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<title>The Gnome Chemistry Utils: gcu::Chain Class Reference</title>
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<div id="projectname">The Gnome Chemistry Utils
 <span id="projectnumber">0.14.2</span>
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<li class="navelem"><a class="el" href="namespacegcu.html">gcu</a></li><li class="navelem"><a class="el" href="classgcu_1_1Chain.html">Chain</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<p><code>#include <<a class="el" href="chain_8h_source.html">gcu/chain.h</a>></code></p>
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Inheritance diagram for gcu::Chain:</div>
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<tr class="heading"><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a8b5a4259a56f4eac2931cc9222dd41e6"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a8b5a4259a56f4eac2931cc9222dd41e6">Chain</a> (<a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond, <a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom=NULL, <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Type=ChainType)</td></tr>
<tr class="memitem:a48352b681d8c26d1f101e0f1f46e751c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a48352b681d8c26d1f101e0f1f46e751c">Chain</a> (<a class="el" href="classgcu_1_1Molecule.html">Molecule</a> *molecule, <a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond, <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Type=ChainType)</td></tr>
<tr class="memitem:a9fd3f20c12ffe3c17fce015768dde751"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a9fd3f20c12ffe3c17fce015768dde751">Chain</a> (<a class="el" href="classgcu_1_1Molecule.html">Molecule</a> *molecule, <a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom, <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Type=ChainType)</td></tr>
<tr class="memitem:a6952d1dc44218813990f6f1c19c37bf0"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a6952d1dc44218813990f6f1c19c37bf0">~Chain</a> ()</td></tr>
<tr class="memitem:ad1bc651dbdb0f6ba1968c049a87f58dc"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#ad1bc651dbdb0f6ba1968c049a87f58dc">FindCycles</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom)</td></tr>
<tr class="memitem:ac50c029851a0cca23e8b10faccb43f08"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#ac50c029851a0cca23e8b10faccb43f08">FindCycle</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom, <a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond)</td></tr>
<tr class="memitem:a3449a637c0e60112b22f90b6fa95b4b9"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a3449a637c0e60112b22f90b6fa95b4b9">Erase</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom1, <a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom2)</td></tr>
<tr class="memitem:a3e0a4ab81a6d78688b6ee146a22fad72"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a3e0a4ab81a6d78688b6ee146a22fad72">Insert</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom1, <a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom2, <a class="el" href="classgcu_1_1Chain.html">Chain</a> &chain)</td></tr>
<tr class="memitem:a9ba123c66cf0f663e90f2967a263dda2"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a9ba123c66cf0f663e90f2967a263dda2">Extract</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom1, <a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom2, <a class="el" href="classgcu_1_1Chain.html">Chain</a> &chain)</td></tr>
<tr class="memitem:a4212d690960806d4211d28076bc95956"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a4212d690960806d4211d28076bc95956">Reverse</a> ()</td></tr>
<tr class="memitem:a37a98dd53d5d52868e6e6db39f21a72e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a37a98dd53d5d52868e6e6db39f21a72e">AddBond</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *start, <a class="el" href="classgcu_1_1Atom.html">Atom</a> *end)</td></tr>
<tr class="memitem:a817e6e3e481dff040192ca0f237563ae"><td class="memItemLeft" align="right" valign="top">unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a817e6e3e481dff040192ca0f237563ae">GetUnsaturations</a> ()</td></tr>
<tr class="memitem:ad47d041d0e908602ec35453ce46833a3"><td class="memItemLeft" align="right" valign="top">unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#ad47d041d0e908602ec35453ce46833a3">GetHeteroatoms</a> ()</td></tr>
<tr class="memitem:ae54189912eaaf4f02d7a03b3658fc671"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#ae54189912eaaf4f02d7a03b3658fc671">Contains</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom)</td></tr>
