="gcp::Molecule::BuildContextualMenu" ref="a246671cab3357c6ba9c0daf76f50440c" args="(GtkUIManager *UIManager, gcu::Object *object, double x, double y)" -->
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<td class="memname">bool gcp::Molecule::BuildContextualMenu </td>
<td>(</td>
<td class="paramtype">GtkUIManager * </td>
<td class="paramname"> <em>UIManager</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classgcu_1_1Object.html">gcu::Object</a> * </td>
<td class="paramname"> <em>object</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>x</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>y</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>UIManager</em> </td><td>the GtkUIManager to populate. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>object</em> </td><td>the Object on which occured the mouse click. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>x coordinate of the mouse click. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>y coordinate of the mouse click.</td></tr>
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</dd>
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<p>This method is called to build the contextual menu for the molecule. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>true if something is added to the UIManager, false otherwise. </dd></dl>
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<a class="anchor" id="a29c0359b1705958310b289c77e34d65a"></a><!-- doxytag: member="gcp::Molecule::BuildInChI" ref="a29c0359b1705958310b289c77e34d65a" args="()" -->
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<p>Builds the InChI for the molecule. </p>
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<td class="paramname"> <em>Mol</em></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>Mol</em> </td><td>the OpenBabel molecule used for export.</td></tr>
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<p>Builds an OpenBabel molecule from this instance. The new molecule is built trying to guess appropriate z coordinates so that stereochemistry is preserved. </p>
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<a class="anchor" id="a1718e45650220f838c37b92c29c782cb"></a><!-- doxytag: member="gcp::Molecule::BuildOBMol2D" ref="a1718e45650220f838c37b92c29c782cb" args="(OpenBabel::OBMol &Mol)" -->
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<td class="memname">void gcp::Molecule::BuildOBMol2D </td>
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<td class="paramtype">OpenBabel::OBMol & </td>
<td class="paramname"> <em>Mol</em></td>
<td> ) </td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>Mol</em> </td><td>the OpenBabel molecule used for export.</td></tr>
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<p>Builds a 2D OpenBabel molecule from this instance. </p>
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<a class="anchor" id="a2cd7d99ad18b2693bc3f4a5697494972"></a><!-- doxytag: member="gcp::Molecule::BuildSMILES" ref="a2cd7d99ad18b2693bc3f4a5697494972" args="()" -->
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<p>Builds the SMILES representation for the molecule and opens a new <a class="el" href="classgcp_1_1StringDlg.html">StringDlg</a> instance displaying it. </p>
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<a class="anchor" id="a80e413512fc8fa7e77e805ea01bdaef3"></a><!-- doxytag: member="gcp::Molecule::CheckCrossings" ref="a80e413512fc8fa7e77e805ea01bdaef3" args="(Bond *pBond)" -->
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<td class="paramname"> <em>pBond</em></td>
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<dl><dt><b>Parameters:</b></dt><dd>
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<tr><td valign="top"></td><td valign="top"><em>pBond</em> </td><td>a bond in the molecule.</td></tr>
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<p>Checks if any other bond in the molecule crosses <em>pBond</em>, and notify both bonds that they are crossing. </p>
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<p>Removes all children from the molecule, resulting in a empty molecule. </p>
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<p>Opens a Ghemical window with a copy of the molecule trying to preserve the stereochemistry as far as possible. </p>
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<td><code> [inline]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the id string of the child used for alignment if any, or an empty string. </dd></dl>
<p>Definition at line <a class="el" href="gcp_2molecule_8h_source.html#l00183">183</a> of file <a class="el" href="gcp_2molecule_8h_source.html">gcp/molecule.h</a>.</p>
<p>References <a class="el" href="object_8h_source.html#l00164">gcu::Object::GetId()</a>.</p>
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<td class="paramtype">double </td>
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<dl><dt><b>Parameters:</b></dt><dd>
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<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>the x coordinate </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the y coordinate </td></tr>
