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<div class="textblock"><code>#include <openbabel/babelconfig.h></code><br/>
<code>#include <vector></code><br/>
<code>#include <string></code><br/>
<code>#include <<a class="el" href="base_8h_source.shtml">openbabel/base.h</a>></code><br/>
<code>#include <<a class="el" href="residue_8h_source.shtml">openbabel/residue.h</a>></code><br/>
<code>#include <<a class="el" href="vector3_8h_source.shtml">openbabel/math/vector3.h</a>></code><br/>
</div><div class="textblock"><div class="dynheader">
This graph shows which files directly or indirectly include this file:</div>
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<div class="center"><img src="atom_8h__dep__incl.png" border="0" usemap="#atom_8hdep" alt=""/></div>
<map name="atom_8hdep" id="atom_8hdep">
<area shape="rect" id="node3" href="bond_8h.shtml" title="Handle bonds." alt="" coords="315,83,381,112"/><area shape="rect" id="node5" href="mol_8h.shtml" title="Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue. (the main header for Open Babel)..." alt="" coords="385,160,444,189"/><area shape="rect" id="node7" href="atom_8cpp.shtml" title="Handle OBAtom class." alt="" coords="123,237,208,267"/><area shape="rect" id="node11" href="builder_8cpp.shtml" title="Handle OBBuilder class." alt="" coords="5,237,99,267"/><area shape="rect" id="node13" href="chargemodel_8cpp.shtml" title="Base class for molecular partial charge models." alt="" coords="475,237,611,267"/><area shape="rect" id="node15" href="forcefield_8cpp.shtml" title="Handle OBForceField class." alt="" coords="232,237,344,267"/><area shape="rect" id="node17" href="grid_8cpp.shtml" title="Handle grids of values." alt="" coords="635,237,709,267"/><area shape="rect" id="node19" href="pointgroup_8cpp.shtml" title="Brute-force point group detection." alt="" coords="733,237,853,267"/><area shape="rect" id="node24" href="residue_8cpp.shtml" title="Handle macromolecule residues." alt="" coords="468,160,567,189"/><area shape="rect" id="node9" href="bond_8cpp.shtml" title="Handle OBBond class." alt="" coords="368,237,451,267"/></map>
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</div>
<p><a href="atom_8h_source.shtml">Go to the source code of this file.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAtom.shtml">OBAtom</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Atom class. <a href="classOpenBabel_1_1OBAtom.shtml#details">More...</a><br/></td></tr>
<tr><td colspan="2"><h2><a name="namespaces"></a>
Namespaces</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">namespace  </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml">OpenBabel</a></td></tr>
<tr><td colspan="2"><h2><a name="define-members"></a>
Defines</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#a7049a943ce03181c7004fe9ecd798f40">OB_4RING_ATOM</a>   (1<<1)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#a54cf51e4021ce031b9a9bd20e053cead">OB_3RING_ATOM</a>   (1<<2)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#ac08352e8abee93573a66f692f0827bd3">OB_AROMATIC_ATOM</a>   (1<<3)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#a5f2ffc18f5cc3589dd1978252169f11e">OB_RING_ATOM</a>   (1<<4)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#a4cfdf58a49dd4ebfab6d8dada02fef43">OB_CSTEREO_ATOM</a>   (1<<5)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#a7a0c4ca8c736e743fda131e25de50a26">OB_ACSTEREO_ATOM</a>   (1<<6)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#acb984613554c9199387e3039b6cf4e8c">OB_DONOR_ATOM</a>   (1<<7)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#a86c329377a02eb7b0d5e015a6d0b1099">OB_ACCEPTOR_ATOM</a>   (1<<8)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#a57a10e2d6bfa530e787d7e13cc9da15d">OB_CHIRAL_ATOM</a>   (1<<9)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#a2cac237d3ceb0758f76448ba35cf4fa5">OB_POS_CHIRAL_ATOM</a>   (1<<10)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#a28504d751913b6affc112690765c1ea6">OB_NEG_CHIRAL_ATOM</a>   (1<<11)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#aad40730c29a0be944d55f5b3e3f98ac9">OB_ATOM_HAS_NO_H</a>   (1<<12)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="atom_8h.shtml#ac41fb93bbf43756058cf90930dae22f1">OB_ATOM_NOT_H_DEFICIENT</a>   (1<<13)</td></tr>
<tr><td colspan="2"><h2><a name="typedef-members"></a>
Typedefs</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef OBAtom </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#ac0863bf2485bd66ba3afa6e50ddc20f6">OBNodeBase</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef std::vector< OBBond * ><br class="typebreak"/>
::iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#a54495d3eb8f9749d0237e6bda59e0abe">OBBondIterator</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef std::vector< OBAtom * ><br class="typebreak"/>
::iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceOpenBabel.shtml#aed11ccd81d7abaccbdf10486a5ae0402">OBAtomIterator</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Handle atoms. </p>
</div><hr/><h2>Define Documentation</h2>
<a class="anchor" id="a7049a943ce03181c7004fe9ecd798f40"></a><!-- doxytag: member="atom.h::OB_4RING_ATOM" ref="a7049a943ce03181c7004fe9ecd798f40" args="" -->
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<td class="memname">#define OB_4RING_ATOM   (1<<1)</td>
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</div>
<div class="memdoc">
<p>Atom is in a 4-membered ring. </p>
</div>
</div>
<a class="anchor" id="a54cf51e4021ce031b9a9bd20e053cead"></a><!-- doxytag: member="atom.h::OB_3RING_ATOM" ref="a54cf51e4021ce031b9a9bd20e053cead" args="" -->
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<td class="memname">#define OB_3RING_ATOM   (1<<2)</td>
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<div class="memdoc">
<p>Atom is in a 3-membered ring. </p>
</div>
</div>
<a class="anchor" id="ac08352e8abee93573a66f692f0827bd3"></a><!-- doxytag: member="atom.h::OB_AROMATIC_ATOM" ref="ac08352e8abee93573a66f692f0827bd3" args="" -->
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<td class="memname">#define OB_AROMATIC_ATOM   (1<<3)</td>
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<p>Atom is aromatic. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a4ef863ca7ed29e266960966a66dc8fb8">OBAtom::IsAromatic()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a3d29498c15007d9b6729e26784f23a5b">OBAtom::SetAromatic()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a2fcf3bf429f36281a43c879e40e75f34">OBAtom::UnsetAromatic()</a>.</p>
</div>
</div>
<a class="anchor" id="a5f2ffc18f5cc3589dd1978252169f11e"></a><!-- doxytag: member="atom.h::OB_RING_ATOM" ref="a5f2ffc18f5cc3589dd1978252169f11e" args="" -->
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<td class="memname">#define OB_RING_ATOM   (1<<4)</td>
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<div class="memdoc">
<p>Atom is in a ring. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#aa17842bd610dc8b2ede2fe324738fe5b">OBAtom::IsInRing()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a9ca260c28f84147e45c377cdb2254144">OBAtom::IsInRingSize()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#ae6a016e7f67cf564e5f80254c425f65c">OBAtom::SetInRing()</a>.</p>
</div>
</div>
<a class="anchor" id="a4cfdf58a49dd4ebfab6d8dada02fef43"></a><!-- doxytag: member="atom.h::OB_CSTEREO_ATOM" ref="a4cfdf58a49dd4ebfab6d8dada02fef43" args="" -->
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<td class="memname">#define OB_CSTEREO_ATOM   (1<<5)</td>
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</div>
<div class="memdoc">
<p>Atom has clockwise SMILES chiral stereochemistry (i.e., "@@") </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a8844e382c76003229ee5fdd0341aacee">OBAtom::HasChiralitySpecified()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a4d1f38bbe03483629778078dcc4e75a0">OBAtom::IsClockwise()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#adf069c94123595712cb7fa847b87e449">OBAtom::SetClockwiseStereo()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#afdf42f73fe8a0cec0db3c3e544830fcc">OBAtom::UnsetStereo()</a>.</p>
</div>
</div>
<a class="anchor" id="a7a0c4ca8c736e743fda131e25de50a26"></a><!-- doxytag: member="atom.h::OB_ACSTEREO_ATOM" ref="a7a0c4ca8c736e743fda131e25de50a26" args="" -->
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<td class="memname">#define OB_ACSTEREO_ATOM   (1<<6)</td>
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<div class="memdoc">
<p>Atom has anticlockwise SMILES chiral stereochemistry (i.e., "@") </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a8844e382c76003229ee5fdd0341aacee">OBAtom::HasChiralitySpecified()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#af3abb70d4f818b9c3e416928afa2e844">OBAtom::IsAntiClockwise()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#af328f0aa99465103074b1d336c393919">OBAtom::SetAntiClockwiseStereo()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#afdf42f73fe8a0cec0db3c3e544830fcc">OBAtom::UnsetStereo()</a>.</p>
</div>
</div>
<a class="anchor" id="acb984613554c9199387e3039b6cf4e8c"></a><!-- doxytag: member="atom.h::OB_DONOR_ATOM" ref="acb984613554c9199387e3039b6cf4e8c" args="" -->
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<td class="memname">#define OB_DONOR_ATOM   (1<<7)</td>
