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<li class="navelem"><a class="el" href="namespaceOpenBabel.shtml">OpenBabel</a> </li>
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<div class="title">OBAlign Class Reference</div> </div>
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<!-- doxytag: class="OpenBabel::OBAlign" -->
<p><code>#include <<a class="el" href="align_8h_source.shtml">openbabel/math/align.h</a>></code></p>
<p><a href="classOpenBabel_1_1OBAlign-members.shtml">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td colspan="2"><div class="groupHeader">Constructors</div></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a2bc7af7892ce336cbeb8a6295823a150">OBAlign</a> (bool includeH=false, bool symmetry=true)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a50daf56049eaa97c3159bceca10d5886">OBAlign</a> (const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> &refmol, const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> &targetmol, bool includeH=false, bool symmetry=true)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#afe0c5f1d18b1dd06c009eb59213412d7">OBAlign</a> (const vector< <a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> > &ref, const vector< <a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> > &target)</td></tr>
<tr><td colspan="2"><div class="groupHeader">Partial Setup</div></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a7909c3a4140da2417bd5e35d02afa272">SetRef</a> (const vector< <a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> > &ref)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a44c3cb229020cd0d2270cb63b6251650">SetTarget</a> (const vector< <a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> > &target)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#ac56e2c2ffd9fdf7448b3bda78cdc9549">SetRefMol</a> (const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> &refmol)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a2a325b0a2af5bbc3511c6f536e686e21">SetTargetMol</a> (const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> &targetmol)</td></tr>
<tr><td colspan="2"><div class="groupHeader">Execute the alignment</div></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a946a73d3de978fd930793711f23e00b3">Align</a> ()</td></tr>
<tr><td colspan="2"><div class="groupHeader">Access the result of the alignment</div></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a060c746a125272a535ec8f6b59f5338a">GetRMSD</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenBabel_1_1matrix3x3.shtml">matrix3x3</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a53e6707da019dfa88df1e8c1aeeb6f67">GetRotMatrix</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">vector< <a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a6a9ca08185bebf3307c4a1acd31e58c3">GetAlignment</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBAlign.shtml#a3748ab33ffd81acda5060963bdae971a">UpdateCoords</a> (<a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> *target)</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Perform a least-squares alignment of two molecules or two vectors of <a class="el" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> objects. </p>
<p>This class may be used to perform a least-squares alignment of two <a class="el" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> objects or two vector<vector3> objects. The Kabsch algorithm is used for the alignment.</p>
<p>During the alignment, the Target is aligned to the Reference. Note that mutiple alignments to the same Reference will be much faster than multiple alignments to the same Target. When carrying out multiple alignments, a single <a class="el" href="classOpenBabel_1_1OBAlign.shtml" title="Perform a least-squares alignment of two molecules or two vectors of vector3 objects.">OBAlign</a> instance should be reused by calling <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a44c3cb229020cd0d2270cb63b6251650">SetTarget()</a> or <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a2a325b0a2af5bbc3511c6f536e686e21">SetTargetMol()</a> for each additional Target and then calling <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a946a73d3de978fd930793711f23e00b3">Align()</a>.</p>
<p>When aligning molecules, the atoms of the two molecules must be in the same order for the results to be sensible. By default, hydrogens are not included in the least-squares fitting procedure (set <code>includeH</code> to true if you wish to include them) and so the resulting RMSD is the heavy-atom RMSD (which is usually what you want).</p>
<p>By default, symmetry is taken into account when comparing molecules. For example, if a benzene is flipped by 180 degrees along one of its 2-fold symmetry axes, it will only have an RMSD of 0 (with respect to its original orientation) if symmetry is enabled. To turn off handling of symmetry set <code>symmetry</code> to false (this will speed up the alignment).</p>
<p>Note that neither the Target nor the Reference are modified by the algorithm. As a result, to update a TargetMol with the new coordinates from the alignment, you need to use <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a3748ab33ffd81acda5060963bdae971a">UpdateCoords()</a>.</p>
