Author: bugman
Date: Tue Sep 30 16:37:24 2008
New Revision: 7454
URL: http://svn.gna.org/viewcvs/relax?rev=7454&view=rev
Log:
Removed a pile of unused and significantly out of date functions.
Modified:
branches/pipe_refs/generic_fns/pcs.py
branches/pipe_refs/generic_fns/rdc.py
Modified: branches/pipe_refs/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/pipe_refs/generic_fns/pcs.py?rev=7454&r1=7453&r2=7454&view=diff
==============================================================================
--- branches/pipe_refs/generic_fns/pcs.py (original)
+++ branches/pipe_refs/generic_fns/pcs.py Tue Sep 30 16:37:24 2008
@@ -140,81 +140,6 @@
spin.relax_sim_data.append(values)
-def back_calc(ri_label=None, frq_label=None, frq=None):
- """Function for back calculating relaxation data."""
-
- # Arguments.
- self.run = run
- self.ri_label = ri_label
- self.frq_label = frq_label
- self.frq = frq
-
- # Test if the run exists.
- if not self.run in ds.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if sequence data is loaded.
- if not ds.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # 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)
-
-
- # Global (non-residue specific) data.
- #####################################
-
- # Global data flag.
- self.global_flag = 1
-
- # Initialise the global data if necessary.
- self.data_init(ds)
-
- # Update the global data.
- self.update_data_structures_pipe(ri_label, frq_label, frq)
-
-
- # Residue specific data.
- ########################
-
- # Global data flag.
- self.global_flag = 0
-
- # Function type.
- function_type = ds.run_types[ds.run_names.index(self.run)]
-
- # Specific back-calculate function setup.
- back_calculate = self.relax.specific_setup.setup('back_calc',
function_type)
-
- # 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]
-
- # Skip deselected residues.
- if not data.select:
- continue
-
- # Store a copy of all the data in 'ds.res[self.run][i]' for backing
up if the back_calculation function fails.
- back_up = deepcopy(data)
-
- # Initialise all data structures.
- self.update_data_structures_spin(data, ri_label, frq_label, frq)
-
- # Back-calculate the relaxation value.
- try:
- value = back_calculate(run=self.run, index=i,
ri_label=self.ri_label, frq_label=frq_label, frq=self.frq)
- except:
- # Restore the data.
- ds.res[self.run][i] = deepcopy(back_up)
- del back_up
- raise
-
- # Update all data structures.
- self.update_data_structures_spin(data, ri_label, frq_label, frq,
value)
-
-
def centre(atom_id=None, pipe=None):
"""Specify the atom in the loaded structure corresponding to the
paramagnetic centre.
@@ -453,100 +378,6 @@
# Return the list of names.
return names
-
-
-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
-
- # Test if the run exists.
- if not self.run in ds.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if the sequence data is loaded.
- if not ds.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # 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]
-
- # Global data flag.
- self.global_flag = 0
-
- # 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:
- continue
-
- # Relaxation data and errors.
- data.relax_data.pop(index)
- data.relax_error.pop(index)
-
- # Update the number of relaxation data points.
- data.num_ri = data.num_ri - 1
-
- # Delete ri_label from the data types.
- data.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:
- # Update the number of frequencies.
- data.num_frq = data.num_frq - 1
-
- # Update the frequency labels.
- data.frq_labels.pop(frq_index)
-
- # Update the frequency array.
- data.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()
-
-
-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
-
- # Test if the run exists.
- if not self.run in ds.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if the sequence data is loaded.
- if not ds.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # 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)
-
- # 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)
def find_index(data, ri_label, frq_label):
@@ -761,56 +592,3 @@
return 'The relaxation data'
if name == 'relax_error':
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
-
- # Unpack the data_type tuple.
- self.ri_label, self.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])
-
- # Get the data.
- if index != None:
- value = ds.res[self.run][i].relax_data[index]
- error = ds.res[self.run][i].relax_error[index]
-
- # Return the data.
- return value, error
-
-
-def write(ri_label=None, frq_label=None, file=None, dir=None, force=0):
- """Function for writing relaxation data."""
-
- # Arguments.
- self.run = run
- self.ri_label = ri_label
- self.frq_label = frq_label
-
- # Test if the run exists.
- if not self.run in ds.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if the sequence data is loaded.
- if not ds.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # 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)
-
- # Create the file name if none is given.