<tr><td valign="top"></td><td valign="top"><em>z</em> </td><td>the z coordinate (not used)</td></tr>
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<dl class="return"><dt><b>Returns:</b></dt><dd>a pointer to n atom at or near position defined by the coordinates passed as parameters or NULL if none is found in the molecule. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#aa47c38061c6a2e51947d89c86fbae630">gcu::Object</a>.</p>
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<a class="anchor" id="ae6df1b3fd7f5068a82f1c9f33d0c2542"></a><!-- doxytag: member="gcp::Molecule::GetAtomsNumber" ref="ae6df1b3fd7f5068a82f1c9f33d0c2542" args="() const " -->
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<dl class="return"><dt><b>Returns:</b></dt><dd>the number of atoms in the molecule. Atoms groups are counted for one only, whatever their real atomic composition. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Molecule.html#a6ad0da2f365b11e8693fae4d24b45030">gcu::Molecule</a>.</p>
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<a class="anchor" id="a43d905bf39d2e97f943d7594a7795515"></a><!-- doxytag: member="gcp::Molecule::GetInChI" ref="a43d905bf39d2e97f943d7594a7795515" args="()" -->
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<dl class="return"><dt><b>Returns:</b></dt><dd>the InChI. The returned string should not be freed (it's a const char*). Molecules with fragments are not currently supported. </dd></dl>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the raw formula as a string. Molecules with fragments are not currently supported. </dd></dl>
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<a class="anchor" id="a141ffeeff75f342eb90fb5aec87e4e81"></a><!-- doxytag: member="gcp::Molecule::GetYAlign" ref="a141ffeeff75f342eb90fb5aec87e4e81" args="()" -->
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<p>Used to retrieve the y coordinate for alignment. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>y coordinate used for the molecule alignment. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#aedeec6e6b66e1a35e6d2f3ef75c94a09">gcu::Object</a>.</p>
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<a class="anchor" id="af3abe215c266c862151b4301ea30495f"></a><!-- doxytag: member="gcp::Molecule::Load" ref="af3abe215c266c862151b4301ea30495f" args="(xmlNodePtr node)" -->
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<td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
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<tr><td valign="top"></td><td valign="top"><em>node</em> </td><td>a pointer to the xmlNode containing the serialized molecule.</td></tr>
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<p>Used to load a molecule in memory. The Mlecule instance must already exist. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>true on succes, false otherwise. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#aa3ee33c25154d8e7bbe1e39de970c489">gcu::Object</a>.</p>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pMolecule</em> </td><td>a molecule. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>RemoveDuplicates</em> </td><td>whether duplicate atoms should be unififed or not.</td></tr>
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<p>Adds all children from <em>pMolecule</em> in this instance, and removes one of the atoms for each pair of duplicates (atoms with same atomic number and position) if <em>RemoveDuplicates</em> is true. This might fail when it would end with hypervalent atoms. On success <em>pMolecule</em> is deleted. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>true on success, false otherwise. </dd></dl>
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<a class="anchor" id="a37c6ce6b2910d96e6afa5bcdf42c1de3"></a><!-- doxytag: member="gcp::Molecule::OnLoaded" ref="a37c6ce6b2910d96e6afa5bcdf42c1de3" args="()" -->
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<p>Updates all cycles after loading. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#af972c30c9990923c34c54754654c3e72">gcu::Object</a>.</p>
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<td class="paramname"> <em>Signal</em>, </td>
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<dl><dt><b>Parameters:</b></dt><dd>
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<tr><td valign="top"></td><td valign="top"><em>Signal</em> </td><td>the appropriate SignalId </td></tr>
<tr><td valign="top"></td><td valign="top"><em>Child</em> </td><td>the child which emitted the signal or NULL</td></tr>
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<p>Signals the molecule that at least one of its children changed.</p>
<dl class="return"><dt><b>Returns:</b></dt><dd>true to propagate the signal to the parent. </dd></dl>
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<a class="anchor" id="ab30b793e3003aec4969b0b349ec82ac5"></a><!-- doxytag: member="gcp::Molecule::OpenCalc" ref="ab30b793e3003aec4969b0b349ec82ac5" args="()" -->