<tr class="memitem:af7abd79ef09c751b751978a16248b5e2"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#af7abd79ef09c751b751978a16248b5e2">Contains</a> (<a class="el" href="classgcu_1_1Bond.html">Bond</a> *pBond)</td></tr>
<tr class="memitem:a41c88d5be7504a416e5d1da2cd088302"><td class="memItemLeft" align="right" valign="top">unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a41c88d5be7504a416e5d1da2cd088302">GetLength</a> ()</td></tr>
<tr class="memitem:a8673fd54a49ad9beb99b641fc770b97e"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a8673fd54a49ad9beb99b641fc770b97e">GetMeanBondLength</a> ()</td></tr>
<tr class="memitem:a562f70d1331071b5f4d4819644f64592"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a562f70d1331071b5f4d4819644f64592">GetFirstAtom</a> ()</td></tr>
<tr class="memitem:a4e43fccf28cbef4304bebae341b5453b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a4e43fccf28cbef4304bebae341b5453b">GetNextAtom</a> (<a class="el" href="classgcu_1_1Atom.html">Atom</a> *pAtom)</td></tr>
<tr class="memitem:a1644982524595342b02a318143a3322d"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a1644982524595342b02a318143a3322d">Name</a> ()</td></tr>
<tr class="memitem:a87aad41d5d5b560df9038d7c917844a5"><td class="memItemLeft" align="right" valign="top">unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a87aad41d5d5b560df9038d7c917844a5">BuildLength</a> (unsigned *cycle_size=NULL, unsigned *cycle_pos=NULL)</td></tr>
<tr class="inherit_header pub_methods_classgcu_1_1Object"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classgcu_1_1Object')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classgcu_1_1Object.html">gcu::Object</a></td></tr>
<tr class="memitem:a6f15e766fdfb066008bd4b0779574549 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a6f15e766fdfb066008bd4b0779574549">Object</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id=OtherType)</td></tr>
<tr class="memitem:a3e575300e517594b0c2c161d6e704352 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a3e575300e517594b0c2c161d6e704352">~Object</a> ()</td></tr>
<tr class="memitem:a9c900a7a382cad4a995edbb10b8f179d inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a9c900a7a382cad4a995edbb10b8f179d">GetType</a> () const </td></tr>
<tr class="memitem:ac45cdb13cf013066a3704054c9d06ed0 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ac45cdb13cf013066a3704054c9d06ed0">SetId</a> (gchar const *Id)</td></tr>
<tr class="memitem:aef94f9435a51669a518b5a713f24e7ca inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">char const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aef94f9435a51669a518b5a713f24e7ca">GetId</a> () const </td></tr>
<tr class="memitem:ad054f1ae4f0cd697765aa4d2007521b2 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ad054f1ae4f0cd697765aa4d2007521b2">AddChild</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *object)</td></tr>
<tr class="memitem:adf610a8402000e9f9ae9ad0135c1d7da inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#adf610a8402000e9f9ae9ad0135c1d7da">GetMolecule</a> () const </td></tr>
<tr class="memitem:adaba7d20336b8036b6bfb7ef3884880a inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#adaba7d20336b8036b6bfb7ef3884880a">GetReaction</a> () const </td></tr>
<tr class="memitem:a841968632d00e5d879694ee84737225b inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a841968632d00e5d879694ee84737225b">GetGroup</a> () const </td></tr>
<tr class="memitem:a274432165e22fa89a375eded192631db inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Document.html">Document</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a274432165e22fa89a375eded192631db">GetDocument</a> () const </td></tr>
<tr class="memitem:ab65facd99621938dfbd6330ccee1e9f7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Application.html">Application</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ab65facd99621938dfbd6330ccee1e9f7">GetApplication</a> () const </td></tr>
<tr class="memitem:a158be0361aaadca1d03fdb5b5d3089b2 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a158be0361aaadca1d03fdb5b5d3089b2">GetParentOfType</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id) const </td></tr>
<tr class="memitem:a026b22b02b09f8f9f535197f2d936c07 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a026b22b02b09f8f9f535197f2d936c07">GetChild</a> (const gchar *Id) const </td></tr>
<tr class="memitem:a5fe8cfbfe83645c292f8895aba4a91d0 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a5fe8cfbfe83645c292f8895aba4a91d0">GetFirstChild</a> (std::map< std::string, <a class="el" href="classgcu_1_1Object.html">Object</a> * >::iterator &i)</td></tr>
