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<title>The Gnome Chemistry Utils: gcu::Molecule Class Reference</title>
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<h1>gcu::Molecule Class Reference</h1><!-- doxytag: class="gcu::Molecule" --><!-- doxytag: inherits="gcu::Object" -->
<p><code>#include <<a class="el" href="gcu_2molecule_8h_source.html">gcu/molecule.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for gcu::Molecule:</div>
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<img src="classgcu_1_1Molecule.gif" usemap="#gcu::Molecule_map" alt=""/>
<map id="gcu::Molecule_map" name="gcu::Molecule_map">
<area href="classgcu_1_1Object.html" alt="gcu::Object" shape="rect" coords="0,0,91,24"/>
<area href="classgcp_1_1Molecule.html" alt="gcp::Molecule" shape="rect" coords="0,112,91,136"/>
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<p><a href="classgcu_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="classgcu_1_1Molecule.html#ab8ac57bf99fc726a3605809ed436cadf">Molecule</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Type=MoleculeType)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#ae98e16c22599f5a5afad714e7479e0ca">Molecule</a> (<a class="el" href="classgcu_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="classgcu_1_1Molecule.html#a27d96d88547230d32ea7f8bfc6601742">~Molecule</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#ab9ec078566194173ab67d60074b6b245">AddChild</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *object)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#a2f277cc2b9f40b2ece88df56c1fe5c95">AddAtom</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#a30a68fe89c3c1f81497ec1498acc1012">AddBond</a> (<a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#aff43b05c6f575fefda0c13a181181379">Remove</a> (<a class="el" href="classgcu_1_1Object.html">gcu::Object</a> *pObject)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#a283c641732a0d9768254d934445efea6">UpdateCycles</a> (<a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#abb8dc72dc84a7c22a553425f0c447195">UpdateCycles</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#a8e2afa9634a94587b3fc6bb01da41784">operator==</a> (<a class="el" href="classgcu_1_1Molecule.html">Molecule</a> const &molecule) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#a6ad0da2f365b11e8693fae4d24b45030">GetAtomsNumber</a> () const </td></tr>
<tr><td colspan="2"><h2>Static Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classgcu_1_1Molecule.html">Molecule</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#a9a41f121b26ddb33a88cdba1302d0644">MoleculeFromFormula</a> (<a class="el" href="classgcu_1_1Document.html">Document</a> *Doc, <a class="el" href="classgcu_1_1Formula.html">Formula</a> const &formula, bool add_pseudo=true)</td></tr>
<tr><td colspan="2"><h2>Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::list< <a class="el" href="classgcu_1_1Cycle.html">Cycle</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#a936ef484763b9a9ace3ced4a847eb251">m_Cycles</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::list< <a class="el" href="classgcu_1_1Chain.html">Chain</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#aa9d30f8cfd6f87fdd84fd07aef21f4b0">m_Chains</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::list< <a class="el" href="classgcu_1_1Atom.html">Atom</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#adcad89ca2f5c358068b466a99ce9a7cd">m_Atoms</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::list< <a class="el" href="classgcu_1_1Bond.html">Bond</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Molecule.html#ab939115e2e636a22de80176dbed6811c">m_Bonds</a></td></tr>
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<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>Represents molecules. </p>
<p>Definition at line <a class="el" href="gcu_2molecule_8h_source.html#l00042">42</a> of file <a class="el" href="gcu_2molecule_8h_source.html">gcu/molecule.h</a>.</p>
<hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="ab8ac57bf99fc726a3605809ed436cadf"></a><!-- doxytag: member="gcu::Molecule::Molecule" ref="ab8ac57bf99fc726a3605809ed436cadf" args="(TypeId Type=MoleculeType)" -->
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<td class="memname">gcu::Molecule::Molecule </td>
<td>(</td>
<td class="paramtype"><a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td>
<td class="paramname"> <em>Type</em> = <code>MoleculeType</code></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>Type</em> </td><td>the type id of a derived class</td></tr>
</table>
</dd>
</dl>
<p>The constructor. The type id may be changed in derived classes, otherwise the argument is not needed, since the default value is enough. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Molecule.html#a87a50241159cfdf8b55cd5f76280cd2a">gcp::Molecule</a>.</p>
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<a class="anchor" id="ae98e16c22599f5a5afad714e7479e0ca"></a><!-- doxytag: member="gcu::Molecule::Molecule" ref="ae98e16c22599f5a5afad714e7479e0ca" args="(Atom *pAtom)" -->
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<td class="memname">gcu::Molecule::Molecule </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"> <em>pAtom</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>pAtom</em> </td><td>Builds a molecule from an atom. If the atom has bonds, the connectivity will be explored and all atoms and bonds found will be added to the molecule. </td></tr>
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</dd>
