Author: bugman
Date: Thu Mar 5 09:53:37 2009
New Revision: 8903
URL: http://svn.gna.org/viewcvs/relax?rev=8903&view=rev
Log:
Merged revisions 8900-8902 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8900 | bugman | 2009-03-04 15:33:51 +0100 (Wed, 04 Mar 2009) | 6 lines
Changed the way the Q-factor is calculated.
The Q-factor is now calculated as Clore's R-factor divided by N. This now
matches the Pales default
mode.
........
r8901 | bugman | 2009-03-04 15:37:49 +0100 (Wed, 04 Mar 2009) | 3 lines
Both Q-factors are now being calculated.
........
r8902 | bugman | 2009-03-04 17:17:28 +0100 (Wed, 04 Mar 2009) | 3 lines
Changed the Q-factors tested in the system tests.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/specific_fns/n_state_model.py
branches/bmrb/test_suite/system_tests/n_state_model.py
Propchange: branches/bmrb/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Mar 5 09:53:37 2009
@@ -1,1 +1,1 @@
-/1.3:1-8898
+/1.3:1-8902
Modified: branches/bmrb/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/n_state_model.py?rev=8903&r1=8902&r2=8903&view=diff
==============================================================================
--- branches/bmrb/specific_fns/n_state_model.py (original)
+++ branches/bmrb/specific_fns/n_state_model.py Thu Mar 5 09:53:37 2009
@@ -730,6 +730,7 @@
# Q-factor list.
cdp.q_factors_rdc = []
+ cdp.q_factors_rdc_norm2 = []
# Loop over the alignments.
for i in xrange(len(cdp.align_tensors)):
@@ -738,6 +739,8 @@
sse = 0.0
# Spin loop.
+ dj = None
+ N = 0
for spin in spin_loop():
# Skip deselected spins.
if not spin.select:
@@ -750,19 +753,44 @@
# Sum of squares.
sse = sse + (spin.rdc[i] - spin.rdc_bc[i])**2
- # Sum the RDCs squared (for normalisation).
+ # Sum the RDCs squared (for one type of normalisation).
D2_sum = D2_sum + spin.rdc[i]**2
+ # Gyromagnetic ratios.
+ gx = return_gyromagnetic_ratio(spin.heteronuc_type)
+ gh = return_gyromagnetic_ratio(spin.proton_type)
+
+ # Calculate the RDC dipolar constant (in Hertz, and the 3
comes from the alignment tensor), and append it to the list.
+ dj_new = 3.0/(2.0*pi) * dipolar_constant(gx, gh, spin.r)
+ if dj and dj_new != dj:
+ raise RelaxError, "All the RDCs must come from the same
nucleus type."
+ else:
+ dj = dj_new
+
+ # Increment the number of data sets.
+ N = N + 1
+
+ # Normalisation factor of 2Da^2(4 + 3R)/5.
+ D = dj * cdp.align_tensors[i].tensor_diag
+ Da = 1.0/3.0 * (D[2,2] - (D[0,0]+D[1,1])/2.0)
+ Dr = 1.0/3.0 * (D[0,0] - D[1,1])
+ R = Dr / Da
+ norm = 2.0 * (Da)**2 * (4.0 + 3.0*R**2)/5.0
+
# The Q-factor for the alignment.
- Q = sqrt(sse / D2_sum)
+ Q = sqrt(sse / N / norm)
cdp.q_factors_rdc.append(Q)
+ cdp.q_factors_rdc_norm2.append(sqrt(sse / D2_sum))
# The total Q-factor.
cdp.q_rdc = 0.0
+ cdp.q_rdc_norm2 = 0.0
for Q in cdp.q_factors_rdc:
cdp.q_rdc = cdp.q_rdc + Q**2
- cdp.q_rdc = cdp.q_rdc / len(cdp.q_factors_rdc)
- cdp.q_rdc = sqrt(cdp.q_rdc)
+ for Q in cdp.q_factors_rdc_norm2:
+ cdp.q_rdc_norm2 = cdp.q_rdc_norm2 + Q**2
+ cdp.q_rdc = sqrt(cdp.q_rdc / len(cdp.q_factors_rdc))
+ cdp.q_rdc_norm2 = sqrt(cdp.q_rdc_norm2 /
len(cdp.q_factors_rdc_norm2))
def __q_factors_pcs(self):
Modified: branches/bmrb/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/n_state_model.py?rev=8903&r1=8902&r2=8903&view=diff
==============================================================================
--- branches/bmrb/test_suite/system_tests/n_state_model.py (original)
+++ branches/bmrb/test_suite/system_tests/n_state_model.py Thu Mar 5
09:53:37 2009
@@ -131,7 +131,7 @@
self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.000152207413184)
self.assertAlmostEqual(cdp.chi2, 783.530808266)
self.assertAlmostEqual(cdp.q_pcs, 0.063345784112045375)
- self.assertAlmostEqual(cdp.q_rdc, 0.15076645625705937)
+ self.assertAlmostEqual(cdp.q_rdc, 0.084926009099013003)
def test_align_fit_pcs(self):
@@ -227,7 +227,7 @@
self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.00029833)
self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.00015125)
self.assertAlmostEqual(cdp.chi2, 23.5877482365) #
Pales: 23.709
- self.assertAlmostEqual(cdp.q_rdc, 0.14049691097282743/2.) #
Pales (Q Saupe): 0.079
+ self.assertAlmostEqual(cdp.q_rdc, 0.078460000413257444) #
Pales (Q Saupe): 0.079
def test_lactose_n_state(self):
r8903 - in /branches/bmrb: ./ specific_fns/n_state_model.py test_suite/system_tests/n_state_model.py