Author: bugman
Date: Mon Jan 7 16:28:13 2008
New Revision: 4434
URL: http://svn.gna.org/viewcvs/relax?rev=4434&view=rev
Log:
Merged revisions 4430-4433 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r4430 | bugman | 2008-01-07 15:52:55 +0100 (Mon, 07 Jan 2008) | 5 lines
Bug fix for the read() and test_labels() methods of the
specific_fns.relax_data.Rx_data class.
The arguments are not placed into self!
........
r4431 | bugman | 2008-01-07 15:58:52 +0100 (Mon, 07 Jan 2008) | 5 lines
Many fixes for the specific_fns.relax_data.find_index() function.
This function now fits into the new relax design.
........
r4432 | bugman | 2008-01-07 16:01:23 +0100 (Mon, 07 Jan 2008) | 3 lines
Bug fix. Updated all the calls to self.find_index().
........
r4433 | bugman | 2008-01-07 16:06:07 +0100 (Mon, 07 Jan 2008) | 6 lines
Bug fix for the J(w) mapping system tests trying to set the nucleus type.
The call to self.relax.interpreter._Nuclei.nuclei() has been replaced with
a call to
self.relax.interpreter._Value.set().
........
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/specific_fns/relax_data.py
branches/N_state_model/test_suite/system_tests/jw_mapping.py
Propchange: branches/N_state_model/
------------------------------------------------------------------------------
Binary property 'svnmerge-integrated' - no diff available.
Modified: branches/N_state_model/specific_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/relax_data.py?rev=4434&r1=4433&r2=4434&view=diff
==============================================================================
--- branches/N_state_model/specific_fns/relax_data.py (original)
+++ branches/N_state_model/specific_fns/relax_data.py Mon Jan 7 16:28:13 2008
@@ -284,8 +284,8 @@
data1 = relax_data_store.res[run1][i]
data2 = relax_data_store.res[run2][i]
- # Find the index corresponding to 'self.ri_label' and
'self.frq_label'.
- index = self.find_index(data1)
+ # Find the index corresponding to 'ri_label' and 'frq_label'.
+ index = self.find_index(data1, ri_label, frq_label)
# Catch any problems.
if index == None:
@@ -414,8 +414,8 @@
# Global data flag.
self.global_flag = 0
- # Find the index corresponding to 'self.ri_label' and
'self.frq_label'.
- index = self.find_index(data)
+ # Find the index corresponding to 'ri_label' and 'frq_label'.
+ index = self.find_index(data, ri_label, frq_label)
# Catch any problems.
if index == None:
@@ -480,29 +480,31 @@
self.relax.generic.value.write_data(self.run, (self.ri_label,
self.frq_label), sys.stdout, return_value=self.return_value)
- def find_index(self, data):
- """Function for finding the index corresponding to self.ri_label and
self.frq_label."""
+ def find_index(self, data, ri_label, frq_label):
+ """Function for finding the index corresponding to ri_label and
frq_label.
+
+ @param data: The class instance containing the ri_label and
frq_label variables.
+ @type data: PipeContainer or SpinContainer
+ @param ri_label: The relaxation data type, ie 'R1', 'R2', or
'NOE'.
+ @type ri_label: str
+ @param frq_label: The field strength label.
+ @type frq_label: str
+ @return: The index corresponding to the relaxation data.
If there is no
+ relaxation data corresponding to the labels,
None is returned.
+ @type return: None or int
+ """
# No data.num_ri data structure.
- if self.global_flag == 1:
- if not data.num_ri.has_key(self.relax):
- return None
- else:
- if not hasattr(data, 'num_ri'):
- return None
+ if not hasattr(data, 'num_ri'):
+ return None
# Initialise.
index = None
# Find the index.
- if self.global_flag == 1:
- for j in xrange(data.num_ri[self.run]):
- if self.ri_label == data.ri_labels[self.run][j] and
self.frq_label == data.frq_labels[self.run][data.remap_table[self.run][j]]:
- index = j
- else:
- for j in xrange(data.num_ri):
- if self.ri_label == data.ri_labels[j] and self.frq_label ==
data.frq_labels[data.remap_table[j]]:
- index = j
+ for j in xrange(data.num_ri):
+ if ri_label == data.ri_labels[j] and frq_label ==
data.frq_labels[data.remap_table[j]]:
+ index = j
# Return the index.
return index
@@ -547,9 +549,9 @@
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
- # Test if relaxation data corresponding to 'self.ri_label' and
'self.frq_label' already exists.
- if self.test_labels():
- raise RelaxRiError, (self.ri_label, self.frq_label)
+ # Test if relaxation data corresponding to 'ri_label' and
'frq_label' already exists.
+ if self.test_labels(ri_label, frq_label):
+ raise RelaxRiError, (ri_label, frq_label)
# Minimum number of columns.
min_col_num = max(mol_name_col, res_num_col, res_name_col,
spin_num_col, spin_name_col, data_col, error_col)
@@ -654,7 +656,7 @@
value = None
error = None
- # Find the index corresponding to 'self.ri_label' and
'self.frq_label'.
+ # Find the index corresponding to 'ri_label' and 'frq_label'.
index = self.find_index(relax_data_store.res[self.run][i])
# Get the data.
@@ -666,8 +668,8 @@
return value, error
- def test_labels(self):
- """Test if data corresponding to 'self.ri_label' and
'self.frq_label' currently exists.
+ def test_labels(self, ri_label, frq_label):
+ """Test if data corresponding to 'ri_label' and 'frq_label'
currently exists.
@return: The answer to the question of whether relaxation
data exists corresponding to
the given labels.
@@ -682,8 +684,8 @@
# Loop over the relaxation data.
for j in xrange(spin.num_ri):
- # Test if the relaxation data matches 'self.ri_label' and
'self.frq_label'.
- if self.ri_label == spin.ri_labels[j] and self.frq_label ==
spin.frq_labels[spin.remap_table[j]]:
+ # Test if the relaxation data matches 'ri_label' and
'frq_label'.
+ if ri_label == spin.ri_labels[j] and frq_label ==
spin.frq_labels[spin.remap_table[j]]:
return True
# No match.
@@ -776,7 +778,7 @@
self.data_init(spin)
# Find the index corresponding to 'ri_label' and 'frq_label'.
- index = self.find_index(spin)
+ index = self.find_index(spin, ri_label, frq_label)
# Append empty data.
if index == None:
Modified: branches/N_state_model/test_suite/system_tests/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/jw_mapping.py?rev=4434&r1=4433&r2=4434&view=diff
==============================================================================
--- branches/N_state_model/test_suite/system_tests/jw_mapping.py (original)
+++ branches/N_state_model/test_suite/system_tests/jw_mapping.py Mon Jan 7
16:28:13 2008
@@ -75,12 +75,10 @@
for dataSet in xrange(len(dataPaths)):
self.relax.interpreter._Relax_data.read(dataTypes[dataSet][0],
dataTypes[dataSet][1], dataTypes[dataSet][2], dataPaths[dataSet])
- # Nuclei type.
- self.relax.interpreter._Nuclei.nuclei('N')
-
- # Set r and csa.
+ # Set r, csa, and the nucleus type.
self.relax.interpreter._Value.set(NH_BOND_LENGTH, 'bond_length')
self.relax.interpreter._Value.set(N15_CSA, 'csa')
+ self.relax.interpreter._Value.set('N', 'nucleus')
# Select the frequency.
self.relax.interpreter._Jw_mapping.set_frq(frq=600.0 * 1e6)
r4434 - in /branches/N_state_model: ./ specific_fns/relax_data.py test_suite/system_tests/jw_mapping.py