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<p>Opens GChemCalc with the formula for the molecule. Molecules with fragments are not currently supported. </p>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>pObject</em> </td><td>an atom, a bond, or a fragment in the molecule.</td></tr>
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<p>Removes an atom, a bond, or a fragment from a molecule. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Molecule.html#aff43b05c6f575fefda0c13a181181379">gcu::Molecule</a>.</p>
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<td class="paramname"> <em>xml</em></td>
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<td> const<code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>xml</em> </td><td>the xmlDoc used to save the document.</td></tr>
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<p>Used to save the molecule to the xmlDoc. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>the xmlNode containing the serialized molecule. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#aad462441e79fbd93e158f8294a198d11">gcu::Object</a>.</p>
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<dl><dt><b>Parameters:</b></dt><dd>
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<tr><td valign="top"></td><td valign="top"><em>child</em> </td><td>the child used for alignment.</td></tr>
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<p>Selects the child used for alignment, which might be an atom or group of atoms, or a bond. For bonds, the center of the bonds is used, a while for the others a call to their <a class="el" href="classgcu_1_1Object.html#aedeec6e6b66e1a35e6d2f3ef75c94a09">gcu::Object::GetYAlign()</a> method will be used. </p>
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<p>Builds the InChI for the molecule if necessary and opens a new <a class="el" href="classgcp_1_1StringDlg.html">StringDlg</a> instance displaying it. </p>
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<a class="anchor" id="a875bedb82db0d14800ec16b811ca87da"></a><!-- doxytag: member="gcp::Molecule::ShowWebBase" ref="a875bedb82db0d14800ec16b811ca87da" args="(char const *uri_start, char const *uri_end)" -->
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<td class="memname">void gcp::Molecule::ShowWebBase </td>
<td>(</td>
<td class="paramtype">char const * </td>
<td class="paramname"> <em>uri_start</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">char const * </td>
<td class="paramname"> <em>uri_end</em></td><td> </td>
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<td>)</td>
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<dl><dt><b>Parameters:</b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"></td><td valign="top"><em>uri_start</em> </td><td>the first part of the URI to open. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>uri_end</em> </td><td>the last part of the URI to open.</td></tr>
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<p>Opens a web browser with an URI constructed from both arguments and the InChI for the molecule ntercalated between <em>uri_start</em> and <em>uri_end</em>. </p>
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<a class="anchor" id="a7f6eb1535a5b6ae36d8d5a7bfe1ecce5"></a><!-- doxytag: member="gcp::Molecule::Transform2D" ref="a7f6eb1535a5b6ae36d8d5a7bfe1ecce5" args="(gcu::Matrix2D &m, double x, double y)" -->
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<td class="memname">void gcp::Molecule::Transform2D </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Matrix2D.html">gcu::Matrix2D</a> & </td>
<td class="paramname"> <em>m</em>, </td>
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<td class="paramtype">double </td>
<td class="paramname"> <em>x</em>, </td>
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<td class="paramtype">double </td>
<td class="paramname"> <em>y</em></td><td> </td>
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<td>)</td>
<td></td><td></td><td><code> [virtual]</code></td>
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<dl><dt><b>Parameters:</b></dt><dd>
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<tr><td valign="top"></td><td valign="top"><em>m</em> </td><td>the Matrix2D of the transformation. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>x</em> </td><td>the x component of the center of the transformation. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>y</em> </td><td>the y component of the center of the transformation.</td></tr>
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<p>Used to move and/or transform the molecule taking care of hydrogen atoms positions around heteroatoms. </p>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#a69ad6edf7d50950b036f09d9ff86f849">gcu::Object</a>.</p>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="gcp_2molecule_8h_source.html">gcp/molecule.h</a></li>
</ul>
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<hr size="1"/><address style="text-align: right;"><small>Generated on Sun Sep 6 18:33:54 2009 for The Gnome Chemistry Utils by
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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