<tr class="memitem:a70ff8a33f72e424f3c39b3d0edbe9903 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a70ff8a33f72e424f3c39b3d0edbe9903">GetNextChild</a> (std::map< std::string, <a class="el" href="classgcu_1_1Object.html">Object</a> * >::iterator &i)</td></tr>
<tr class="memitem:ab70083d7ebb2cf32180c5383b5bb428c inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ab70083d7ebb2cf32180c5383b5bb428c">GetDescendant</a> (const char *Id) const </td></tr>
<tr class="memitem:abacb2c2002726a3237ffbd0e50e3df52 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#abacb2c2002726a3237ffbd0e50e3df52">GetParent</a> () const </td></tr>
<tr class="memitem:a0ffe1f48151c92f167eeec303277e45c inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a0ffe1f48151c92f167eeec303277e45c">SetParent</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *Parent)</td></tr>
<tr class="memitem:aad462441e79fbd93e158f8294a198d11 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aad462441e79fbd93e158f8294a198d11">Save</a> (xmlDocPtr xml) const </td></tr>
<tr class="memitem:aa3ee33c25154d8e7bbe1e39de970c489 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aa3ee33c25154d8e7bbe1e39de970c489">Load</a> (xmlNodePtr node)</td></tr>
<tr class="memitem:a7ae5e90dd76580aee332c6ef59e89298 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a7ae5e90dd76580aee332c6ef59e89298">GetCoords</a> (double *x, double *y, double *z=NULL) const </td></tr>
<tr class="memitem:af5505430c421604ff7e26e4414197fbc inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#af5505430c421604ff7e26e4414197fbc">Move</a> (double x, double y, double z=0.)</td></tr>
<tr class="memitem:a69ad6edf7d50950b036f09d9ff86f849 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a69ad6edf7d50950b036f09d9ff86f849">Transform2D</a> (<a class="el" href="classgcu_1_1Matrix2D.html">Matrix2D</a> &m, double x, double y)</td></tr>
<tr class="memitem:a07de41cb137a650b51920d6186fc82d7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a07de41cb137a650b51920d6186fc82d7">SaveChildren</a> (xmlDocPtr xml, xmlNodePtr node) const </td></tr>
<tr class="memitem:a5f99b290d7e48c38738342dfc984865d inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a5f99b290d7e48c38738342dfc984865d">SaveId</a> (xmlNodePtr node) const </td></tr>
<tr class="memitem:ad533d866f1478a972a1896499e5659a5 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#ad533d866f1478a972a1896499e5659a5">GetNodeByProp</a> (xmlNodePtr node, char const *Property, char const *Id)</td></tr>
<tr class="memitem:aa19f11cca83189a955f0a7bf2919562b inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aa19f11cca83189a955f0a7bf2919562b">GetNextNodeByProp</a> (xmlNodePtr node, char const *Property, char const *Id)</td></tr>
<tr class="memitem:a4e8712098d673c958fb0c72488058f80 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a4e8712098d673c958fb0c72488058f80">GetNodeByName</a> (xmlNodePtr node, char const *<a class="el" href="classgcu_1_1Object.html#ae19033807f4b7ee9321f308bb0ffd3b9">Name</a>)</td></tr>
<tr class="memitem:a2dc10bf48d3ebfe86853cace21e9abf2 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">xmlNodePtr </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a2dc10bf48d3ebfe86853cace21e9abf2">GetNextNodeByName</a> (xmlNodePtr node, char const *<a class="el" href="classgcu_1_1Object.html#ae19033807f4b7ee9321f308bb0ffd3b9">Name</a>)</td></tr>
<tr class="memitem:a28f682a2891b17ae57c5f346c95d6f50 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a28f682a2891b17ae57c5f346c95d6f50">HasChildren</a> () const </td></tr>
<tr class="memitem:a5e3d6fbdc8b10a9dbf43de2c052fff05 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">unsigned </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a5e3d6fbdc8b10a9dbf43de2c052fff05">GetChildrenNumber</a> () const </td></tr>
<tr class="memitem:aa47c38061c6a2e51947d89c86fbae630 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aa47c38061c6a2e51947d89c86fbae630">GetAtomAt</a> (double x, double y, double z=0.)</td></tr>
<tr class="memitem:af1da4274cbbf0ca56bf8d380743d49e7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#af1da4274cbbf0ca56bf8d380743d49e7">Build</a> (std::set< <a class="el" href="classgcu_1_1Object.html">Object</a> * > const &Children) throw (std::invalid_argument)</td></tr>
<tr class="memitem:aedeec6e6b66e1a35e6d2f3ef75c94a09 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aedeec6e6b66e1a35e6d2f3ef75c94a09">GetYAlign</a> ()</td></tr>
<tr class="memitem:acc55e92f84843058139d3a729aa6afcb inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#acc55e92f84843058139d3a729aa6afcb">BuildContextualMenu</a> (<a class="el" href="classgcu_1_1UIManager.html">UIManager</a> *uim, <a class="el" href="classgcu_1_1Object.html">Object</a> *object, double x, double y)</td></tr>
