Author: bugman
Date: Tue Aug 27 12:27:06 2013
New Revision: 20696
URL: http://svn.gna.org/viewcvs/relax?rev=20696&view=rev
Log:
The TP02 model R1rho off-resonance test data creation script now creates
files of the R1 relaxation data.
These files are needed for the system tests, as R1 data needs to be read.
Added:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_500MHz.out
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_800MHz.out
Modified:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.log
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.py
Added:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_500MHz.out
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_500MHz.out?rev=20696&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_500MHz.out
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_500MHz.out
Tue Aug 27 12:27:06 2013
@@ -1,0 +1,3 @@
+# mol_name res_num res_name spin_num spin_name value
error
+None 1 Trp None N
1 0.1
+None 2 Lys None N
1.1 0.1
Added:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_800MHz.out
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_800MHz.out?rev=20696&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_800MHz.out
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1_800MHz.out
Tue Aug 27 12:27:06 2013
@@ -1,0 +1,3 @@
+# mol_name res_num res_name spin_num spin_name value
error
+None 1 Trp None N
1.2 0.1
+None 2 Lys None N
1.3 0.1
Modified:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.log
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.log?rev=20696&r1=20695&r2=20696&view=diff
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.log
(original)
+++
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.log
Tue Aug 27 12:27:06 2013
@@ -1,7 +1,7 @@
- relax repository checkout r20641
+ relax repository checkout r20695
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp
Molecular dynamics by NMR data analysis
@@ -40,7 +40,7 @@
from numpy import array, float64
# relax module imports.
-from lib.software.sparky import write_list
+from lib.spectrum.sparky import write_list
# Setup for 2 spin systems.
@@ -50,6 +50,7 @@
spin_lock_offset = 110.0 # The spin-lock frequency in ppm.
r1rho_prime = array([[10.0, 15.0], [12.0, 18.0]], float64) # The R1rho'
value per spin and per field.
r1 = array([[1.0, 1.2], [1.1, 1.3]], float64) # The R1 value per spin and
per field.
+r1_err = 0.1
pA = 0.7654321
kex = 1234.56789
delta_omega = array([7.0, 9.0], float64) # The chemical shift difference
in ppm.
@@ -73,6 +74,18 @@
frq = 2.0 * pi * frqs[frq_index]
dw = delta_omega * frq
omega_rf = spin_lock_offset * frq
+
+ # Set up the data for the R1 file.
+ label = 'R1_%s' % frq_label[frq_index]
+ pipe.create(label, 'mf')
+ cdp.ri_ids = ['r1']
+ for i in range(len(res_names)):
+ spin.create(res_name=res_names[i], res_num=res_nums[i],
spin_name=atom1_names[i])
+ cdp.mol[0].res[i].spin[0].ri_data = {}
+ cdp.mol[0].res[i].spin[0].ri_data_err = {}
+ cdp.mol[0].res[i].spin[0].ri_data['r1'] = r1[i, frq_index]
+ cdp.mol[0].res[i].spin[0].ri_data_err['r1'] = r1_err
+ relax_data.write(ri_id='r1', file='%s.out'%label, force=True)
# Frequency dependent parameters.
omega_a = w1 - 0.5*dw
@@ -103,10 +116,10 @@
# The rate.
nomen = pA * pB * dw[spin_index]**2 * kex
denom = omega_aeff2[spin_index] * omega_beff2[spin_index] /
omega_eff2[spin_index] + kex**2
- rx = r1[spin_index][frq_index] * cos_theta2 + sin_theta2 *
(r1rho_prime[spin_index][frq_index] + nomen / denom)
+ rx = r1[spin_index, frq_index] * cos_theta2 + sin_theta2 *
(r1rho_prime[spin_index, frq_index] + nomen / denom)
# The peak intensity.
- intensities.append(i0[spin_index][frq_index] *
exp(-rx*times[time_index]))
+ intensities.append(i0[spin_index, frq_index] *
exp(-rx*times[time_index]))
# Create a Sparky .list file.
if time_index == 0 and spin_lock_index == 0:
@@ -118,6 +131,15 @@
if name:
write_list(file_prefix=name, dir=None, res_names=res_names,
res_nums=res_nums, atom1_names=atom1_names, atom2_names=atom2_names, w1=w1,
w2=w2, data_height=intensities)
----------------------------------------------------------------------------------------------------
+
+relax> pipe.create(pipe_name='R1_500MHz', pipe_type='mf', bundle=None)
+
+relax> spin.create(spin_name='N', spin_num=None, res_name='Trp', res_num=1,
mol_name=None)
+
+relax> spin.create(spin_name='N', spin_num=None, res_name='Lys', res_num=2,
mol_name=None)
+
+relax> relax_data.write(ri_id='r1', file='R1_500MHz.out', dir=None,
bc=False, force=True)
+Opening the file 'R1_500MHz.out' for writing.
