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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqUtils-module.html">Package SeqUtils</a> ::
<a href="Bio.SeqUtils.ProtParam-module.html">Module ProtParam</a> ::
Class ProteinAnalysis
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class ProteinAnalysis</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis">source code</a></span></p>
<p>This class contains methods for protein analysis. The class init
method takes only one argument, the protein sequence as a string and
build a sequence object using the Bio.Seq module. This is done just to
make sure the sequence is a protein sequence and not anything else.</p>
<p>methods:</p>
<p>count_amino_acids:</p>
<p>Simply counts the number times an amino acid is repeated in the
protein sequence. Returns a dictionary {AminoAcid:Number} and also stores
the dictionary in self.amino_acids_content.</p>
<p>get_amino_acids_percent:</p>
<p>The same as count_amino_acids only returns the Number in percentage of
entire sequence. Returns a dictionary and stores the dictionary in
self.amino_acids_content_percent.</p>
<p>molecular_weight: Calculates the molecular weight of a protein.</p>
<p>aromaticity:</p>
<p>Calculates the aromaticity value of a protein according to Lobry,
1994. It is simply the relative frequency of Phe+Trp+Tyr.</p>
<p>instability_index:</p>
<p>Implementation of the method of Guruprasad et al. (Protein Engineering
4:155-161,1990). This method tests a protein for stability. Any value
above 40 means the protein is unstable (=has a short half life).</p>
<p>flexibility: Implementation of the flexibility method of Vihinen et
al. (Proteins. 1994 Jun;19(2):141-9).</p>
<p>isoelectric_point: This method uses the module IsoelectricPoint to
calculate the pI of a protein.</p>
<p>secondary_structure_fraction: This methods returns a list of the
fraction of amino acids which tend to be in Helix, Turn or Sheet. Amino
acids in helix: V, I, Y, F, W, L. Amino acids in Turn: N, P, G, S. Amino
acids in sheet: E, M, A, L. The list contains 3 values: [Helix, Turn,
Sheet].</p>
<p>protein_scale(Scale, WindwonSize, Edge):</p>
<p>An amino acid scale is defined by a numerical value assigned to each
type of amino acid. The most frequently used scales are the
hydrophobicity or hydrophilicity scales and the secondary structure
conformational parameters scales, but many other scales exist which are
based on different chemical and physical properties of the amino acids.
You can set several parameters that control the computation of a scale
profile, such as the window size and the window edge relative weight
value. WindowSize: The window size is the length of the interval to use
for the profile computation. For a window size n, we use the i- ( n-1)/2
neighboring residues on each side of residue it compute the score for
residue i. The score for residue is the sum of the scale values for
these amino acids, optionally weighted according to their position in
the window. Edge: The central amino acid of the window always has a
weight of 1. By default, the amino acids at the remaining window
positions have the same weight, but you can make the residue at the
center of the window have a larger weight than the others by setting the
edge value for the residues at the beginning and end of the interval to
a value between 0 and 1. For instance, for Edge=0.4 and a window size of
5 the weights will be: 0.4, 0.7, 1.0, 0.7, 0.4. The method returns a
list of values which can be plotted to view the change along a protein
sequence. Many scales exist. Just add your favorites to the
ProtParamData modules.</p>
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
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<td><span class="summary-sig"><a name="count_amino_acids"></a><span class="summary-sig-name">count_amino_acids</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a name="get_amino_acids_percent"></a><span class="summary-sig-name">get_amino_acids_percent</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a name="molecular_weight"></a><span class="summary-sig-name">molecular_weight</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a name="aromaticity"></a><span class="summary-sig-name">aromaticity</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a name="instability_index"></a><span class="summary-sig-name">instability_index</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a name="flexibility"></a><span class="summary-sig-name">flexibility</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a name="_weight_list"></a><span class="summary-sig-name">_weight_list</span>(<span class="summary-sig-arg">self</span>,
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<span class="summary-sig-arg">edge</span>)</span></td>
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<td><span class="summary-sig"><a name="protein_scale"></a><span class="summary-sig-name">protein_scale</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">ParamDict</span>,
<span class="summary-sig-arg">Window</span>,
<span class="summary-sig-arg">Edge</span>=<span class="summary-sig-default">1.0</span>)</span></td>
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<td><span class="summary-sig"><a name="isoelectric_point"></a><span class="summary-sig-name">isoelectric_point</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a name="secondary_structure_fraction"></a><span class="summary-sig-name">secondary_structure_fraction</span>(<span class="summary-sig-arg">self</span>)</span></td>
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