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<a class="anchor" id="a27d96d88547230d32ea7f8bfc6601742"></a><!-- doxytag: member="gcu::Molecule::~Molecule" ref="a27d96d88547230d32ea7f8bfc6601742" args="()" -->
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<td class="memname">virtual gcu::Molecule::~Molecule </td>
<td>(</td>
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<td> ) </td>
<td><code> [virtual]</code></td>
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<p>The destructor. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Molecule.html#a617ada73c8a4f5180b895cab04debcc2">gcp::Molecule</a>.</p>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a2f277cc2b9f40b2ece88df56c1fe5c95"></a><!-- doxytag: member="gcu::Molecule::AddAtom" ref="a2f277cc2b9f40b2ece88df56c1fe5c95" args="(Atom *pAtom)" -->
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<td class="memname">virtual void gcu::Molecule::AddAtom </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">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 in <a class="el" href="classgcp_1_1Molecule.html#ab6d82e3990b47e5a066e0eb2f629ad92">gcp::Molecule</a>.</p>
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<a class="anchor" id="a30a68fe89c3c1f81497ec1498acc1012"></a><!-- doxytag: member="gcu::Molecule::AddBond" ref="a30a68fe89c3c1f81497ec1498acc1012" args="(Bond *pBond)" -->
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<td class="memname">virtual void gcu::Molecule::AddBond </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">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 in <a class="el" href="classgcp_1_1Molecule.html#a47ebe171afdd3a3f8aed5bade9c3a5bc">gcp::Molecule</a>.</p>
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<a class="anchor" id="ab9ec078566194173ab67d60074b6b245"></a><!-- doxytag: member="gcu::Molecule::AddChild" ref="ab9ec078566194173ab67d60074b6b245" args="(Object *object)" -->
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<td class="memname">void gcu::Molecule::AddChild </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Object.html">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>an object, generally an atom or a bond.</td></tr>
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<p>Adds an object (which might be an atom or a bond) to the molecule. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Molecule.html#ae382280cbed9d5428b41e64c3cc7cf5e">gcp::Molecule</a>.</p>
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<a class="anchor" id="a6ad0da2f365b11e8693fae4d24b45030"></a><!-- doxytag: member="gcu::Molecule::GetAtomsNumber" ref="a6ad0da2f365b11e8693fae4d24b45030" args="() const " -->
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<td class="memname">virtual unsigned gcu::Molecule::GetAtomsNumber </td>
<td>(</td>
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<td> const<code> [inline, virtual]</code></td>
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<dl class="return"><dt><b>Returns:</b></dt><dd>the number of atoms in the molecule. </dd></dl>
<p>Reimplemented in <a class="el" href="classgcp_1_1Molecule.html#ae6df1b3fd7f5068a82f1c9f33d0c2542">gcp::Molecule</a>.</p>
<p>Definition at line <a class="el" href="gcu_2molecule_8h_source.html#l00107">107</a> of file <a class="el" href="gcu_2molecule_8h_source.html">gcu/molecule.h</a>.</p>
<p>References <a class="el" href="gcu_2molecule_8h_source.html#l00132">m_Atoms</a>.</p>
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<a class="anchor" id="a9a41f121b26ddb33a88cdba1302d0644"></a><!-- doxytag: member="gcu::Molecule::MoleculeFromFormula" ref="a9a41f121b26ddb33a88cdba1302d0644" args="(Document *Doc, Formula const &formula, bool add_pseudo=true)" -->
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<td class="memname">static <a class="el" href="classgcu_1_1Molecule.html">Molecule</a>* gcu::Molecule::MoleculeFromFormula </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Document.html">Document</a> * </td>
<td class="paramname"> <em>Doc</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Formula.html">Formula</a> const & </td>
<td class="paramname"> <em>formula</em>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"> <em>add_pseudo</em> = <code>true</code></td><td> </td>
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<td>)</td>
<td></td><td></td><td><code> [static]</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>Doc</em> </td><td>a document. </td></tr>
<tr><td valign="top"></td><td valign="top"><em>formula</em> </td><td>a formula </td></tr>
<tr><td valign="top"></td><td valign="top"><em>add_pseudo</em> </td><td>tells if a pseudo atom (with Z = 0) has to be added (used when building a <a class="el" href="classgcu_1_1Residue.html">gcu::Residue</a> instance).</td></tr>
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<p>Tries to build a molecule from a formula, adding bonds between atoms. Atoms coordinates are not calculated. </p>
<dl class="return"><dt><b>Returns:</b></dt><dd>a molecule on success or NULL. </dd></dl>
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<a class="anchor" id="a8e2afa9634a94587b3fc6bb01da41784"></a><!-- doxytag: member="gcu::Molecule::operator==" ref="a8e2afa9634a94587b3fc6bb01da41784" args="(Molecule const &molecule) const " -->
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<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Molecule.html">Molecule</a> const & </td>
<td class="paramname"> <em>molecule</em></td>
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<td> const</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>molecule</em> </td><td>a molecule. </td></tr>
