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<a href="Bio-module.html">Package Bio</a> ::
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Module ResidueDepth'
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<h1 class="epydoc">Module ResidueDepth'</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Calculation of residue depth using command line tool MSMS.
This module uses Michel Sanner's MSMS program for the surface calculation
(specifically commands msms and pdb_to_xyzr). See:
http://mgltools.scripps.edu/packages/MSMS
Residue depth is the average distance of the atoms of a residue from
the solvent accessible surface.
Residue Depth:
>>> rd = ResidueDepth(model, pdb_file)
>>> print rd[(chain_id, res_id)]
Direct MSMS interface:
Typical use:
>>> surface = get_surface("1FAT.pdb")
Surface is a Numeric array with all the surface
vertices.
Distance to surface:
>>> dist = min_dist(coord, surface)
where coord is the coord of an atom within the volume
bound by the surface (ie. atom depth).
To calculate the residue depth (average atom depth
of the atoms in a residue):
>>> rd = residue_depth(residue, surface)
</pre>
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<a href="Bio.PDB.ResidueDepth%27.ResidueDepth-class.html" class="summary-name">ResidueDepth</a><br />
Calculate residue and CA depth for all residues.
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<td><span class="summary-sig"><a name="_read_vertex_array"></a><span class="summary-sig-name">_read_vertex_array</span>(<span class="summary-sig-arg">filename</span>)</span><br />
Read the vertex list into a Numeric array.</td>
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<td><span class="summary-sig"><a name="ca_depth"></a><span class="summary-sig-name">ca_depth</span>(<span class="summary-sig-arg">residue</span>,
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<td><span class="summary-sig"><a href="Bio.PDB.ResidueDepth%27-module.html#get_surface" class="summary-sig-name">get_surface</a>(<span class="summary-sig-arg">pdb_file</span>,
<span class="summary-sig-arg">PDB_TO_XYZR</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">pdb_to_xyzr</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">MSMS</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">msms</code><code class="variable-quote">'</code></span>)</span><br />
Return a Numeric array that represents the vertex list of the
molecular surface.</td>
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<td><span class="summary-sig"><a name="min_dist"></a><span class="summary-sig-name">min_dist</span>(<span class="summary-sig-arg">coord</span>,
<span class="summary-sig-arg">surface</span>)</span><br />
Return minimum distance between coord and surface.</td>
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<td><span class="summary-sig"><a href="Bio.PDB.ResidueDepth%27-module.html#residue_depth" class="summary-sig-name">residue_depth</a>(<span class="summary-sig-arg">residue</span>,
<span class="summary-sig-arg">surface</span>)</span><br />
Return average distance to surface for all atoms in a residue, ie.</td>
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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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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_surface</span>(<span class="sig-arg">pdb_file</span>,
<span class="sig-arg">PDB_TO_XYZR</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">pdb_to_xyzr</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">MSMS</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">msms</code><code class="variable-quote">'</code></span>)</span>
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<p>Return a Numeric array that represents the vertex list of the
molecular surface.</p>
<p>PDB_TO_XYZR --- pdb_to_xyzr executable (arg. to os.system) MSMS ---
msms executable (arg. to os.system)</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">residue_depth</span>(<span class="sig-arg">residue</span>,
<span class="sig-arg">surface</span>)</span>
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><span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html#residue_depth">source code</a></span>
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<p>Return average distance to surface for all atoms in a residue, ie. the
residue depth.</p>
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