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<a href="Bio-module.html">Package Bio</a> ::
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Module Vector'
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module Vector'</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html">source code</a></span></p>
<p>Vector class, including rotation-related functions.</p>
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<span class="summary-type"> </span>
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<a href="Bio.PDB.Vector%27.Vector-class.html" class="summary-name">Vector</a><br />
3D vector
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<td><span class="summary-sig"><a href="Bio.PDB.Vector%27-module.html#calc_angle" class="summary-sig-name">calc_angle</a>(<span class="summary-sig-arg">v1</span>,
<span class="summary-sig-arg">v2</span>,
<span class="summary-sig-arg">v3</span>)</span><br />
Calculate the angle between 3 vectors representing 3 connected
points.</td>
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<span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#calc_angle">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.Vector%27-module.html#calc_dihedral" class="summary-sig-name">calc_dihedral</a>(<span class="summary-sig-arg">v1</span>,
<span class="summary-sig-arg">v2</span>,
<span class="summary-sig-arg">v3</span>,
<span class="summary-sig-arg">v4</span>)</span><br />
Calculate the dihedral angle between 4 vectors representing 4
connected points.</td>
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<span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#calc_dihedral">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="m2rotaxis"></a><span class="summary-sig-name">m2rotaxis</span>(<span class="summary-sig-arg">m</span>)</span><br />
Return angles, axis pair that corresponds to rotation matrix m.</td>
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<span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#m2rotaxis">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.Vector%27-module.html#refmat" class="summary-sig-name">refmat</a>(<span class="summary-sig-arg">p</span>,
<span class="summary-sig-arg">q</span>)</span><br />
Return a (left multiplying) matrix that mirrors p onto q.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#refmat">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.Vector%27-module.html#rotaxis" class="summary-sig-name">rotaxis</a>(<span class="summary-sig-arg">theta</span>,
<span class="summary-sig-arg">vector</span>)</span><br />
Calculate a left multiplying rotation matrix that rotates theta rad
around vector.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#rotaxis">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.Vector%27-module.html#rotaxis2m" class="summary-sig-name">rotaxis2m</a>(<span class="summary-sig-arg">theta</span>,
<span class="summary-sig-arg">vector</span>)</span><br />
Calculate a left multiplying rotation matrix that rotates theta rad
around vector.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#rotaxis">source code</a></span>
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<span class="summary-type">3x3 Numeric array</span>
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<td><span class="summary-sig"><a href="Bio.PDB.Vector%27-module.html#rotmat" class="summary-sig-name">rotmat</a>(<span class="summary-sig-arg">p</span>,
<span class="summary-sig-arg">q</span>)</span><br />
Return a (left multiplying) matrix that rotates p onto q.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#rotmat">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.Vector%27-module.html#vector_to_axis" class="summary-sig-name">vector_to_axis</a>(<span class="summary-sig-arg">line</span>,
<span class="summary-sig-arg">point</span>)</span><br />
Returns the vector between a point and the closest point on a line
(ie.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#vector_to_axis">source code</a></span>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.PDB'"><code class="variable-quote">'</code><code class="variable-string">Bio.PDB</code><code class="variable-quote">'</code></code>
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<a name="calc_angle"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">calc_angle</span>(<span class="sig-arg">v1</span>,
<span class="sig-arg">v2</span>,
<span class="sig-arg">v3</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#calc_angle">source code</a></span>
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<p>Calculate the angle between 3 vectors representing 3 connected
points.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>v1</code></strong>, <strong class="pname"><code>v2</code></strong>, <strong class="pname"><code>v3</code></strong> - the tree points that define the angle</li>
</ul></dd>
<dt>Returns: float</dt>
<dd>angle</dd>
</dl>
</td></tr></table>
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<a name="calc_dihedral"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">calc_dihedral</span>(<span class="sig-arg">v1</span>,