<tr class="memitem:acf16b429a6875e5620fa8051446ef34c inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#acf16b429a6875e5620fa8051446ef34c">EmitSignal</a> (<a class="el" href="namespacegcu.html#af13348b065987fa4ca74ca0fb1ffa48e">SignalId</a> Signal)</td></tr>
<tr class="memitem:a1ad183ecf7e5b5c42db100da03221e46 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a1ad183ecf7e5b5c42db100da03221e46">OnSignal</a> (<a class="el" href="namespacegcu.html#af13348b065987fa4ca74ca0fb1ffa48e">SignalId</a> Signal, <a class="el" href="classgcu_1_1Object.html">Object</a> *Child)</td></tr>
<tr class="memitem:a8b4da97be50a4ceea941ab8aa8ece825 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a8b4da97be50a4ceea941ab8aa8ece825">Lock</a> (bool state=true)</td></tr>
<tr class="memitem:a4094e3d8cf58a6f9de9cb6c6b6fed8c8 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a4094e3d8cf58a6f9de9cb6c6b6fed8c8">IsLocked</a> ()</td></tr>
<tr class="memitem:a79e87eb91afb57ebf188fdc3753cba7d inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a79e87eb91afb57ebf188fdc3753cba7d">GetFirstLink</a> (std::set< <a class="el" href="classgcu_1_1Object.html">Object</a> * >::iterator &i)</td></tr>
<tr class="memitem:a61b227220c2b831b7196d2bd61201bdc inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a61b227220c2b831b7196d2bd61201bdc">GetNextLink</a> (std::set< <a class="el" href="classgcu_1_1Object.html">Object</a> * >::iterator &i)</td></tr>
<tr class="memitem:a0173055f0ba60038d9d913b5f09bb354 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a0173055f0ba60038d9d913b5f09bb354">Link</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *object)</td></tr>
<tr class="memitem:a606a257c41cd9cc177c98958fdf2ae3d inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a606a257c41cd9cc177c98958fdf2ae3d">Unlink</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *object)</td></tr>
<tr class="memitem:a786610ff1992e4aa1acff883b5479ec7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a786610ff1992e4aa1acff883b5479ec7">OnUnlink</a> (<a class="el" href="classgcu_1_1Object.html">Object</a> *object)</td></tr>
<tr class="memitem:a97106b6ec695ac946d0a1d04293eef79 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a97106b6ec695ac946d0a1d04293eef79">GetPossibleAncestorTypes</a> (std::set< <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> > &types) const </td></tr>
<tr class="memitem:a47862fe83b1c3739ee37b8af81550644 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a47862fe83b1c3739ee37b8af81550644">SetProperty</a> (unsigned property, char const *value)</td></tr>
<tr class="memitem:a9f612121600c791abbee16bb539975d7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a9f612121600c791abbee16bb539975d7">GetProperty</a> (unsigned property) const </td></tr>
<tr class="memitem:af972c30c9990923c34c54754654c3e72 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#af972c30c9990923c34c54754654c3e72">OnLoaded</a> ()</td></tr>
<tr class="memitem:a01ea0147ad675e139ddea7aaa2af503c inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a01ea0147ad675e139ddea7aaa2af503c">SetDirty</a> (bool dirty=true)</td></tr>
<tr class="memitem:adce3873de56ddf2abe7dba89e127fc06 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#adce3873de56ddf2abe7dba89e127fc06">Clear</a> ()</td></tr>
<tr class="memitem:a373cd8efa4af70cdbc4a77086aee82c7 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a373cd8efa4af70cdbc4a77086aee82c7">Identity</a> ()</td></tr>
<tr class="memitem:aceff810bb8bfad7f9a7152eef3dfe46e inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual char const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aceff810bb8bfad7f9a7152eef3dfe46e">HasPropertiesDialog</a> () const </td></tr>
<tr class="memitem:a8f3da29ebe1fcc1534ac65b724f3582f inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a8f3da29ebe1fcc1534ac65b724f3582f">CanSelect</a> () const </td></tr>
<tr class="memitem:a67e3c8ee2104cd937aea48dabde7d319 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a67e3c8ee2104cd937aea48dabde7d319">NotifyEmpty</a> ()</td></tr>
<tr class="memitem:a45b59346e78b7a9927d379bb65df1710 inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a45b59346e78b7a9927d379bb65df1710">ShowPropertiesDialog</a> ()</td></tr>
<tr class="memitem:a71e2333cf4d47abdd272a8709361829f inherit pub_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a71e2333cf4d47abdd272a8709361829f">GetDirty</a> (void) const </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:acb5f7fb52cf019721daf6e761cdea6ae"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="classgcu_1_1Atom.html">Atom</a> *, <a class="el" href="structgcu_1_1ChainElt.html">ChainElt</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#acb5f7fb52cf019721daf6e761cdea6ae">m_Bonds</a></td></tr>
