Author: semor
Date: Tue Dec 18 22:18:29 2007
New Revision: 4214
URL: http://svn.gna.org/viewcvs/relax?rev=4214&view=rev
Log:
Synced the file specific_fns/consistency_tests.py from the file
specific_fns/jw_mapping.py.
This file was first created as a copy of the file specific_fns/jw_mapping.py
but was never updated.
Now, the two files are identical. It will thus be easier to modify this new
version which
incorporates many aspects of the 1.3 line redesign.
Modified:
branches/consistency_tests_1.3/specific_fns/consistency_tests.py
Modified: branches/consistency_tests_1.3/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/consistency_tests.py?rev=4214&r1=4213&r2=4214&view=diff
==============================================================================
--- branches/consistency_tests_1.3/specific_fns/consistency_tests.py
(original)
+++ branches/consistency_tests_1.3/specific_fns/consistency_tests.py Tue Dec
18 22:18:29 2007
@@ -28,17 +28,13 @@
from data import Data as relax_data_store
from base_class import Common_functions
from maths_fns.jw_mapping import Mapping
-from relax_errors import RelaxError, RelaxFuncSetupError, RelaxNoRunError,
RelaxNoSequenceError, RelaxNoValueError, RelaxNucleusError
-
-
-# The relax data storage object.
+from relax_errors import RelaxError, RelaxFuncSetupError, RelaxNoPipeError,
RelaxNoSequenceError, RelaxNoValueError, RelaxNucleusError
+from physical_constants import N15_CSA, NH_BOND_LENGTH
class Jw_mapping(Common_functions):
- def __init__(self, relax):
+ def __init__(self):
"""Class containing functions specific to reduced spectral density
mapping."""
-
- self.relax = relax
def calculate(self, run=None, print_flag=1, sim_index=None):
@@ -208,6 +204,7 @@
"""
Reduced spectral density mapping default values
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ These default values are found in the file 'physical_constants.py'.
_______________________________________________________________________________________
| | |
|
@@ -216,18 +213,18 @@
| | |
|
| 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):
@@ -253,7 +250,7 @@
# Loop over residue data:
for residue in relax_data_store.res[run]:
-
+
# Check for sufficient data
if not hasattr(residue, 'relax_data'):
residue.select = 0
@@ -395,7 +392,7 @@
value.append(self.default_value('r'))
# Initilise data.
- if not hasattr(relax_data_store.res[self.run][index], 'csa') or
not hasattr(relax_data_store.res[self.run][index], 'csa'):
+ if not hasattr(relax_data_store.res[self.run][index], 'csa') or
not hasattr(relax_data_store.res[self.run][index], 'r'):
self.data_init(relax_data_store.res[self.run][index])
# CSA and Bond length.
@@ -436,7 +433,7 @@
# Test if the run exists.
if not self.run in relax_data_store.run_names:
- raise RelaxNoRunError, self.run
+ raise RelaxNoPipeError, self.run
# Test if the run type is set to 'jw'.
function_type =
relax_data_store.run_types[relax_data_store.run_names.index(self.run)]
@@ -585,7 +582,7 @@
# Test if the run exists.
if not self.run in relax_data_store.run_names:
- raise RelaxNoRunError, self.run
+ raise RelaxNoPipeError, self.run
# Test if sequence data is loaded.
if not relax_data_store.res.has_key(self.run):
@@ -663,16 +660,18 @@
ri_error = []
if hasattr(relax_data_store, 'num_ri'):
for i in xrange(relax_data_store.num_ri[self.run]):
- # Find the residue specific data corresponding to i.
- index = None
- for j in xrange(data.num_ri):
- if data.ri_labels[j] ==
relax_data_store.ri_labels[self.run][i] and
data.frq_labels[data.remap_table[j]] ==
relax_data_store.frq_labels[self.run][relax_data_store.remap_table[self.run][i]]:
- index = j
-
- # Data exists for this data type.
try:
+ # Find the residue specific data corresponding to i.
+ index = None
+ for j in xrange(data.num_ri):
+ if data.ri_labels[j] ==
relax_data_store.ri_labels[self.run][i] and
data.frq_labels[data.remap_table[j]] ==
relax_data_store.frq_labels[self.run][relax_data_store.remap_table[self.run][i]]:
+ index = j
+
+ # Data exists for this data type.
ri.append(`data.relax_data[index]`)
ri_error.append(`data.relax_error[index]`)
+
+ # No data exists for this data type.
except:
ri.append(None)
ri_error.append(None)
@@ -769,20 +768,23 @@
# Relaxation data and errors.
ri = []
ri_error = []
- for k in xrange(relax_data_store.num_ri[self.run]):
- # Find the residue specific data corresponding to k.
- index = None
- for l in xrange(data.num_ri):
- if data.ri_labels[l] ==
relax_data_store.ri_labels[self.run][k] and
data.frq_labels[data.remap_table[l]] ==
relax_data_store.frq_labels[self.run][relax_data_store.remap_table[self.run][k]]:
- index = l
-
- # Data exists for this data type.
- try:
- ri.append(`data.relax_sim_data[i][index]`)
- ri_error.append(`data.relax_error[index]`)
- except:
- ri.append(None)
- ri_error.append(None)
+ if hasattr(self.relax.data, 'num_ri'):
+ for k in xrange(relax_data_store.num_ri[self.run]):
+ try:
+ # Find the residue specific data corresponding
to k.
+ index = None
+ for l in xrange(data.num_ri):
+ if data.ri_labels[l] ==
relax_data_store.ri_labels[self.run][k] and
data.frq_labels[data.remap_table[l]] ==
relax_data_store.frq_labels[self.run][relax_data_store.remap_table[self.run][k]]:
+ index = l
+
+ # Data exists for this data type.
+ ri.append(`data.relax_sim_data[i][index]`)
+ ri_error.append(`data.relax_error[index]`)
+
+ # No data exists for this data type.
+ except:
+ ri.append(None)
+ ri_error.append(None)
# Write the line.
self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='sim_'+`i`, nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
r4214 - /branches/consistency_tests_1.3/specific_fns/consistency_tests.py