コード例 #1
0
    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)
コード例 #2
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    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)
コード例 #3
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    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)