def persistence_length(self, start=1, end=None, return_guess=False):
"""
Calculates the persistence length (Lp) of given section of the model.
Persistence length is calculated according to [Bystricky2004]_ :
.. math::
<r^2> = 2 \\times Lp^2 \\times (\\frac{Lc}{Lp} - 1 + e^{\\frac{-Lc}{Lp}})
with the contour length as :math:`Lc = \\frac{d}{c}` where :math:`d` is
the genomic dstance in bp and :math:`c` the linear mass density of the
chromatin (in bp/nm).
:param 1 start: start particle from which to calculate the persistence
length
:param None end: end particle from which to calculate the persistence
length. Uses the last particle by default
:param False return_guess: Computes persistence length using the
approximation :math:`Lp=\\frac{Lc}{Lp}`
:returns: persistence length, or 2 times the Kuhn length
"""
clength = float(self.contour())
end = end or len(self)
sq_length = float(self._square_distance(start, end))
guess = sq_length / clength
if return_guess:
return guess # incredible!
kuhn = newton_raphson(guess, clength, sq_length)
return 2 * kuhn
def persistence_length(self, start=1, end=None, return_guess=False):
"""
Calculates the persistence length (Lp) of given section of the model.
Persistence length is calculated according to [Bystricky2004]_ :
.. math::
<r^2> = 2 \\times Lp^2 \\times (\\frac{Lc}{Lp} - 1 + e^{\\frac{-Lc}{Lp}})
with the contour length as :math:`Lc = \\frac{d}{c}` where :math:`d` is
the genomic dstance in bp and :math:`c` the linear mass density of the
chromatin (in bp/nm).
:param 1 start: start particle from which to calculate the persistence
length
:param None end: end particle from which to calculate the persistence
length. Uses the last particle by default
:param False return_guess: Computes persistence length using the
approximation :math:`Lp=\\frac{Lc}{Lp}`
:returns: persistence length, or 2 times the Kuhn length
"""
clength = float(self.contour())
end = end or len(self)
sq_length = float(self._square_distance(start, end))
guess = sq_length / clength
if return_guess:
return guess # incredible!
kuhn = newton_raphson(guess, clength, sq_length)
return 2 * kuhn