<dl class="since"><dt><b>Since:</b></dt><dd>version 2.3 </dd></dl>
</div><hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="a2bc7af7892ce336cbeb8a6295823a150"></a><!-- doxytag: member="OpenBabel::OBAlign::OBAlign" ref="a2bc7af7892ce336cbeb8a6295823a150" args="(bool includeH=false, bool symmetry=true)" -->
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<td class="memname"><a class="el" href="classOpenBabel_1_1OBAlign.shtml">OBAlign</a> </td>
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<td class="paramtype">bool </td>
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<p>If this constructor is used, the Target and Reference must be set using SetRef/SetRefMol and SetTarget/SetTargetMol before running the alignment. </p>
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<a class="anchor" id="a50daf56049eaa97c3159bceca10d5886"></a><!-- doxytag: member="OpenBabel::OBAlign::OBAlign" ref="a50daf56049eaa97c3159bceca10d5886" args="(const OBMol &refmol, const OBMol &targetmol, bool includeH=false, bool symmetry=true)" -->
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<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> & </td>
<td class="paramname"><em>refmol</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> & </td>
<td class="paramname"><em>targetmol</em>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>includeH</em> = <code>false</code>, </td>
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<p>Align two molecules. </p>
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<a class="anchor" id="afe0c5f1d18b1dd06c009eb59213412d7"></a><!-- doxytag: member="OpenBabel::OBAlign::OBAlign" ref="afe0c5f1d18b1dd06c009eb59213412d7" args="(const vector< vector3 > &ref, const vector< vector3 > &target)" -->
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<td>(</td>
<td class="paramtype">const vector< <a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> > & </td>
<td class="paramname"><em>ref</em>, </td>
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<td class="paramtype">const vector< <a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> > & </td>
<td class="paramname"><em>target</em> </td>
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<p>Align two vectors of <a class="el" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> objects. </p>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a7909c3a4140da2417bd5e35d02afa272"></a><!-- doxytag: member="OpenBabel::OBAlign::SetRef" ref="a7909c3a4140da2417bd5e35d02afa272" args="(const vector< vector3 > &ref)" -->
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<td class="memname">void SetRef </td>
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<p>Set the Reference (to which the Target will be aligned) in terms of a vector of <a class="el" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> objects. Note that it is faster to perform multiple alignments to the same Reference, rather than multiple alignments to the same Target. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBRMSDConformerScore.shtml#af48ac6558d86f5b0d3e7981ee51033a8">OBRMSDConformerScore::Score()</a>.</p>
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<a class="anchor" id="a44c3cb229020cd0d2270cb63b6251650"></a><!-- doxytag: member="OpenBabel::OBAlign::SetTarget" ref="a44c3cb229020cd0d2270cb63b6251650" args="(const vector< vector3 > &target)" -->
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<td class="memname">void SetTarget </td>
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<td class="paramtype">const vector< <a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> > & </td>
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<p>Set the Target (which will be aligned to the Reference) in terms of a vector of <a class="el" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> objects. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBRMSDConformerScore.shtml#af48ac6558d86f5b0d3e7981ee51033a8">OBRMSDConformerScore::Score()</a>.</p>
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<a class="anchor" id="ac56e2c2ffd9fdf7448b3bda78cdc9549"></a><!-- doxytag: member="OpenBabel::OBAlign::SetRefMol" ref="ac56e2c2ffd9fdf7448b3bda78cdc9549" args="(const OBMol &refmol)" -->
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<td class="memname">void SetRefMol </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> & </td>
<td class="paramname"><em>refmol</em></td><td>)</td>
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<p>Set the Reference Molecule (to which the Target Molecule must be aligned). Note that is faster to perform multiple alignments to the same Reference Molecule, rather than multple alignments to the same Target Molecule. </p>
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<a class="anchor" id="a2a325b0a2af5bbc3511c6f536e686e21"></a><!-- doxytag: member="OpenBabel::OBAlign::SetTargetMol" ref="a2a325b0a2af5bbc3511c6f536e686e21" args="(const OBMol &targetmol)" -->
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<td class="memname">void SetTargetMol </td>
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<td class="paramtype">const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> & </td>