<tr class="memitem:a335946bc030113d283a351caac1ecae0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgcu_1_1Molecule.html">Molecule</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Chain.html#a335946bc030113d283a351caac1ecae0">m_Molecule</a></td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_static_methods_classgcu_1_1Object"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classgcu_1_1Object')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classgcu_1_1Object.html">gcu::Object</a></td></tr>
<tr class="memitem:aea6734ca6bde8ae3e0788db43928f42e inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#aea6734ca6bde8ae3e0788db43928f42e">AddType</a> (std::string TypeName, <a class="el" href="classgcu_1_1Object.html">Object</a> *(*CreateFunc)(), <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> id=OtherType)</td></tr>
<tr class="memitem:a3645f28b3df32308f135ec5b0aac0793 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a3645f28b3df32308f135ec5b0aac0793">AddAlias</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> id, std::string TypeName)</td></tr>
<tr class="memitem:a0d3837f66eccae5ce73573ca95930dbc inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classgcu_1_1Object.html">Object</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a0d3837f66eccae5ce73573ca95930dbc">CreateObject</a> (const std::string &TypeName, <a class="el" href="classgcu_1_1Object.html">Object</a> *parent=NULL)</td></tr>
<tr class="memitem:a6038f7f7c0f58cd1aa12bd8237ac1024 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a6038f7f7c0f58cd1aa12bd8237ac1024">GetTypeId</a> (const std::string &<a class="el" href="classgcu_1_1Object.html#ae19033807f4b7ee9321f308bb0ffd3b9">Name</a>)</td></tr>
<tr class="memitem:a9e57005d5129e341ce3dcd4d3c188eaf inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a9e57005d5129e341ce3dcd4d3c188eaf">GetTypeName</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id)</td></tr>
<tr class="memitem:a47d2dd181c9934ab4671c526a251295f inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a47d2dd181c9934ab4671c526a251295f">AddMenuCallback</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id, <a class="el" href="namespacegcu.html#aea85ee1e0ab66342f28448b2e7a9174d">BuildMenuCb</a> cb)</td></tr>
<tr class="memitem:a3eb4fd4787f224f5e7e3e5f8d1fc2abb inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a3eb4fd4787f224f5e7e3e5f8d1fc2abb">AddRule</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> type1, <a class="el" href="namespacegcu.html#a19c49d12e7c0a96ae2be6c6c33c44b47">RuleId</a> rule, <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> type2)</td></tr>
<tr class="memitem:a13348c710f80100519c94d10dff3d0e0 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a13348c710f80100519c94d10dff3d0e0">AddRule</a> (const std::string &type1, <a class="el" href="namespacegcu.html#a19c49d12e7c0a96ae2be6c6c33c44b47">RuleId</a> rule, const std::string &type2)</td></tr>
<tr class="memitem:a96a3ea77a33f4721399f00e6b341cde2 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static const std::set< <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a96a3ea77a33f4721399f00e6b341cde2">GetRules</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> type, <a class="el" href="namespacegcu.html#a19c49d12e7c0a96ae2be6c6c33c44b47">RuleId</a> rule)</td></tr>
<tr class="memitem:a44d44e134f05976140e8e4686b0cd936 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static const std::set< <a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a44d44e134f05976140e8e4686b0cd936">GetRules</a> (const std::string &type, <a class="el" href="namespacegcu.html#a19c49d12e7c0a96ae2be6c6c33c44b47">RuleId</a> rule)</td></tr>
<tr class="memitem:a8159c48a642f3410913e635e23d77f24 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a8159c48a642f3410913e635e23d77f24">SetCreationLabel</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id, std::string Label)</td></tr>
<tr class="memitem:a90c6d068fdbea8cffe8690f177b5c939 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static const std::string & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a90c6d068fdbea8cffe8690f177b5c939">GetCreationLabel</a> (<a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> Id)</td></tr>
<tr class="memitem:a591fb1674ad415be983b6810ef484326 inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static const std::string & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a591fb1674ad415be983b6810ef484326">GetCreationLabel</a> (const std::string &TypeName)</td></tr>
