Author: bugman
Date: Sun Feb 22 23:03:48 2009
New Revision: 8862
URL: http://svn.gna.org/viewcvs/relax?rev=8862&view=rev
Log:
Converted the rest of the generic_fns.relax_data module to the 1.3 line relax
design.
Modified:
1.3/generic_fns/relax_data.py
Modified: 1.3/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/relax_data.py?rev=8862&r1=8861&r2=8862&view=diff
==============================================================================
--- 1.3/generic_fns/relax_data.py (original)
+++ 1.3/generic_fns/relax_data.py Sun Feb 22 23:03:48 2009
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2008 Edward d'Auvergne
#
+# Copyright (C) 2003-2009 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -31,6 +31,7 @@
from data import Relax_data_store; ds = Relax_data_store()
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_index_loop, spin_loop
from generic_fns import pipes
+from generic_fns import value
from relax_errors import RelaxError, RelaxNoRiError, RelaxNoSequenceError,
RelaxNoSpinError, RelaxRiError
from relax_io import extract_data, strip
import specific_fns
@@ -162,7 +163,7 @@
raise RelaxNoSequenceError
# Test if relaxation data corresponding to 'ri_label' and 'frq_label'
already exists.
- if test_labels():
+ if test_labels(ri_label, frq_label):
raise RelaxRiError, (ri_label, frq_label)
@@ -295,7 +296,7 @@
def data_init(container, global_flag=False):
- """Function for initialising the data structures for a spin container.
+ """Initialise the data structures for a spin container.
@param container: The data pipe or spin data container
(PipeContainer or SpinContainer).
@type container: class instance
@@ -403,12 +404,13 @@
def delete(ri_label=None, frq_label=None):
- """Function for deleting relaxation data corresponding to ri_label and
frq_label."""
-
- # Arguments.
- self.run = run
- self.ri_label = ri_label
- self.frq_label = frq_label
+ """Delete relaxation data corresponding to the Ri and frequency labels.
+
+ @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
+ """
# Test if the current pipe exists.
pipes.test()
@@ -417,67 +419,62 @@
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
- # Test if data corresponding to 'self.ri_label' and 'self.frq_label'
exists.
- if not self.test_labels():
- raise RelaxNoRiError, (self.ri_label, self.frq_label)
-
- # Loop over the sequence.
- for i in xrange(len(ds.res[self.run])):
- # Remap the data structure 'ds.res[self.run][i]'.
- data = ds.res[self.run][i]
-
+ # Test if data corresponding to 'ri_label' and 'frq_label' exists.
+ if not test_labels(ri_label, frq_label):
+ raise RelaxNoRiError, (ri_label, frq_label)
+
+ # Loop over the spins.
+ for spin in spin_loop():
# Global data flag.
- self.global_flag = 0
+ global_flag = False
# Find the index corresponding to 'ri_label' and 'frq_label'.
- index = self.find_index(data, ri_label, frq_label)
+ index = find_index(spin, ri_label, frq_label)
# Catch any problems.
if index == None:
continue
# Relaxation data and errors.
- data.relax_data.pop(index)
- data.relax_error.pop(index)
+ spin.relax_data.pop(index)
+ spin.relax_error.pop(index)
# Update the number of relaxation data points.
- data.num_ri = data.num_ri - 1
+ spin.num_ri = spin.num_ri - 1
# Delete ri_label from the data types.
- data.ri_labels.pop(index)
+ spin.ri_labels.pop(index)
# Update the remap table.
- data.remap_table.pop(index)
-
- # Find if there is other data corresponding to 'self.frq_label'
- frq_index = data.frq_labels.index(self.frq_label)
- if not frq_index in data.remap_table:
+ spin.remap_table.pop(index)
+
+ # Find if there is other data corresponding to 'frq_label'
+ frq_index = spin.frq_labels.index(frq_label)
+ if not frq_index in spin.remap_table:
# Update the number of frequencies.
- data.num_frq = data.num_frq - 1
+ spin.num_frq = spin.num_frq - 1
# Update the frequency labels.
- data.frq_labels.pop(frq_index)
+ spin.frq_labels.pop(frq_index)
# Update the frequency array.
- data.frq.pop(frq_index)
+ spin.frq.pop(frq_index)
# Update the NOE R1 translation table.
- data.noe_r1_table.pop(index)
- for j in xrange(data.num_ri):
- if data.noe_r1_table[j] > index:
- data.noe_r1_table[j] = data.noe_r1_table[j] - 1
-
- # Clean up the runs.
- self.relax.generic.runs.eliminate_unused_runs()
+ spin.noe_r1_table.pop(index)
+ for j in xrange(spin.num_ri):
+ if spin.noe_r1_table[j] > index:
+ spin.noe_r1_table[j] = spin.noe_r1_table[j] - 1
def display(ri_label=None, frq_label=None):
- """Function for displaying relaxation data corresponding to ri_label and
frq_label."""
