Author: bugman
Date: Sun Feb 22 23:06:04 2009
New Revision: 8863
URL: http://svn.gna.org/viewcvs/relax?rev=8863&view=rev
Log:
Merged revisions 8833-8862 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8861 | bugman | 2009-02-22 23:00:08 +0100 (Sun, 22 Feb 2009) | 3 lines
Fixed some circular import issues.
........
r8862 | bugman | 2009-02-22 23:03:48 +0100 (Sun, 22 Feb 2009) | 3 lines
Converted the rest of the generic_fns.relax_data module to the 1.3 line
relax design.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/generic_fns/minimise.py
branches/bmrb/generic_fns/relax_data.py
branches/bmrb/generic_fns/value.py
Propchange: branches/bmrb/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Sun Feb 22 23:06:04 2009
@@ -1,1 +1,1 @@
-/1.3:1-8832
+/1.3:1-8862
Modified: branches/bmrb/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/minimise.py?rev=8863&r1=8862&r2=8863&view=diff
==============================================================================
--- branches/bmrb/generic_fns/minimise.py (original)
+++ branches/bmrb/generic_fns/minimise.py Sun Feb 22 23:06:04 2009
@@ -30,7 +30,7 @@
from generic_fns.mol_res_spin import spin_loop
from generic_fns import pipes
from relax_errors import RelaxError
-from specific_fns.setup import get_specific_fn
+import specific_fns
def reset_min_stats(data_pipe=None, spin=None):
@@ -122,8 +122,8 @@
cdp = pipes.get_pipe()
# Specific calculate function setup.
- calculate = get_specific_fn('calculate', cdp.pipe_type)
- overfit_deselect = get_specific_fn('overfit_deselect', cdp.pipe_type)
+ calculate = specific_fns.setup.get_specific_fn('calculate',
cdp.pipe_type)
+ overfit_deselect =
specific_fns.setup.get_specific_fn('overfit_deselect', cdp.pipe_type)
# Deselect residues lacking data:
overfit_deselect()
@@ -166,8 +166,8 @@
cdp = pipes.get_pipe()
# Specific grid search function.
- grid_search = get_specific_fn('grid_search', cdp.pipe_type)
- overfit_deselect = get_specific_fn('overfit_deselect', cdp.pipe_type)
+ grid_search = specific_fns.setup.get_specific_fn('grid_search',
cdp.pipe_type)
+ overfit_deselect =
specific_fns.setup.get_specific_fn('overfit_deselect', cdp.pipe_type)
# Deselect residues lacking data:
overfit_deselect()
@@ -217,8 +217,8 @@
cdp = pipes.get_pipe()
# Specific minimisation function.
- minimise = get_specific_fn('minimise', cdp.pipe_type)
- overfit_deselect = get_specific_fn('overfit_deselect', cdp.pipe_type)
+ minimise = specific_fns.setup.get_specific_fn('minimise', cdp.pipe_type)
+ overfit_deselect =
specific_fns.setup.get_specific_fn('overfit_deselect', cdp.pipe_type)
# Deselect residues lacking data:
overfit_deselect()
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=8863&r1=8862&r2=8863&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Sun Feb 22 23:06:04 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)
Modified: branches/bmrb/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/value.py?rev=8863&r1=8862&r2=8863&view=diff
==============================================================================
--- branches/bmrb/generic_fns/value.py (original)
+++ branches/bmrb/generic_fns/value.py Sun Feb 22 23:06:04 2009
@@ -33,7 +33,7 @@
from generic_fns.sequence import write_header, write_line
from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoSequenceError, RelaxNoSpinError, RelaxParamSetError, RelaxValueError
from relax_io import extract_data, open_write_file, strip
-from specific_fns.setup import get_specific_fn
+import specific_fns
def copy(pipe_from=None, pipe_to=None, param=None):
@@ -66,7 +66,7 @@
raise RelaxNoSequenceError, pipe_to
# Specific value and error returning function.
- return_value = get_specific_fn('return_value', pipes.get_type(pipe_from))
+ return_value = specific_fns.setup.get_specific_fn('return_value',
pipes.get_type(pipe_from))
# Test if the data exists for pipe_to.
for spin in spin_loop(pipe_to):
@@ -126,7 +126,7 @@
"""
# Specific functions.
- is_spin_param = get_specific_fn('is_spin_param', pipes.get_type())
+ is_spin_param = specific_fns.setup.get_specific_fn('is_spin_param',
pipes.get_type())
# Initialise.
spin_params = []
@@ -245,7 +245,7 @@
min_stat = False
# Specific v
- return_value = get_specific_fn('return_value', pipes.get_type())
+ return_value = specific_fns.setup.get_specific_fn('return_value',
pipes.get_type())
# Specific set function.
set = set_spin_params
@@ -364,8 +364,8 @@
pipes.test()
# Specific functions.
- return_value = get_specific_fn('return_value', pipes.get_type())
- set_non_spin_params = get_specific_fn('set_non_spin_params',
pipes.get_type())
+ return_value = specific_fns.setup.get_specific_fn('return_value',
pipes.get_type())
+ set_non_spin_params =
specific_fns.setup.get_specific_fn('set_non_spin_params', pipes.get_type())
# The parameters have been specified.
if param:
@@ -453,10 +453,10 @@
"""
# Specific functions.
- data_init = get_specific_fn('data_init', pipes.get_type())
- default_value = get_specific_fn('default_value', pipes.get_type())
- return_data_name = get_specific_fn('return_data_name', pipes.get_type())
- set_update = get_specific_fn('set_update', pipes.get_type())
+ data_init = specific_fns.setup.get_specific_fn('data_init',
pipes.get_type())
+ default_value = specific_fns.setup.get_specific_fn('default_value',
pipes.get_type())
+ return_data_name =
specific_fns.setup.get_specific_fn('return_data_name', pipes.get_type())
+ set_update = specific_fns.setup.get_specific_fn('set_update',
pipes.get_type())
# Setting the model parameters prior to minimisation.
@@ -601,7 +601,7 @@
# Get the value and error returning function if required.
if not return_value:
- return_value = get_specific_fn('return_value', pipes.get_type())
+ return_value = specific_fns.setup.get_specific_fn('return_value',
pipes.get_type())
# Format string.
format = "%-30s%-30s"
r8863 - in /branches/bmrb: ./ generic_fns/minimise.py generic_fns/relax_data.py generic_fns/value.py