<tr class="memitem:a380275771a250b94785e43286525c74e inherit pub_static_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="namespacegcu.html#af13348b065987fa4ca74ca0fb1ffa48e">SignalId</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a380275771a250b94785e43286525c74e">CreateNewSignalId</a> ()</td></tr>
<tr class="inherit_header pro_methods_classgcu_1_1Object"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classgcu_1_1Object')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classgcu_1_1Object.html">gcu::Object</a></td></tr>
<tr class="memitem:a98a9025b609f6ba46ab3b273792ee51e inherit pro_methods_classgcu_1_1Object"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classgcu_1_1Dialog.html">Dialog</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgcu_1_1Object.html#a98a9025b609f6ba46ab3b273792ee51e">BuildPropertiesDialog</a> ()</td></tr>
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<a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>This class is used to represent chains of atoms. </p>
<p>Definition at line <a class="el" href="chain_8h_source.html#l00059">59</a> of file <a class="el" href="chain_8h_source.html">chain.h</a>.</p>
</div><h2>Constructor & Destructor Documentation</h2>
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<td class="memname">gcu::Chain::Chain </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td>
<td class="paramname"><em>pBond</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>pAtom</em> = <code>NULL</code>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td>
<td class="paramname"><em>Type</em> = <code>ChainType</code> </td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pBond</td><td>a bond. </td></tr>
<tr><td class="paramname">pAtom</td><td>an atom. </td></tr>
<tr><td class="paramname">Type</td><td>an optional type id used when constructing a derived type (i. e. a cycle).</td></tr>
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<p>Constructs a <a class="el" href="classgcu_1_1Chain.html">Chain</a> starting from a bond and an optional atom. Choosing the atom forces the direction of the chain, otherwise, the first atom will be the first atom of the bond. </p>
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<td class="memname">gcu::Chain::Chain </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgcu_1_1Molecule.html">Molecule</a> * </td>
<td class="paramname"><em>molecule</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td>
<td class="paramname"><em>pBond</em>, </td>
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<td class="paramtype"><a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td>
<td class="paramname"><em>Type</em> = <code>ChainType</code> </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">molecule</td><td>a molecule. </td></tr>
<tr><td class="paramname">pBond</td><td>a bond in the molecule or NULL. </td></tr>
<tr><td class="paramname">Type</td><td>an optional type id used when constructing a derived type</td></tr>
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<p>Explores a molecule and find all cycles, starting from pBond or an empty chain if pBond is NULL. </p>
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<td class="memname">gcu::Chain::Chain </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Molecule.html">Molecule</a> * </td>
<td class="paramname"><em>molecule</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>pAtom</em>, </td>
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<td class="paramtype"><a class="el" href="namespacegcu.html#a4a6abffbefdd6abf047dca4e63b0bac5">TypeId</a> </td>
<td class="paramname"><em>Type</em> = <code>ChainType</code> </td>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">molecule</td><td>a molecule. </td></tr>
<tr><td class="paramname">pAtom</td><td>an atom in the molecule. </td></tr>
<tr><td class="paramname">Type</td><td>an optional type id used when constructing a derived type</td></tr>
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<p>Explores a molecule and find all cycles, starting from pAtom or an empty chain if pAtom is NULL. </p>
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<td class="memname">virtual gcu::Chain::~Chain </td>
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<p>The destructor. </p>
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<h2>Member Function Documentation</h2>
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<td class="memname">void gcu::Chain::AddBond </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>start</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>end</em> </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">start</td><td>an atom. </td></tr>
