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)
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)
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)