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<dl class="return"><dt><b>Returns:</b></dt><dd>true if the molecules have identical atoms and the connection framework between the atoms. </dd></dl>
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<a class="anchor" id="aff43b05c6f575fefda0c13a181181379"></a><!-- doxytag: member="gcu::Molecule::Remove" ref="aff43b05c6f575fefda0c13a181181379" args="(gcu::Object *pObject)" -->
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<td class="memname">virtual void gcu::Molecule::Remove </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Object.html">gcu::Object</a> * </td>
<td class="paramname"> <em>pObject</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>pObject</em> </td><td>an atom or a bond in the molecule.</td></tr>
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<p>Removes an atom or a bond from a molecule. </p>
<p>Reimplemented in <a class="el" href="classgcp_1_1Molecule.html#a2ef5c5ded47d687ab48351ac4412b599">gcp::Molecule</a>.</p>
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<a class="anchor" id="abb8dc72dc84a7c22a553425f0c447195"></a><!-- doxytag: member="gcu::Molecule::UpdateCycles" ref="abb8dc72dc84a7c22a553425f0c447195" args="()" -->
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<td class="memname">void gcu::Molecule::UpdateCycles </td>
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<p>Updates the cycles list after a change. </p>
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<a class="anchor" id="a283c641732a0d9768254d934445efea6"></a><!-- doxytag: member="gcu::Molecule::UpdateCycles" ref="a283c641732a0d9768254d934445efea6" args="(Bond *pBond)" -->
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<td class="memname">void gcu::Molecule::UpdateCycles </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td>
<td class="paramname"> <em>pBond</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>pBond</em> </td><td>a bond in the molecule.</td></tr>
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</dd>
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<p>Updates the cycles list after a change, starting the exploration from <em>pBond</em>. </p>
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<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="adcad89ca2f5c358068b466a99ce9a7cd"></a><!-- doxytag: member="gcu::Molecule::m_Atoms" ref="adcad89ca2f5c358068b466a99ce9a7cd" args="" -->
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<td class="memname">std::list<<a class="el" href="classgcu_1_1Atom.html">Atom</a>*> <a class="el" href="classgcu_1_1Molecule.html#adcad89ca2f5c358068b466a99ce9a7cd">gcu::Molecule::m_Atoms</a><code> [protected]</code></td>
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<p>The atoms in the molecule. </p>
<p>Definition at line <a class="el" href="gcu_2molecule_8h_source.html#l00132">132</a> of file <a class="el" href="gcu_2molecule_8h_source.html">gcu/molecule.h</a>.</p>
<p>Referenced by <a class="el" href="gcu_2molecule_8h_source.html#l00107">GetAtomsNumber()</a>.</p>
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<a class="anchor" id="ab939115e2e636a22de80176dbed6811c"></a><!-- doxytag: member="gcu::Molecule::m_Bonds" ref="ab939115e2e636a22de80176dbed6811c" args="" -->
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<td class="memname">std::list<<a class="el" href="classgcu_1_1Bond.html">Bond</a>*> <a class="el" href="classgcu_1_1Molecule.html#ab939115e2e636a22de80176dbed6811c">gcu::Molecule::m_Bonds</a><code> [protected]</code></td>
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<p>The bonds in the molecule. </p>
<p>Definition at line <a class="el" href="gcu_2molecule_8h_source.html#l00136">136</a> of file <a class="el" href="gcu_2molecule_8h_source.html">gcu/molecule.h</a>.</p>
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<a class="anchor" id="aa9d30f8cfd6f87fdd84fd07aef21f4b0"></a><!-- doxytag: member="gcu::Molecule::m_Chains" ref="aa9d30f8cfd6f87fdd84fd07aef21f4b0" args="" -->
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<td class="memname">std::list<<a class="el" href="classgcu_1_1Chain.html">Chain</a>*> <a class="el" href="classgcu_1_1Molecule.html#aa9d30f8cfd6f87fdd84fd07aef21f4b0">gcu::Molecule::m_Chains</a><code> [protected]</code></td>
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<p>The non cyclic chains contained in the molecules (not used at the moment). </p>
<p>Definition at line <a class="el" href="gcu_2molecule_8h_source.html#l00128">128</a> of file <a class="el" href="gcu_2molecule_8h_source.html">gcu/molecule.h</a>.</p>
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<a class="anchor" id="a936ef484763b9a9ace3ced4a847eb251"></a><!-- doxytag: member="gcu::Molecule::m_Cycles" ref="a936ef484763b9a9ace3ced4a847eb251" args="" -->
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<td class="memname">std::list<<a class="el" href="classgcu_1_1Cycle.html">Cycle</a>*> <a class="el" href="classgcu_1_1Molecule.html#a936ef484763b9a9ace3ced4a847eb251">gcu::Molecule::m_Cycles</a><code> [protected]</code></td>
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<p>The cycles contained in the molecules. </p>
<p>Definition at line <a class="el" href="gcu_2molecule_8h_source.html#l00124">124</a> of file <a class="el" href="gcu_2molecule_8h_source.html">gcu/molecule.h</a>.</p>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="gcu_2molecule_8h_source.html">gcu/molecule.h</a></li>
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<hr size="1"/><address style="text-align: right;"><small>Generated on Sun Sep 6 18:33:55 2009 for The Gnome Chemistry Utils by
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