Author: bugman
Date: Mon Aug 6 13:36:02 2007
New Revision: 3354
URL: http://svn.gna.org/viewcvs/relax?rev=3354&view=rev
Log:
Application of Sebastien Morin's patch to convert all default CSA values to
-172 ppm.
For the patch, see the post at
https://mail.gna.org/public/relax-devel/2007-07/msg00060.html.
The patch 'patch__default_csa__l1.2_r3351' makes uniform the use of the CSA
value (now -172 ppm
everywhere) and fixes the test-suite (in jw_mapping) to account for this
change.
Modified:
1.2/prompt/value.py
1.2/specific_fns/jw_mapping.py
1.2/specific_fns/model_free.py
1.2/test_suite/jw_mapping.py
1.2/test_suite/model_free.py
Modified: 1.2/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/value.py?rev=3354&r1=3353&r2=3354&view=diff
==============================================================================
--- 1.2/prompt/value.py (original)
+++ 1.2/prompt/value.py Mon Aug 6 13:36:02 2007
@@ -343,10 +343,10 @@
To set the CSA value of all residues in the reduced spectral density
mapping run '600MHz' to
- -170 ppm, type:
-
- relax> value.set('600MHz', -170 * 1e-6, 'csa')
- relax> value.set('600MHz', value=-170 * 1e-6, param='csa')
+ -172 ppm, type:
+
+ relax> value.set('600MHz', -172 * 1e-6, 'csa')
+ relax> value.set('600MHz', value=-172 * 1e-6, param='csa')
To set the NH bond length of all residues in the model-free run 'm5'
to 1.02 Angstroms,
Modified: 1.2/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/jw_mapping.py?rev=3354&r1=3353&r2=3354&view=diff
==============================================================================
--- 1.2/specific_fns/jw_mapping.py (original)
+++ 1.2/specific_fns/jw_mapping.py Mon Aug 6 13:36:02 2007
@@ -209,7 +209,7 @@
| | |
|
| Bond length | 'r' | 1.02 *
1e-10 |
| | |
|
- | CSA | 'csa' | -170 * 1e-6
|
+ | CSA | 'csa' | -172 * 1e-6
|
|_______________________________________|______________|______________________________|
"""
@@ -220,7 +220,7 @@
# CSA.
if param == 'CSA':
- return -170 * 1e-6
+ return -172 * 1e-6
def num_instances(self, run=None):
Modified: 1.2/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=3354&r1=3353&r2=3354&view=diff
==============================================================================
--- 1.2/specific_fns/model_free.py (original)
+++ 1.2/specific_fns/model_free.py Mon Aug 6 13:36:02 2007
@@ -925,7 +925,7 @@
| | |
|
| Bond length | 'r' | 1.02
* 1e-10 |
| | |
|
- | CSA | 'csa' | -170
* 1e-6 |
+ | CSA | 'csa' | -172
* 1e-6 |
|_______________________________________|____________________|________________________|
"""
@@ -960,7 +960,7 @@
# CSA.
elif param == 'CSA':
- return -170 * 1e-6
+ return -172 * 1e-6
def delete(self, run):
Modified: 1.2/test_suite/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/jw_mapping.py?rev=3354&r1=3353&r2=3354&view=diff
==============================================================================
--- 1.2/test_suite/jw_mapping.py (original)
+++ 1.2/test_suite/jw_mapping.py Mon Aug 6 13:36:02 2007
@@ -67,8 +67,8 @@
def calc_integrity(self):
# Correct jw values:
- j0 = [4.0958793960056238e-09, 3.7976266046729745e-09]
- jwx = [1.85720953886864e-10, 1.6450121628270092e-10]
+ j0 = [4.0703318681008998e-09, 3.7739393907014834e-09]
+ jwx = [1.8456254300773903e-10, 1.6347516082378241e-10]
jwh = [1.5598167512718012e-12, 2.9480536599037041e-12]
