def save_linearSigma(self, filename, blobLen=5):
"""
Generates a plot of how the Sigma parameter changes as we move
along the linear amino acid sequence in blobLen size steps. This uses a sliding window
approach and calculates the average within that window.
Recall that sigma is defined as
NCPR^2/FCR (net charge per residue squared divided by the fraction of charged residues)
INPUT:
--------------------------------------------------------------------------------
filename | Name of the file to write
bloblen | Set the windowsize (DEFAULT = 5)
OUTPUT:
--------------------------------------------------------------------------------
Nothing, but creates a .png file at the filename location
"""
plotting.save_linearplot(
plotting.build_sigma_plot,
self.SeqObj,
blobLen,
filename)
def save_linearHydropathy(self, filename, blobLen=5):
"""
Generates a plot of how the mean hydropathy changes as we move
along the linear amino acid sequence in blobLen size steps. This uses a sliding window
approach and calculates the average within that window.
Hydropathy here is calculated using a NORMALIZED Kyte-Doolittle scale, where 1 is
the most hydrophobic and 0 the least.
INPUT:
--------------------------------------------------------------------------------
filename | Name of the file to write
bloblen | Set the windowsize (DEFAULT = 5)
OUTPUT:
--------------------------------------------------------------------------------
Nothing, but creates a .png file at the filename location
"""
plotting.save_linearplot(
plotting.build_hydropathy_plot,
self.SeqObj,
blobLen,
filename)
def save_linearFCR(self, filename, blobLen=5):
"""
Generates a plot of how the FCR (fraction of charged residues) changes as we move
along the linear amino acid sequence in blobLen size steps. This uses a sliding window
approach and calculates the average within that window.
INPUT:
--------------------------------------------------------------------------------
filename | Name of the file to write
bloblen | Set the windowsize (DEFAULT = 5)
OUTPUT:
--------------------------------------------------------------------------------
Nothing, but creates a .png file at the filename location
"""
plotting.save_linearplot(
plotting.build_FCR_plot,
self.SeqObj,
blobLen,
filename)
