def show_linearNCPR(self, blobLen=5, getFig=False):
"""
Generates a plot of how the NCPR (net charge per residue) 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:
--------------------------------------------------------------------------------
bloblen | Set the windowsize (DEFAULT = 5)
getFig | Do you want to get the matplotlib figure object (DEFAULY = FALSE)
OUTPUT:
--------------------------------------------------------------------------------
Nothing, but the plot is displayed on screen
"""
return plotting.show_linearplot(
plotting.build_NCPR_plot, self.SeqObj, blobLen, getFig)
def show_linearHydropathy(self, blobLen=5, getFig=False):
"""
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:
--------------------------------------------------------------------------------
bloblen | Set the windowsize (DEFAULT = 5)
getFig | Do you want to get the matplotlib figure object (DEFAULY = FALSE)
OUTPUT:
--------------------------------------------------------------------------------
Nothing, but the plot is displayed on screen
"""
return plotting.show_linearplot(
plotting.build_hydropathy_plot, self.SeqObj, blobLen, getFig)
def show_linearSigma(self, blobLen=5, getFig=False):
"""
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:
--------------------------------------------------------------------------------
bloblen | Set the windowsize (DEFAULT = 5)
getFig | Do you want to get the matplotlib figure object (DEFAULY = FALSE)
OUTPUT:
--------------------------------------------------------------------------------
Nothing, but the plot is displayed on screen
"""
return plotting.show_linearplot(
plotting.build_sigma_plot, self.SeqObj, blobLen, getFig)