<tr><td class="paramname">end</td><td>an atom.</td></tr>
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<p>Adds the two atoms and the bond between them to the chain. The two atoms must be bonded. </p>
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<td class="memname">unsigned gcu::Chain::BuildLength </td>
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<td class="paramtype">unsigned * </td>
<td class="paramname"><em>cycle_size</em> = <code>NULL</code>, </td>
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<td class="paramtype">unsigned * </td>
<td class="paramname"><em>cycle_pos</em> = <code>NULL</code> </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">cycle_size</td><td>where to store a cycle size if a cycle is encountered </td></tr>
<tr><td class="paramname">cycle_pos</td><td>where to store a cycle position if a cycle is encountered</td></tr>
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<p>Finds the longest chani starting from first bond and ending when a cycle is found or at the chain end. </p>
<dl class="section return"><dt>Returns</dt><dd>the evaluated chain length. </dd></dl>
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<td class="memname">bool gcu::Chain::Contains </td>
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<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 class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pAtom</td><td>an atom.</td></tr>
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<dl class="section return"><dt>Returns</dt><dd>true if pAtom is in the chain. </dd></dl>
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<td class="memname">bool gcu::Chain::Contains </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 class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pBond</td><td>a bond.</td></tr>
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<dl class="section return"><dt>Returns</dt><dd>true if pBond is in the chain. </dd></dl>
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<td class="memname">virtual void gcu::Chain::Erase </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>pAtom1</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>pAtom2</em> </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pAtom1</td><td>an atom in the source chain. </td></tr>
<tr><td class="paramname">pAtom2</td><td>an atom in the source chain.</td></tr>
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<p>Erases a sub-chain. One of the atoms must already be one of the chain ends. </p>
<p>Reimplemented in <a class="el" href="classgcu_1_1Cycle.html#a55e6be78f330b5c3d650b2df4c122b92">gcu::Cycle</a>.</p>
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<td class="memname">void gcu::Chain::Extract </td>
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<td class="paramname"><em>pAtom1</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>pAtom2</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Chain.html">Chain</a> & </td>
<td class="paramname"><em>chain</em> </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pAtom1</td><td>an atom in the chain. </td></tr>
<tr><td class="paramname">pAtom2</td><td>an atom in the chain. </td></tr>
<tr><td class="paramname">chain</td><td>the target chain.</td></tr>
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<p>Extracts a sub-chain to the chain variable which should be empty before the call. </p>
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<td class="memname">bool gcu::Chain::FindCycle </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>pAtom</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Bond.html">Bond</a> * </td>
<td class="paramname"><em>pBond</em> </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pAtom</td><td>an atom. </td></tr>
<tr><td class="paramname">pBond</td><td>a bond.</td></tr>
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<p>Searches for a cycle containing the atom pAtom and the bond pBond. pAtom must be one of the ends of pBond. If a cycle is found, it is added to the molecule cycles list. </p>
<dl class="section return"><dt>Returns</dt><dd>true on success, false otherwise. </dd></dl>
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<td class="memname">void gcu::Chain::FindCycles </td>
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<td class="paramname"><em>pAtom</em></td><td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pAtom</td><td>an atom.</td></tr>
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<p>Searches all cycles in a molecule starting from <a class="el" href="classgcu_1_1Atom.html">Atom</a> pAtom. Found cycles are added to the molecule cycles list. </p>