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<p>Atom is an electron donor. </p>
</div>
</div>
<a class="anchor" id="a86c329377a02eb7b0d5e015a6d0b1099"></a><!-- doxytag: member="atom.h::OB_ACCEPTOR_ATOM" ref="a86c329377a02eb7b0d5e015a6d0b1099" args="" -->
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<td class="memname">#define OB_ACCEPTOR_ATOM   (1<<8)</td>
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<div class="memdoc">
<p>Atom is an electron acceptor. </p>
</div>
</div>
<a class="anchor" id="a57a10e2d6bfa530e787d7e13cc9da15d"></a><!-- doxytag: member="atom.h::OB_CHIRAL_ATOM" ref="a57a10e2d6bfa530e787d7e13cc9da15d" args="" -->
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<td class="memname">#define OB_CHIRAL_ATOM   (1<<9)</td>
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<div class="memdoc">
<p>Atom is chiral. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#af328f0aa99465103074b1d336c393919">OBAtom::SetAntiClockwiseStereo()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#ad4e5a4c67101743f644b047b632d058b">OBAtom::SetChiral()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#adf069c94123595712cb7fa847b87e449">OBAtom::SetClockwiseStereo()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#aea322d9d450ee48fb2e89a4f7c34deda">OBAtom::SetNegativeStereo()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a6ddbbbc5f8e185c43e634a0425311275">OBAtom::SetPositiveStereo()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#afdf42f73fe8a0cec0db3c3e544830fcc">OBAtom::UnsetStereo()</a>.</p>
</div>
</div>
<a class="anchor" id="a2cac237d3ceb0758f76448ba35cf4fa5"></a><!-- doxytag: member="atom.h::OB_POS_CHIRAL_ATOM" ref="a2cac237d3ceb0758f76448ba35cf4fa5" args="" -->
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<td class="memname">#define OB_POS_CHIRAL_ATOM   (1<<10)</td>
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<p>Atom has + chiral volume. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a63911efd550113b275239d322670986d">OBAtom::HasChiralVolume()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a9880a080dd0bce244291bde514b67d20">OBAtom::IsPositiveStereo()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a6ddbbbc5f8e185c43e634a0425311275">OBAtom::SetPositiveStereo()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#afdf42f73fe8a0cec0db3c3e544830fcc">OBAtom::UnsetStereo()</a>.</p>
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<a class="anchor" id="a28504d751913b6affc112690765c1ea6"></a><!-- doxytag: member="atom.h::OB_NEG_CHIRAL_ATOM" ref="a28504d751913b6affc112690765c1ea6" args="" -->
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<td class="memname">#define OB_NEG_CHIRAL_ATOM   (1<<11)</td>
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<p>Atom has - chiral volume. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a63911efd550113b275239d322670986d">OBAtom::HasChiralVolume()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a61e5344c34c172e9b889e59255aff6de">OBAtom::IsNegativeStereo()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#aea322d9d450ee48fb2e89a4f7c34deda">OBAtom::SetNegativeStereo()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#afdf42f73fe8a0cec0db3c3e544830fcc">OBAtom::UnsetStereo()</a>.</p>
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<a class="anchor" id="aad40730c29a0be944d55f5b3e3f98ac9"></a><!-- doxytag: member="atom.h::OB_ATOM_HAS_NO_H" ref="aad40730c29a0be944d55f5b3e3f98ac9" args="" -->
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<td class="memname">#define OB_ATOM_HAS_NO_H   (1<<12)</td>
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<p>Atom has no hydrogen attached. Temporary use only during input of some formats. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a1a92c9eb656eb9ef43f03c717a38adc3">OBAtom::ForceNoH()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a55e8f858833eee0408aee7b0f1b9c22c">OBAtom::HasNoHForced()</a>.</p>
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<a class="anchor" id="ac41fb93bbf43756058cf90930dae22f1"></a><!-- doxytag: member="atom.h::OB_ATOM_NOT_H_DEFICIENT" ref="ac41fb93bbf43756058cf90930dae22f1" args="" -->
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<td class="memname">#define OB_ATOM_NOT_H_DEFICIENT   (1<<13)</td>
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<p>Atom is not hydrogen deficient. (for SMILES input) </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a03e54abd32434bd610bfd4430d91b7b9">OBAtom::ForceImplH()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a8920c0ef5c32f64887d09c3b2da857d5">OBAtom::HasImplHForced()</a>.</p>
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