コード例 #1
0
ファイル: macro_base.py プロジェクト: pombredanne/relax
    def classic_order_param(self, res_num, s2, colour_start, colour_end, colour_list):
        """Function for generating the bond width and colours for order parameters."""

        # The bond width (aiming for a width range of 2 to 0 for S2 values of 0.0 to 1.0).
        if s2 <= 0.0:
            width = 2.0
        else:
            width = 2.0 * (1.0 - s2**2)

        # Catch invalid widths.
        if width <= 0.0:
            width = 0.001

        # Colour value (quartic).
        colour_value = s2 ** 4

        # Catch invalid colours.
        if colour_value < 0.0:
            colour_value = 0.0
        elif colour_value > 1.0:
            colour_value = 1.0

        # Default colours.
        if colour_start == None:
            colour_start = 'red'
        if colour_end == None:
            colour_end = 'yellow'

        # Get the RGB colour array.
        rgb_array = linear_gradient(colour_value, colour_start, colour_end, colour_list)

        # Colour the peptide bond.
        self.classic_colour(res_num, width, rgb_array)
コード例 #2
0
ファイル: macro_base.py プロジェクト: pombredanne/relax
    def classic_correlation_time(self, res_num, te, colour_start, colour_end, colour_list):
        """Function for generating the bond width and colours for correlation times."""

        # The te value in picoseconds.
        te = te * 1e12

        # The bond width (aiming for a width range of 2 to 0 for te values of 0 to 10 ns).
        width = 2.0 - 200.0 / (te + 100.0)

        # Catch invalid widths.
        if width <= 0.0:
            width = 0.001

        # Colour value (hyperbolic).
        colour_value = 1.0 / (te / 100.0 + 1.0)

        # Catch invalid colours.
        if colour_value < 0.0:
            colour_value = 0.0
        elif colour_value > 1.0:
            colour_value = 1.0

        # Default colours.
        if colour_start == None:
            colour_start = 'turquoise'
        if colour_end == None:
            colour_end = 'blue'

        # Get the RGB colour array (swap the colours because of the inverted hyperbolic colour value).
        rgb_array = linear_gradient(colour_value, colour_end, colour_start, colour_list)

        # Colour the peptide bond.
        self.classic_colour(res_num, width, rgb_array)
コード例 #3
0
ファイル: macro_base.py プロジェクト: pombredanne/relax
    def classic_rex(self, res_num, rex, colour_start, colour_end, colour_list):
        """Function for generating the bond width and colours for correlation times."""

        # The 1st spectrometer frequency.
        if not hasattr(cdp, 'spectrometer_frq'):
            raise RelaxError("No spectrometer frequency information is present in the current data pipe.")
        if hasattr(cdp, 'ri_ids'):
            frq = cdp.spectrometer_frq[cdp.ri_ids[0]]
        else:       # Take the highest frequency, if all else fails.
            frqs = sorted(cdp.spectrometer_frq.values())
            frq = frqs[-1]

        # The Rex value.
        rex = rex * (2.0 * pi * frq)**2

        # The bond width (aiming for a width range of 2 to 0 for Rex values of 0 to 25 s^-1).
        width = 2.0 - 2.0 / (rex/5.0 + 1.0)

        # Catch invalid widths.
        if width <= 0.0:
            width = 0.001

        # Colour value (hyperbolic).
        colour_value = 1.0 / (rex + 1.0)

        # Catch invalid colours.
        if colour_value < 0.0:
            colour_value = 0.0
        elif colour_value > 1.0:
            colour_value = 1.0

        # Default colours.
        if colour_start == None:
            colour_start = 'yellow'
        if colour_end == None:
            colour_end = 'red'

        # Get the RGB colour array (swap the colours because of the inverted hyperbolic colour value).
        rgb_array = linear_gradient(colour_value, colour_end, colour_start, colour_list)

        # Colour the peptide bond.
        self.classic_colour(res_num, width, rgb_array)