<span class="sig-arg">v2</span>,
<span class="sig-arg">v3</span>,
<span class="sig-arg">v4</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#calc_dihedral">source code</a></span>
</td>
</tr></table>
<p>Calculate the dihedral angle between 4 vectors representing 4
connected points. The angle is in ]-pi, pi].</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>v1</code></strong>, <strong class="pname"><code>v2</code></strong>, <strong class="pname"><code>v3</code></strong>, <strong class="pname"><code>v4</code></strong> - the four points that define the dihedral angle</li>
</ul></dd>
</dl>
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<a name="refmat"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">refmat</span>(<span class="sig-arg">p</span>,
<span class="sig-arg">q</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#refmat">source code</a></span>
</td>
</tr></table>
<p>Return a (left multiplying) matrix that mirrors p onto q.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>mirror=refmat(p,q)
<span class="py-prompt">>>> </span>qq=p.left_multiply(mirror)
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> q, qq <span class="py-comment"># q and qq should be the same</span></pre>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>p,q</code></strong> (<a href="Bio.PDB.Vector%27.Vector-class.html"
class="link">Vector</a>)</li>
</ul></dd>
<dt>Returns:</dt>
<dd>The mirror operation, a 3x3 Numeric array.</dd>
</dl>
</td></tr></table>
</div>
<a name="rotaxis"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">rotaxis</span>(<span class="sig-arg">theta</span>,
<span class="sig-arg">vector</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#rotaxis">source code</a></span>
</td>
</tr></table>
<p>Calculate a left multiplying rotation matrix that rotates theta rad
around vector.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>m=rotaxis(pi, Vector(1,0,0))
<span class="py-prompt">>>> </span>rotated_vector=any_vector.left_multiply(m)</pre>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>theta</code></strong> (float) - the rotation angle</li>
<li><strong class="pname"><code>vector</code></strong> (<a href="Bio.PDB.Vector%27.Vector-class.html"
class="link">Vector</a>) - the rotation axis</li>
</ul></dd>
<dt>Returns:</dt>
<dd>The rotation matrix, a 3x3 Numeric array.</dd>
</dl>
</td></tr></table>
</div>
<a name="rotaxis2m"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">rotaxis2m</span>(<span class="sig-arg">theta</span>,
<span class="sig-arg">vector</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#rotaxis">source code</a></span>
</td>
</tr></table>
<p>Calculate a left multiplying rotation matrix that rotates theta rad
around vector.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>m=rotaxis(pi, Vector(1,0,0))
<span class="py-prompt">>>> </span>rotated_vector=any_vector.left_multiply(m)</pre>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>theta</code></strong> (float) - the rotation angle</li>
<li><strong class="pname"><code>vector</code></strong> (<a href="Bio.PDB.Vector%27.Vector-class.html"
class="link">Vector</a>) - the rotation axis</li>
</ul></dd>
<dt>Returns:</dt>
<dd>The rotation matrix, a 3x3 Numeric array.</dd>
</dl>
</td></tr></table>
</div>
<a name="rotmat"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">rotmat</span>(<span class="sig-arg">p</span>,
<span class="sig-arg">q</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#rotmat">source code</a></span>
</td>
</tr></table>
<p>Return a (left multiplying) matrix that rotates p onto q.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>r=rotmat(p,q)
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> q, p.left_multiply(r)</pre>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>p</code></strong> (<a href="Bio.PDB.Vector%27.Vector-class.html"
class="link">Vector</a>) - moving vector</li>
<li><strong class="pname"><code>q</code></strong> (<a href="Bio.PDB.Vector%27.Vector-class.html"
class="link">Vector</a>) - fixed vector</li>
</ul></dd>
<dt>Returns: 3x3 Numeric array</dt>
<dd>rotation matrix that rotates p onto q</dd>
</dl>
</td></tr></table>
</div>
<a name="vector_to_axis"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">vector_to_axis</span>(<span class="sig-arg">line</span>,
<span class="sig-arg">point</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#vector_to_axis">source code</a></span>
</td>
</tr></table>
<p>Returns the vector between a point and the closest point on a line
(ie. the perpendicular projection of the point on the line).</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>line</code></strong> (<a href="Bio.PDB.Vector%27.Vector-class.html"
class="link">Vector</a>) - vector defining a line</li>
<li><strong class="pname"><code>point</code></strong> (<a href="Bio.PDB.Vector%27.Vector-class.html"
class="link">Vector</a>) - vector defining the point</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
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