gjankowiak/tsa_saxs
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

comments

Browse source
This commit is contained in:
Gaspard Jankowiak 2024-03-05 11:13:14 +01:00
parent 7ac1b17832
commit 807d1d1a64
1 changed files with 23 additions and 6 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

29
Minimization/PLUV.py
View file

@ -119,11 +119,13 @@ def water_volume(T) :
######################################################### #########################################################
#@njit(parallel=True) #@njit(parallel=True)
def FTreal_erf(q, mu, d, sig) : def FTreal_erf(q, mu, d, sig) :
""" FTreal_erf(q, mu, d, sig) """
return np.where(q==0, 1, np.sin(q*d/2.)/(q*d/2.) * np.exp(-(q*sig)**2/2.) * np.cos(q*mu) ) return np.where(q==0, 1, np.sin(q*d/2.)/(q*d/2.) * np.exp(-(q*sig)**2/2.) * np.cos(q*mu) )
######################################################### #########################################################
#@njit(parallel=True) #@njit(parallel=True)
def FTreal_gauss(q, mu, sig) : def FTreal_gauss(q, mu, sig) :
""" FTreal_gauss(q, mu, sig) """
return np.exp(-(q*sig)**2/2.) * np.cos(q*mu) return np.exp(-(q*sig)**2/2.) * np.cos(q*mu)
######################################################### #########################################################
@ -275,11 +277,23 @@ class SDP_POPC_RecBuf:
self.T, self.V_BW, self.T, self.V_BW,
self.Con] = PAR self.Con] = PAR
# [Example 1], fixed parameters:
# Norm 1e5 # Normalization
# n_TR 0.0 # Tris fraction
# d_TR 1.0 # Tris width (nm)
# s_TR 0.29 # Tris position (nm)
# d_CH 0.90 # CH position (nm)
# s_CH 0.305 # CH width (nm)
# r12 0.81 # V_CH/V_CH2
# T 37 # Temperature (°C)
# [example 1] fixed
Cw = CONST_p0_Cw + CONST_p1_Cw*self.T + CONST_p2_Cw*self.T**2 + CONST_p3_Cw*self.T**3 Cw = CONST_p0_Cw + CONST_p1_Cw*self.T + CONST_p2_Cw*self.T**2 + CONST_p3_Cw*self.T**3
xtris = CONST_ctris / Cw # mole fraction of free TRIS in bulk xtris = CONST_ctris / Cw # mole fraction of free TRIS in bulk
xEDTA = CONST_cEDTA / Cw # mole fraction of free EDTA in bulk xEDTA = CONST_cEDTA / Cw # mole fraction of free EDTA in bulk
# Volumes # Volumes
# [example 1] fixed
self.V_L = lipid_volume(self.T) self.V_L = lipid_volume(self.T)
V_HW = water_volume(self.T) V_HW = water_volume(self.T)
V_HC = self.V_L - ( (1-CONST_x_PG) * CONST_V_HL_PC + CONST_x_PG * CONST_V_HL_PG ) V_HC = self.V_L - ( (1-CONST_x_PG) * CONST_V_HL_PC + CONST_x_PG * CONST_V_HL_PG )
@ -288,6 +302,7 @@ class SDP_POPC_RecBuf:
self.D_C = V_HC / self.A_L self.D_C = V_HC / self.A_L
# Quasi-molecular volumes # Quasi-molecular volumes
# [example 1] r12 fixed
V_CH2 = V_HC / ( CONST_n_CH2 + CONST_n_CH*self.r12 + CONST_n_CH3*self.r32 ) # Volume of CH2 groups V_CH2 = V_HC / ( CONST_n_CH2 + CONST_n_CH*self.r12 + CONST_n_CH3*self.r32 ) # Volume of CH2 groups
V_CH = V_CH2 * self.r12 # Volume of CH groups V_CH = V_CH2 * self.r12 # Volume of CH groups
V_CH3 = V_CH2 * self.r32 # Volume of CH3 groups V_CH3 = V_CH2 * self.r32 # Volume of CH3 groups
@ -296,13 +311,15 @@ class SDP_POPC_RecBuf:
self.V_PCN = CONST_V_HL_PC * self.r_PCN # Volume of PCN group self.V_PCN = CONST_V_HL_PC * self.r_PCN # Volume of PCN group
self.V_Chol = CONST_V_HL_PC * (1-self.r_PCN-self.r_CG) # Volume of CholCH3 group self.V_Chol = CONST_V_HL_PC * (1-self.r_PCN-self.r_CG) # Volume of CholCH3 group
V_PG1 = CONST_V_HL_PG * 0.16 # Kucerka 2012 # CONST
V_PG2 = CONST_V_HL_PG * ( 1 - 0.51 - 0.16) # Kucerka 2012 CONST_V_PG1 = CONST_V_HL_PG * 0.16 # Kucerka 2012
CONST_V_PG2 = CONST_V_HL_PG * ( 1 - 0.51 - 0.16) # Kucerka 2012
############### X-ray scattering lengths (nm) ############### X-ray scattering lengths (nm)
# [example 1] rho_sol fixed
rho_sol = ( CONST_b_HW + xtris*CONST_b_tris + xEDTA*CONST_b_EDTA ) / V_HW rho_sol = ( CONST_b_HW + xtris*CONST_b_tris + xEDTA*CONST_b_EDTA ) / V_HW
drho_Chol = ( (1-CONST_x_PG)*CONST_b_Chol/self.V_Chol + CONST_x_PG*CONST_b_PG2/V_PG2 ) - rho_sol drho_Chol = ( (1-CONST_x_PG)*CONST_b_Chol/self.V_Chol + CONST_x_PG*CONST_b_PG2/CONST_V_PG2 ) - rho_sol
drho_PCN = ( (1-CONST_x_PG)*CONST_b_PCN/self.V_PCN + CONST_x_PG*CONST_b_PG1/V_PG1 ) - rho_sol drho_PCN = ( (1-CONST_x_PG)*CONST_b_PCN/self.V_PCN + CONST_x_PG*CONST_b_PG1/CONST_V_PG1 ) - rho_sol
drho_CG = CONST_b_CG / self.V_CG - rho_sol drho_CG = CONST_b_CG / self.V_CG - rho_sol
drho_TR = CONST_b_tris/ CONST_V_tris - rho_sol drho_TR = CONST_b_tris/ CONST_V_tris - rho_sol
drho_CH = CONST_b_CH / V_CH - rho_sol drho_CH = CONST_b_CH / V_CH - rho_sol
@ -321,8 +338,8 @@ class SDP_POPC_RecBuf:
c_CH3 = np.zeros(HC_array.shape[0],dtype=float) c_CH3 = np.zeros(HC_array.shape[0],dtype=float)
############### c-prefactors ############### c-prefactors
c_Chol = ( (1-CONST_x_PG)*self.V_Chol + CONST_x_PG*V_PG2 ) / self.A_L c_Chol = ( (1-CONST_x_PG)*self.V_Chol + CONST_x_PG*CONST_V_PG2 ) / self.A_L
c_PCN = ( (1-CONST_x_PG)*self.V_PCN + CONST_x_PG*V_PG1 ) / self.A_L c_PCN = ( (1-CONST_x_PG)*self.V_PCN + CONST_x_PG*CONST_V_PG1 ) / self.A_L
c_CG = self.V_CG / self.A_L c_CG = self.V_CG / self.A_L
c_TR = CONST_V_tris*self.n_TR / self.A_L c_TR = CONST_V_tris*self.n_TR / self.A_L