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<td class="memname"><a class="el" href="classgcu_1_1Atom.html">Atom</a>* gcu::Chain::GetFirstAtom </td>
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<dl class="section return"><dt>Returns</dt><dd>the first atom in the chain if any. </dd></dl>
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<td class="memname">unsigned gcu::Chain::GetHeteroatoms </td>
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<dl class="section return"><dt>Returns</dt><dd>the number of heteroatoms in the chain. </dd></dl>
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<dl class="section return"><dt>Returns</dt><dd>the number of bonds in the chain </dd></dl>
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<dl class="section return"><dt>Returns</dt><dd>the mean bond length in the chain. </dd></dl>
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<td class="memname"><a class="el" href="classgcu_1_1Atom.html">Atom</a>* gcu::Chain::GetNextAtom </td>
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<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 class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pAtom</td><td>an atom in the chain. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>the next atom in the chain or NULL if pAtom is the last one. </dd></dl>
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<td class="memname">unsigned gcu::Chain::GetUnsaturations </td>
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<dl class="section return"><dt>Returns</dt><dd>the number of multiple bonds in the chain so not really the unsaturations number. </dd></dl>
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<td class="memname">virtual void gcu::Chain::Insert </td>
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<td class="paramname"><em>pAtom1</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Atom.html">Atom</a> * </td>
<td class="paramname"><em>pAtom2</em>, </td>
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<td class="paramtype"><a class="el" href="classgcu_1_1Chain.html">Chain</a> & </td>
<td class="paramname"><em>chain</em> </td>
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<td>)</td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pAtom1</td><td>an atom in the source chain. </td></tr>
<tr><td class="paramname">pAtom2</td><td>an atom in the source chain. </td></tr>
<tr><td class="paramname">chain</td><td>the source chain.</td></tr>
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</dd>
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<p>Inserts a chain. One of the atoms must already be in the target chain. </p>
<p>Reimplemented in <a class="el" href="classgcu_1_1Cycle.html#a73097fdcd8b726ec27b904fce91523ca">gcu::Cycle</a>.</p>
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<td class="memname">std::string gcu::Chain::Name </td>
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<dl class="section return"><dt>Returns</dt><dd>the localized object generic name. </dd></dl>
<p>Reimplemented from <a class="el" href="classgcu_1_1Object.html#ae19033807f4b7ee9321f308bb0ffd3b9">gcu::Object</a>.</p>
<p>Reimplemented in <a class="el" href="classgcu_1_1Cycle.html#a361ce69c31f92c70e21519ad0ee63a5f">gcu::Cycle</a>.</p>
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<td class="memname">void gcu::Chain::Reverse </td>
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<p>Reverses the chain order. </p>
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<h2>Member Data Documentation</h2>
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<td class="memname">std::map<<a class="el" href="classgcu_1_1Atom.html">Atom</a>*, <a class="el" href="structgcu_1_1ChainElt.html">ChainElt</a>> gcu::Chain::m_Bonds</td>
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<p>The <a class="el" href="structgcu_1_1ChainElt.html">gcu::ChainElt</a> elements in the chain indexed by their common atom. </p>
<p>Definition at line <a class="el" href="chain_8h_source.html#l00205">205</a> of file <a class="el" href="chain_8h_source.html">chain.h</a>.</p>
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<td class="memname"><a class="el" href="classgcu_1_1Molecule.html">Molecule</a>* gcu::Chain::m_Molecule</td>
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<p>The molecule which owns the chain. </p>
<p>Definition at line <a class="el" href="chain_8h_source.html#l00209">209</a> of file <a class="el" href="chain_8h_source.html">chain.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="chain_8h_source.html">chain.h</a></li>
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