Creating the Sparky list file.
Opening the file 'ref_500MHz.list' for writing.
Creating the Sparky list file.
@@ -142,6 +164,15 @@
Opening the file 'nu_5500.0_500MHz.list' for writing.
Creating the Sparky list file.
Opening the file 'nu_6000.0_500MHz.list' for writing.
+
+relax> pipe.create(pipe_name='R1_800MHz', pipe_type='mf', bundle=None)
+
+relax> spin.create(spin_name='N', spin_num=None, res_name='Trp', res_num=1,
mol_name=None)
+
+relax> spin.create(spin_name='N', spin_num=None, res_name='Lys', res_num=2,
mol_name=None)
+
+relax> relax_data.write(ri_id='r1', file='R1_800MHz.out', dir=None,
bc=False, force=True)
+Opening the file 'R1_800MHz.out' for writing.
Creating the Sparky list file.
Opening the file 'ref_800MHz.list' for writing.
Creating the Sparky list file.
Modified:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.py?rev=20696&r1=20695&r2=20696&view=diff
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.py
(original)
+++
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/generate.py
Tue Aug 27 12:27:06 2013
@@ -18,7 +18,7 @@
from numpy import array, float64
# relax module imports.
-from lib.software.sparky import write_list
+from lib.spectrum.sparky import write_list
# Setup for 2 spin systems.
@@ -28,6 +28,7 @@
spin_lock_offset = 110.0 # The spin-lock frequency in ppm.
r1rho_prime = array([[10.0, 15.0], [12.0, 18.0]], float64) # The R1rho'
value per spin and per field.
r1 = array([[1.0, 1.2], [1.1, 1.3]], float64) # The R1 value per spin and
per field.
+r1_err = 0.1
pA = 0.7654321
kex = 1234.56789
delta_omega = array([7.0, 9.0], float64) # The chemical shift difference
in ppm.
@@ -51,6 +52,18 @@
frq = 2.0 * pi * frqs[frq_index]
dw = delta_omega * frq
omega_rf = spin_lock_offset * frq
+
+ # Set up the data for the R1 file.
+ label = 'R1_%s' % frq_label[frq_index]
+ pipe.create(label, 'mf')
+ cdp.ri_ids = ['r1']
+ for i in range(len(res_names)):
+ spin.create(res_name=res_names[i], res_num=res_nums[i],
spin_name=atom1_names[i])
+ cdp.mol[0].res[i].spin[0].ri_data = {}
+ cdp.mol[0].res[i].spin[0].ri_data_err = {}
+ cdp.mol[0].res[i].spin[0].ri_data['r1'] = r1[i, frq_index]
+ cdp.mol[0].res[i].spin[0].ri_data_err['r1'] = r1_err
+ relax_data.write(ri_id='r1', file='%s.out'%label, force=True)
# Frequency dependent parameters.
omega_a = w1 - 0.5*dw
@@ -81,10 +94,10 @@
# The rate.
nomen = pA * pB * dw[spin_index]**2 * kex
denom = omega_aeff2[spin_index] * omega_beff2[spin_index] /
omega_eff2[spin_index] + kex**2
- rx = r1[spin_index][frq_index] * cos_theta2 + sin_theta2 *
(r1rho_prime[spin_index][frq_index] + nomen / denom)
+ rx = r1[spin_index, frq_index] * cos_theta2 + sin_theta2 *
(r1rho_prime[spin_index, frq_index] + nomen / denom)
# The peak intensity.
- intensities.append(i0[spin_index][frq_index] *
exp(-rx*times[time_index]))
+ intensities.append(i0[spin_index, frq_index] *
exp(-rx*times[time_index]))
# Create a Sparky .list file.
if time_index == 0 and spin_lock_index == 0:
r20696 - /branches/relax_disp/test_suite/shared_data/dispersion/r1rho_off_res_tp02/