-
- # Arguments.
- self.run = run
- self.ri_label = ri_label
- self.frq_label = frq_label
+ """Display relaxation data corresponding to the Ri and frequency labels.
+
+ @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
+ """
# Test if the current pipe exists.
pipes.test()
@@ -486,16 +483,16 @@
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
- # Test if data corresponding to 'self.ri_label' and 'self.frq_label'
exists.
- if not self.test_labels():
- raise RelaxNoRiError, (self.ri_label, self.frq_label)
+ # Test if data corresponding to 'ri_label' and 'frq_label' exists.
+ if not test_labels(ri_label, frq_label):
+ raise RelaxNoRiError, (ri_label, frq_label)
# Print the data.
- self.relax.generic.value.write_data(run=self.run, param=(self.ri_label,
self.frq_label), file=sys.stdout, return_value=self.return_value)
+ value.write_data(param=(ri_label, frq_label), file=sys.stdout,
return_value=return_value)
def find_index(data, ri_label, frq_label):
- """Function for finding the index corresponding to ri_label and
frq_label.
+ """Find 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
@@ -525,7 +522,7 @@
def read(ri_label=None, frq_label=None, frq=None, file=None, dir=None,
file_data=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None):
- """Function for reading R1, R2, or NOE relaxation data.
+ """Read R1, R2, or NOE relaxation data from a file.
@param ri_label: The relaxation data type, ie 'R1', 'R2', or
'NOE'.
@type ri_label: str
@@ -681,26 +678,29 @@
return 'The relaxation data errors'
-def return_value(i, data_type):
- """Function for returning the value and error corresponding to
'data_type'."""
-
- # Arguments.
- self.run = run
+def return_value(spin, data_type):
+ """Return the value and error corresponding to 'data_type'.
+
+ @param spin: The spin container.
+ @type spin: SpinContainer instance
+ @param data_type: A tuple of the Ri label and the frequency label.
+ @type data_type: tuple of str of length 2
+ """
# Unpack the data_type tuple.
- self.ri_label, self.frq_label = data_type
+ ri_label, frq_label = data_type
# Initialise.
value = None
error = None
# Find the index corresponding to 'ri_label' and 'frq_label'.
- index = self.find_index(ds.res[self.run][i])
+ index = find_index(spin, ri_label, frq_label)
# Get the data.
if index != None:
- value = ds.res[self.run][i].relax_data[index]
- error = ds.res[self.run][i].relax_error[index]
+ value = spin.relax_data[index]
+ error = spin.relax_error[index]
# Return the data.
return value, error
@@ -709,9 +709,13 @@
def test_labels(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.
- @rtype: bool
+ @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 answer to the question of whether relaxation
data exists corresponding
+ to the given labels.
+ @rtype: bool
"""
# Loop over the spins.
@@ -731,7 +735,7 @@
def update_data_structures_pipe(ri_label=None, frq_label=None, frq=None):
- """Function for updating all relaxation data structures in the current
data pipe.
+ """Update all relaxation data structures in the current data pipe.
@param ri_label: The relaxation data type, ie 'R1', 'R2', or
'NOE'.
@type ri_label: str
@@ -796,7 +800,7 @@
def update_data_structures_spin(spin=None, ri_label=None, frq_label=None,
frq=None, value=None, error=None):
- """Function for updating all relaxation data structures of the given
spin container.
+ """Update all relaxation data structures of the given spin container.
@param spin: The SpinContainer object.
@type spin: class instance
@@ -909,12 +913,7 @@
def write(ri_label=None, frq_label=None, file=None, dir=None, force=False):
- """Function for writing relaxation data."""
-
- # Arguments.
- self.run = run
- self.ri_label = ri_label
- self.frq_label = frq_label
+ """Write relaxation data to a file."""
# Test if the current pipe exists.
pipes.test()
@@ -923,13 +922,13 @@
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
- # Test if data corresponding to 'self.ri_label' and 'self.frq_label'
exists.
- if not self.test_labels():
- raise RelaxNoRiError, (self.ri_label, self.frq_label)
+ # Test if data corresponding to 'ri_label' and 'frq_label' exists.
+ if not test_labels(ri_label, frq_label):
+ raise RelaxNoRiError, (ri_label, frq_label)
# Create the file name if none is given.
if file == None:
- file = self.ri_label + "." + self.frq_label + ".out"
+ file = ri_label + "." + frq_label + ".out"
# Write the data.
- self.relax.generic.value.write(run=self.run, param=(self.ri_label,
self.frq_label), file=file, dir=dir, force=force,
return_value=self.return_value)
+ value.write(param=(ri_label, frq_label), file=file, dir=dir,
force=force, return_value=return_value)
r8862 - /1.3/generic_fns/relax_data.py