# Loop over residues.
@@ -127,7 +127,7 @@
# Set r and csa.
self.relax.interpreter._Value.set(self.run, 1.02 * 1e-10,
'bond_length')
- self.relax.interpreter._Value.set(self.run, -170 * 1e-6, 'csa')
+ self.relax.interpreter._Value.set(self.run, -172 * 1e-6, 'csa')
# Select the frequency.
self.relax.interpreter._Jw_mapping.set_frq(self.run, frq=600.0 * 1e6)
@@ -147,7 +147,7 @@
# Try to set the values.
bond_length = 1.02 * 1e-10
- csa = -170 * 1e-6
+ csa = -172 * 1e-6
self.relax.interpreter._Value.set(self.run, bond_length,
'bond_length')
self.relax.interpreter._Value.set(self.run, csa, 'csa')
Modified: 1.2/test_suite/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/model_free.py?rev=3354&r1=3353&r2=3354&view=diff
==============================================================================
--- 1.2/test_suite/model_free.py (original)
+++ 1.2/test_suite/model_free.py Mon Aug 6 13:36:02 2007
@@ -251,7 +251,7 @@
# Setup other values.
self.relax.interpreter._Diffusion_tensor.init(self.run, 1e-8,
fixed=1)
- self.relax.interpreter._Value.set(self.run, [-170 * 1e-6, 1.02 *
1e-10], ['csa', 'bond_length'])
+ self.relax.interpreter._Value.set(self.run, [-172 * 1e-6, 1.02 *
1e-10], ['csa', 'bond_length'])
# Select the model.
self.relax.interpreter._Model_free.select_model(self.run, model='m4')
@@ -293,7 +293,7 @@
# Setup other values.
self.relax.interpreter._Diffusion_tensor.init(self.run, (1.601 *
1e7, 1.34, 72.4, 90-77.9), param_types=4)
- self.relax.interpreter._Value.set(self.run, [-170 * 1e-6, 1.02 *
1e-10], ['csa', 'bond_length'])
+ self.relax.interpreter._Value.set(self.run, [-172 * 1e-6, 1.02 *
1e-10], ['csa', 'bond_length'])
self.relax.interpreter._Value.set(self.run, [0.8, 50 * 1e-12, 0.0],
['S2', 'te', 'Rex'])
# Select the model.
@@ -332,7 +332,7 @@
self.relax.interpreter._Relax_data.read(self.run, 'NOE', '500',
500.0 * 1e6, 'noe.500.out', dir=path)
# Setup other values.
- self.relax.interpreter._Value.set(self.run, [-170 * 1e-6, 1.02 *
1e-10], ['csa', 'bond_length'])
+ self.relax.interpreter._Value.set(self.run, [-172 * 1e-6, 1.02 *
1e-10], ['csa', 'bond_length'])
# Select the model.
self.relax.interpreter._Model_free.select_model(self.run,
model='tm2')
@@ -1214,10 +1214,10 @@
self.relax.interpreter._Sequence.read(self.run, file='noe.500.out',
dir=path)
# Set the CSA value.
- self.relax.interpreter._Value.set(self.run, -170 * 1e-6, 'csa')
+ self.relax.interpreter._Value.set(self.run, -172 * 1e-6, 'csa')
# Test the value.
- if self.relax.data.res[self.run][1].csa != -170*1e-6:
+ if self.relax.data.res[self.run][1].csa != -172*1e-6:
print "The CSA value has not been set correctly."
return
@@ -1240,10 +1240,10 @@
self.relax.interpreter._Sequence.read(self.run, file='noe.500.out',
dir=path)
# Set the CSA value and bond length simultaneously.
- self.relax.interpreter._Value.set(self.run, [-170 * 1e-6, 1.02 *
1e-10], ['csa', 'bond_length'])
+ self.relax.interpreter._Value.set(self.run, [-172 * 1e-6, 1.02 *
1e-10], ['csa', 'bond_length'])
# Test the CSA value.
- if self.relax.data.res[self.run][1].csa != -170*1e-6:
+ if self.relax.data.res[self.run][1].csa != -172*1e-6:
print "The CSA value has not been set correctly."
return
r3354 - in /1.2: prompt/ specific_fns/ test_suite/