Class ProteinAnalysis

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__

(inherited documentation)

Count standard amino acids, returns a dict.
    
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.

Calculate the amino acid content in percents.

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.

input is the dictionary from CountAA.
output is a dictionary with AA as keys.

Calculate the aromaticity according to Lobry, 1994.

Calculates the aromaticity value of a protein according to Lobry, 1994.
It is simply the relative frequency of Phe+Trp+Tyr.

Calculate the instability index according to Guruprasad et al 1990.

Implementation of the method of Guruprasad et al. 1990 to test a
protein for stability. Any value above 40 means the protein is unstable
(has a short half life). 

See: Guruprasad K., Reddy B.V.B., Pandit M.W.
Protein Engineering 4:155-161(1990).

Calculate the flexibility according to Vihinen, 1994.

No argument to change window size because parameters are specific for a
window=9. The parameters used are optimized for determining the flexibility.

Compute a profile by any amino acid scale.

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.

Similar to expasy's ProtScale: http://www.expasy.org/cgi-bin/protscale.pl

Calculate the isoelectric point.

This method uses the module IsoelectricPoint to calculate the pI of a protein.

Calculate fraction of helix, turn and sheet.

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.

Returns a tuple of three integers (Helix, Turn, Sheet).