Author: bugman
Date: Mon Aug 6 13:28:05 2007
New Revision: 3352
URL: http://svn.gna.org/viewcvs/relax?rev=3352&view=rev
Log:
Application of Sebastien Morin's patch creating the N15_CSA and
NH_BOND_LENGTH constants.
For the patch, see the post at
https://mail.gna.org/public/relax-devel/2007-07/msg00060.html.
The patch 'patch__default_csa_r__l1.3_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. It also adds two
constants for the CSA and NH bond length default values.
Modified:
1.3/physical_constants.py
1.3/prompt/value.py
1.3/specific_fns/jw_mapping.py
1.3/test_suite/system_tests/jw_mapping.py
1.3/test_suite/system_tests/model_free.py
Modified: 1.3/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/physical_constants.py?rev=3352&r1=3351&r2=3352&view=diff
==============================================================================
--- 1.3/physical_constants.py (original)
+++ 1.3/physical_constants.py Mon Aug 6 13:28:05 2007
@@ -32,3 +32,10 @@
# The magnetic constant or the permeability of vacuum.
mu0 = 4.0 * pi * 1e-7
+
+# The 15N CSA in the NH bond (default value).
+N15_CSA = -172 * 1e-6
+
+# The length of the NH bond (default value).
+NH_BOND_LENGTH = 1.02 * 1e-10
+
Modified: 1.3/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/value.py?rev=3352&r1=3351&r2=3352&view=diff
==============================================================================
--- 1.3/prompt/value.py (original)
+++ 1.3/prompt/value.py Mon Aug 6 13:28:05 2007
@@ -345,10 +345,10 @@
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: 1.3/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=3352&r1=3351&r2=3352&view=diff
==============================================================================
--- 1.3/specific_fns/jw_mapping.py (original)
+++ 1.3/specific_fns/jw_mapping.py Mon Aug 6 13:28:05 2007
@@ -29,6 +29,7 @@
from base_class import Common_functions
from maths_fns.jw_mapping import Mapping
from relax_errors import RelaxError, RelaxFuncSetupError, RelaxNoRunError,
RelaxNoSequenceError, RelaxNoValueError, RelaxNucleusError
+from physical_constants import N15_CSA, NH_BOND_LENGTH
# The relax data storage object.
@@ -208,6 +209,7 @@
"""
Reduced spectral density mapping default values
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ These default values are found in the file 'physical_constants.py'.
_______________________________________________________________________________________
| | |
|
@@ -216,18 +218,18 @@
| | |
|
| Bond length | 'r' | 1.02 *
1e-10 |
| | |
|
- | CSA | 'csa' | -170 * 1e-6
|
+ | CSA | 'csa' | -172 * 1e-6
|
|_______________________________________|______________|______________________________|
"""
# Bond length.
if param == 'r':
- return 1.02 * 1e-10
+ return NH_BOND_LENGTH
# CSA.
if param == 'CSA':
- return -170 * 1e-6
+ return N15_CSA
def num_instances(self, run=None):
Modified: 1.3/test_suite/system_tests/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/jw_mapping.py?rev=3352&r1=3351&r2=3352&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/jw_mapping.py (original)
+++ 1.3/test_suite/system_tests/jw_mapping.py Mon Aug 6 13:28:05 2007
@@ -25,7 +25,7 @@
# relax module imports.
from data import Data as relax_data_store
-
+from physical_constants import N15_CSA, NH_BOND_LENGTH
# The relax data storage object.
@@ -76,8 +76,8 @@
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.
@@ -135,8 +135,8 @@
self.relax.interpreter._Nuclei.nuclei('N')
# 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, NH_BOND_LENGTH,
'bond_length')
+ self.relax.interpreter._Value.set(self.run, N15_CSA, 'csa')
# Select the frequency.
self.relax.interpreter._Jw_mapping.set_frq(self.run, frq=600.0 * 1e6)
@@ -155,8 +155,8 @@
self.relax.interpreter._Sequence.read(self.run, file='test_seq',
dir=sys.path[-1] + '/test_suite/system_tests/data')
# Try to set the values.
- bond_length = 1.02 * 1e-10
- csa = -170 * 1e-6
+ bond_length = NH_BOND_LENGTH
+ csa = N15_CSA
self.relax.interpreter._Value.set(self.run, bond_length,
'bond_length')
self.relax.interpreter._Value.set(self.run, csa, 'csa')
Modified: 1.3/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/model_free.py?rev=3352&r1=3351&r2=3352&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/model_free.py (original)
+++ 1.3/test_suite/system_tests/model_free.py Mon Aug 6 13:28:05 2007
@@ -26,6 +26,7 @@
# relax module imports.
from data import Data as relax_data_store
+from physical_constants import N15_CSA, NH_BOND_LENGTH
# The relax data storage object.
@@ -260,7 +261,7 @@
# 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, [N15_CSA,
NH_BOND_LENGTH], ['csa', 'bond_length'])
# Select the model.
self.relax.interpreter._Model_free.select_model(self.run, model='m4')
@@ -303,7 +304,7 @@
# 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, [N15_CSA,
NH_BOND_LENGTH], ['csa', 'bond_length'])
self.relax.interpreter._Value.set(self.run, [0.8, 50 * 1e-12, 0.0],
['S2', 'te', 'Rex'])
# Select the model.
@@ -342,7 +343,7 @@
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, [N15_CSA,
NH_BOND_LENGTH], ['csa', 'bond_length'])
# Select the model.
self.relax.interpreter._Model_free.select_model(self.run,
model='tm2')
@@ -930,7 +931,7 @@
# Setup other values.
self.relax.interpreter._Diffusion_tensor.init(self.run, 10e-9,
fixed=1)
- self.relax.interpreter._Value.set(self.run, 1.02 * 1e-10,
'bond_length')
+ self.relax.interpreter._Value.set(self.run, NH_BOND_LENGTH,
'bond_length')
self.relax.interpreter._Value.set(self.run, -160 * 1e-6, 'csa')
# Select the model-free model.
@@ -1198,10 +1199,10 @@
self.relax.interpreter._Sequence.read(self.run, file='noe.500.out',
dir=path)
# Set the CSA value.
- self.relax.interpreter._Value.set(self.run, 1.02 * 1e-10,
'bond_length')
+ self.relax.interpreter._Value.set(self.run, NH_BOND_LENGTH,
'bond_length')
# Test the value.
- if relax_data_store.res[self.run][1].r != 1.02 * 1e-10:
+ if relax_data_store.res[self.run][1].r != NH_BOND_LENGTH:
print "The bond length has not been set correctly."
return
@@ -1224,10 +1225,10 @@
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, N15_CSA, 'csa')
# Test the value.
- if relax_data_store.res[self.run][1].csa != -170*1e-6:
+ if relax_data_store.res[self.run][1].csa != N15_CSA:
print "The CSA value has not been set correctly."
return
@@ -1250,15 +1251,15 @@
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, [N15_CSA,
NH_BOND_LENGTH], ['csa', 'bond_length'])
# Test the CSA value.
- if relax_data_store.res[self.run][1].csa != -170*1e-6:
+ if relax_data_store.res[self.run][1].csa != N15_CSA:
print "The CSA value has not been set correctly."
return
# Test the bond length.
- if relax_data_store.res[self.run][1].r != 1.02 * 1e-10:
+ if relax_data_store.res[self.run][1].r != NH_BOND_LENGTH:
print "The bond length has not been set correctly."
return
r3352 - in /1.3: ./ prompt/ specific_fns/ test_suite/system_tests/