Author: bugman
Date: Thu Aug 7 16:40:36 2008
New Revision: 7082
URL: http://svn.gna.org/viewcvs/relax?rev=7082&view=rev
Log:
Modified the func_population() target function to handle both RDCs and PCSs.
Modified:
branches/rdc_analysis/maths_fns/n_state_model.py
Modified: branches/rdc_analysis/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/maths_fns/n_state_model.py?rev=7082&r1=7081&r2=7082&view=diff
==============================================================================
--- branches/rdc_analysis/maths_fns/n_state_model.py (original)
+++ branches/rdc_analysis/maths_fns/n_state_model.py Thu Aug 7 16:40:36 2008
@@ -302,7 +302,7 @@
The chi-squared equation
------------------------
- The equation is::
+ The equations are::
___
\ (Dij - Dij(theta)) ** 2
@@ -310,11 +310,21 @@
/__ sigma_ij ** 2
ij
+ ___
+ \ (delta_ij - delta_ij(theta)) ** 2
+ chi^2(theta) = > --------------------------------- ,
+ /__ sigma_ij ** 2
+ ij
+
where:
- theta is the parameter vector,
- - Dij are the measured RDCs,
- - Dij(theta) are the back calculated RDCs,
- - sigma_ij are the RDC errors.
+ - Dij are the measured RDCs for alignment i, spin j,
+ - Dij(theta) are the back calculated RDCs for alignment i, spin
j,
+ - delta_ij are the measured PCSs for alignment i, spin j,
+ - delta_ij(theta) are the back calculated PCSs for alignment i,
spin j,
+ - sigma_ij are the RDC or PCS errors.
+
+ Both chi-squared values sum.
The RDC equation
@@ -330,6 +340,7 @@
where:
- dj is the dipolar constant for spin j,
+ - N is the total number of states or structures,
- pc is the weight or probability associated with state c,
- mu_jc is the unit vector corresponding to spin j and state c,
- Ai is the alignment tensor.
@@ -352,6 +363,38 @@
- r is the distance between the two spins.
+ The PCS equation
+ ----------------
+
+ The PCS equation is::
+
+ _N_
+ \ T
+ delta_ij(theta) = > pc . djc . mu_jc . Ai . mu_jc,
+ /__
+ c=1
+
+ where:
+ - djc is the PCS constant for spin j and state c,
+ - N is the total number of states or structures,
+ - pc is the weight or probability associated with state c,
+ - mu_jc is the unit vector corresponding to spin j and state c,
+ - Ai is the alignment tensor.
+
+ The PCS constant is defined as::
+
+ mu0 15kT 1
+ dj = --- ----- ---- ,
+ 4pi Bo**2 r**3
+
+ where:
+ - mu0 is the permeability of free space,
+ - k is Boltzmann's constant,
+ - T is the absolute temperature,
+ - Bo is the magnetic field strength,
+ - r is the distance between the paramagnetic centre (electron
spin) and the nuclear spin.
+
+
Stored data structures
======================
@@ -363,6 +406,11 @@
----------
The back calculated RDCs. This is a rank-2 tensor with indices {i,
j}.
+
+ delta_ij(theta)
+ ---------------
+
+ The back calculated PCS. This is a rank-2 tensor with indices {i,
j}.
Ai
--
@@ -393,15 +441,31 @@
# Loop over the spin systems j.
for j in xrange(self.num_spins):
- # Calculate the average RDC.
- self.Dij_theta[i, j] = ave_rdc_tensor(self.dip_const[j],
self.mu[j], self.N, self.A[i], weights=self.probs)
-
- # Replace missing data with the back calculated value (to
give a zero chi-squared for the missing element).
- if self.missing_Dij[i, j]:
- self.Dij[i, j] = self.Dij_theta[i, j]
-
- # Calculate and sum the single alignment chi-squared value.
- chi2_sum = chi2_sum + chi2(self.Dij[i], self.Dij_theta[i],
self.rdc_sigma_ij[i])
+ # The back calculated RDC.
+ if self.rdc_flag:
+ # Calculate the average RDC.
+ self.Dij_theta[i, j] = ave_rdc_tensor(self.dip_const[j],
self.mu[j], self.N, self.A[i], weights=self.probs)
+
+ # Replace missing data with the back calculated value
(to give a zero chi-squared for the missing element).
+ if self.missing_Dij[i, j]:
+ self.Dij[i, j] = self.Dij_theta[i, j]
+
+ # The back calculated PCS.
+ if self.pcs_flag:
+ # Calculate the average PCS.
+ self.deltaij_theta[i, j] =
ave_pcs_tensor(self.pcs_const[j], self.mu[j], self.N, self.A[i],
weights=self.probs)
+
+ # Replace missing data with the back calculated value
(to give a zero chi-squared for the missing element).
+ if self.missing_deltaij[i, j]:
+ self.deltaij[i, j] = self.deltaij_theta[i, j]
+
+ # Calculate and sum the single alignment chi-squared value (for
the RDC).
+ if self.rdc_flag:
+ chi2_sum = chi2_sum + chi2(self.Dij[i], self.Dij_theta[i],
self.rdc_sigma_ij[i])
+
+ # Calculate and sum the single alignment chi-squared value (for
the PCS).
+ if self.pcs_flag:
+ chi2_sum = chi2_sum + chi2(self.deltaij[i],
self.deltaij_theta[i], self.pcs_sigma_ij[i])
# Return the chi-squared value.
return chi2_sum
r7082 - /branches/rdc_analysis/maths_fns/n_state_model.py