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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 2acccabecdaec7349b7ed52e909eca3c
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tags: 645f666f9bcd5a90fca523b33c5a78b7
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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Expand All @@ -8,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />

<title>MDAnalysis.analysis.align &mdash; MDAnalysis 0.11.0-dev documentation</title>
<title>MDAnalysis.analysis.align &mdash; MDAnalysis 0.11.0 documentation</title>

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Expand All @@ -27,14 +25,14 @@
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<h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
<span class="c"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
Expand Down Expand Up @@ -146,15 +143,15 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>

<span class="sd"> &gt;&gt;&gt; ref = Universe(PDB_small)</span>
<span class="sd"> &gt;&gt;&gt; mobile = Universe(PSF,DCD)</span>
<span class="sd"> &gt;&gt;&gt; rmsd(mobile.atoms.CA.coordinates(), ref.atoms.CA.coordinates())</span>
<span class="sd"> &gt;&gt;&gt; rmsd(mobile.atoms.CA.positions, ref.atoms.CA.positions)</span>
<span class="sd"> 18.858259026820352</span>

<span class="sd">Note that in this example translations have not been removed. In order</span>
<span class="sd">to look at the pure rotation one needs to superimpose the centres of</span>
<span class="sd">mass (or geometry) first:</span>

<span class="sd"> &gt;&gt;&gt; ref0 = ref.atoms.CA.coordinates() - ref.atoms.CA.centerOfMass()</span>
<span class="sd"> &gt;&gt;&gt; mobile0 = mobile.atoms.CA.coordinates() - mobile.atoms.CA.centerOfMass()</span>
<span class="sd"> &gt;&gt;&gt; ref0 = ref.atoms.CA.positions - ref.atoms.CA.center_of_mass()</span>
<span class="sd"> &gt;&gt;&gt; mobile0 = mobile.atoms.CA.positions - mobile.atoms.CA.center_of_mass()</span>
<span class="sd"> &gt;&gt;&gt; rmsd(mobile0, ref0)</span>
<span class="sd"> 6.8093965864717951</span>

Expand All @@ -172,9 +169,9 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>

<span class="sd">Putting all this together one can superimpose all of *mobile* onto *ref*::</span>

<span class="sd"> &gt;&gt;&gt; mobile.atoms.translate(-mobile.atoms.CA.centerOfMass())</span>
<span class="sd"> &gt;&gt;&gt; mobile.atoms.translate(-mobile.atoms.CA.center_of_mass())</span>
<span class="sd"> &gt;&gt;&gt; mobile.atoms.rotate(R)</span>
<span class="sd"> &gt;&gt;&gt; mobile.atoms.translate(ref.atoms.CA.centerOfMass())</span>
<span class="sd"> &gt;&gt;&gt; mobile.atoms.translate(ref.atoms.CA.center_of_mass())</span>
<span class="sd"> &gt;&gt;&gt; mobile.atoms.write(&quot;mobile_on_ref.pdb&quot;)</span>


Expand All @@ -183,9 +180,9 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>

<span class="sd">To **fit a single structure** with :func:`alignto`::</span>

<span class="sd"> &gt;&gt;&gt; ref = Universe(PSF, PDB_small)</span>
<span class="sd"> &gt;&gt;&gt; mobile = Universe(PSF, DCD) # we use the first frame</span>
<span class="sd"> &gt;&gt;&gt; alignto(mobile, ref, select=&quot;protein and name CA&quot;, mass_weighted=True)</span>
<span class="sd"> &gt;&gt;&gt; ref = Universe(PSF, PDB_small)</span>
<span class="sd"> &gt;&gt;&gt; mobile = Universe(PSF, DCD) # we use the first frame</span>
<span class="sd"> &gt;&gt;&gt; alignto(mobile, ref, select=&quot;protein and name CA&quot;, mass_weighted=True)</span>

<span class="sd">This will change *all* coordinates in *mobile* so that the protein</span>
<span class="sd">C-alpha atoms are optimally superimposed (translation and rotation).</span>
Expand Down Expand Up @@ -402,12 +399,12 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>

<span class="k">if</span> <span class="n">mass_weighted</span><span class="p">:</span>
<span class="n">weights</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">masses</span> <span class="o">/</span> <span class="n">numpy</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">ref_atoms</span><span class="o">.</span><span class="n">masses</span><span class="p">)</span>
<span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span>
<span class="n">mobile_com</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span>
<span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span>
<span class="n">mobile_com</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">weights</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
<span class="n">mobile_com</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">centerOfGeometry</span><span class="p">()</span>
<span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>
<span class="n">mobile_com</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">center_of_geometry</span><span class="p">()</span>

<span class="n">ref_coordinates</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">ref_com</span>
<span class="n">mobile_coordinates</span> <span class="o">=</span> <span class="n">mobile_atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">mobile_com</span>
Expand Down Expand Up @@ -547,7 +544,7 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>

<span class="c"># reference centre of mass system</span>
<span class="c"># (compatibility with pre 1.0 numpy: explicitly cast coords to float32)</span>
<span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
<span class="n">ref_com</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
<span class="n">ref_coordinates</span> <span class="o">=</span> <span class="n">ref_atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">ref_com</span>

<span class="c"># allocate the array for selection atom coords</span>
Expand All @@ -569,7 +566,7 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">ts</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">frames</span><span class="p">):</span>
<span class="c"># shift coordinates for rotation fitting</span>
<span class="c"># selection is updated with the time frame</span>
<span class="n">x_com</span> <span class="o">=</span> <span class="n">traj_atoms</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
<span class="n">x_com</span> <span class="o">=</span> <span class="n">traj_atoms</span><span class="o">.</span><span class="n">center_of_mass</span><span class="p">()</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
<span class="n">traj_coordinates</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">traj_atoms</span><span class="o">.</span><span class="n">coordinates</span><span class="p">()</span> <span class="o">-</span> <span class="n">x_com</span>

<span class="c"># Need to transpose coordinates such that the coordinate array is</span>
Expand Down Expand Up @@ -1015,7 +1012,7 @@ <h1>Source code for MDAnalysis.analysis.align</h1><div class="highlight"><pre>
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