<td class="paramname"><em>targetmol</em></td><td>)</td>
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<p>Set the Target Molecule (which will be aligned to the Reference Molecule). </p>
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<a class="anchor" id="a946a73d3de978fd930793711f23e00b3"></a><!-- doxytag: member="OpenBabel::OBAlign::Align" ref="a946a73d3de978fd930793711f23e00b3" args="()" -->
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<p>Align the Target to the Reference using a least-squares alignment. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBRMSDConformerScore.shtml#af48ac6558d86f5b0d3e7981ee51033a8">OBRMSDConformerScore::Score()</a>.</p>
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<a class="anchor" id="a060c746a125272a535ec8f6b59f5338a"></a><!-- doxytag: member="OpenBabel::OBAlign::GetRMSD" ref="a060c746a125272a535ec8f6b59f5338a" args="()" -->
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<p>Return the root mean squared deviation of the target from the reference. This function should only be called after running the alignment (using <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a946a73d3de978fd930793711f23e00b3">Align()</a>). </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBRMSDConformerScore.shtml#af48ac6558d86f5b0d3e7981ee51033a8">OBRMSDConformerScore::Score()</a>.</p>
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<a class="anchor" id="a53e6707da019dfa88df1e8c1aeeb6f67"></a><!-- doxytag: member="OpenBabel::OBAlign::GetRotMatrix" ref="a53e6707da019dfa88df1e8c1aeeb6f67" args="()" -->
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<td class="memname"><a class="el" href="classOpenBabel_1_1matrix3x3.shtml">matrix3x3</a> GetRotMatrix </td>
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<p>Return the rotation matrix associated with the least squares alignment. This function should only be called after running the alignment (using <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a946a73d3de978fd930793711f23e00b3">Align()</a>).</p>
<p>The following example shows how to use the rotation matrix to rotate all of the atoms in a molecule. </p>
<div class="fragment"><pre class="fragment"> matrix3x3 rotmatrix = align.GetRotMatrix();
<span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 1; i <= mol.<a class="code" href="classOpenBabel_1_1OBMol.shtml#a0c317a10161689c407f29a6fcacdb852">NumAtoms</a>(); ++i) {
vector3 tmpvec = mol.<a class="code" href="classOpenBabel_1_1OBMol.shtml#af2f78686dc35b7f79f44edc55b42d14a">GetAtom</a>(i)->GetVector();
tmpvec *= rotmatrix; <span class="comment">//apply the rotation</span>
mol.<a class="code" href="classOpenBabel_1_1OBMol.shtml#af2f78686dc35b7f79f44edc55b42d14a">GetAtom</a>(i)->SetVector(tmpvec);
}
</pre></div><p> Note that if you wish to use the rotation matrix to find the aligned coordinates (that is, the same coordinates returned by <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a6a9ca08185bebf3307c4a1acd31e58c3">GetAlignment()</a>), you should first translate the set of coordinates to the origin by subtracting the centroid, then apply the rotation, and finally add the centroid of the reference coordinates. </p>
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<a class="anchor" id="a6a9ca08185bebf3307c4a1acd31e58c3"></a><!-- doxytag: member="OpenBabel::OBAlign::GetAlignment" ref="a6a9ca08185bebf3307c4a1acd31e58c3" args="()" -->
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<td class="memname">vector< <a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> > GetAlignment </td>
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<p>Return the actual alignment of the Target to the Reference in terms of a vector of <a class="el" href="classOpenBabel_1_1vector3.shtml" title="Represents a vector in 3-dimensional real space.">vector3</a> objects. If you want an <a class="el" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> with the aligned coordinates, you should use <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a3748ab33ffd81acda5060963bdae971a">UpdateCoords()</a> instead. This function should only be called after running the alignment (using <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a946a73d3de978fd930793711f23e00b3">Align()</a>). </p>
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<a class="anchor" id="a3748ab33ffd81acda5060963bdae971a"></a><!-- doxytag: member="OpenBabel::OBAlign::UpdateCoords" ref="a3748ab33ffd81acda5060963bdae971a" args="(OBMol *target)" -->
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<td class="memname">bool UpdateCoords </td>
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<p>Set the coordinates of an <a class="el" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> to those from the alignment. This function should only be called after running the alignment (using <a class="el" href="classOpenBabel_1_1OBAlign.shtml#a946a73d3de978fd930793711f23e00b3">Align()</a>). </p>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="align_8h_source.shtml">align.h</a></li>
<li><a class="el" href="align_8cpp.shtml">align.cpp</a></li>
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