- if file == None:
- file = self.ri_label + "." + self.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)
Modified: branches/pipe_refs/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/pipe_refs/generic_fns/rdc.py?rev=7454&r1=7453&r2=7454&view=diff
==============================================================================
--- branches/pipe_refs/generic_fns/rdc.py (original)
+++ branches/pipe_refs/generic_fns/rdc.py Tue Sep 30 16:37:24 2008
@@ -31,7 +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 relax_errors import RelaxError, RelaxNoResError, RelaxNoRDCError,
RelaxNoPipeError, RelaxNoSequenceError, RelaxNoSpinError, RelaxRDCError
+from relax_errors import RelaxError, RelaxNoResError, RelaxNoRDCError,
RelaxNoSequenceError, RelaxNoSpinError, RelaxRDCError
from relax_io import extract_data, strip
@@ -139,81 +139,6 @@
spin.relax_sim_data.append(values)
-def back_calc(ri_label=None, frq_label=None, frq=None):
- """Function for back calculating relaxation data."""
-
- # Arguments.
- self.run = run
- self.ri_label = ri_label
- self.frq_label = frq_label
- self.frq = frq
-
- # Test if the run exists.
- if not self.run in ds.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if sequence data is loaded.
- if not ds.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # 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)
-
-
- # Global (non-residue specific) data.
- #####################################
-
- # Global data flag.
- self.global_flag = 1
-
- # Initialise the global data if necessary.
- self.data_init(ds)
-
- # Update the global data.
- self.update_data_structures_pipe(ri_label, frq_label, frq)
-
-
- # Residue specific data.
- ########################
-
- # Global data flag.
- self.global_flag = 0
-
- # Function type.
- function_type = ds.run_types[ds.run_names.index(self.run)]
-
- # Specific back-calculate function setup.
- back_calculate = self.relax.specific_setup.setup('back_calc',
function_type)
-
- # 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]
-
- # Skip deselected residues.
- if not data.select:
- continue
-
- # Store a copy of all the data in 'ds.res[self.run][i]' for backing
up if the back_calculation function fails.
- back_up = deepcopy(data)
-
- # Initialise all data structures.
- self.update_data_structures_spin(data, ri_label, frq_label, frq)
-
- # Back-calculate the relaxation value.
- try:
- value = back_calculate(run=self.run, index=i,
ri_label=self.ri_label, frq_label=frq_label, frq=self.frq)
- except:
- # Restore the data.
- ds.res[self.run][i] = deepcopy(back_up)
- del back_up
- raise
-
- # Update all data structures.
- self.update_data_structures_spin(data, ri_label, frq_label, frq,
value)
-
-
def copy(pipe_from=None, pipe_to=None, ri_label=None, frq_label=None):
"""Copy the relaxation data from one data pipe to another.
@@ -410,100 +335,6 @@
# Return the list of names.
return names
-
-
-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
-
- # Test if the run exists.
- if not self.run in ds.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if the sequence data is loaded.
- if not ds.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # 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]
-
- # Global data flag.
- self.global_flag = 0
-
- # 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:
- continue
-
- # Relaxation data and errors.
- data.relax_data.pop(index)
- data.relax_error.pop(index)
-
- # Update the number of relaxation data points.
- data.num_ri = data.num_ri - 1
-
- # Delete ri_label from the data types.
- data.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:
- # Update the number of frequencies.
- data.num_frq = data.num_frq - 1
-
- # Update the frequency labels.
- data.frq_labels.pop(frq_index)
-
- # Update the frequency array.
- data.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()
-
-
-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
-
- # Test if the run exists.
- if not self.run in ds.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if the sequence data is loaded.
- if not ds.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # 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)
-
- # 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)
def find_index(data, ri_label, frq_label):
@@ -720,31 +551,6 @@
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
-
- # Unpack the data_type tuple.
- self.ri_label, self.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])
-
- # Get the data.
- if index != None:
- value = ds.res[self.run][i].relax_data[index]
- error = ds.res[self.run][i].relax_error[index]
-
- # Return the data.
- return value, error
-
-
def test_labels(ri_label, frq_label):
"""Test if data corresponding to 'ri_label' and 'frq_label' currently
exists.
@@ -945,31 +751,3 @@
for j in xrange(cont.num_ri):
if cont.ri_labels[j] == 'NOE' and
cont.frq_labels[cont.remap_table[i]] == cont.frq_labels[cont.remap_table[j]]:
cont.noe_r1_table[j] = i
-
-
-def write(ri_label=None, frq_label=None, file=None, dir=None, force=0):
- """Function for writing relaxation data."""
-
- # Arguments.
- self.run = run
- self.ri_label = ri_label
- self.frq_label = frq_label
-
- # Test if the run exists.
- if not self.run in ds.run_names:
- raise RelaxNoPipeError, self.run
-
- # Test if the sequence data is loaded.
- if not ds.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # 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)
-
- # Create the file name if none is given.
- if file == None:
- file = self.ri_label + "." + self.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)
r7454 - in /branches/pipe_refs/generic_fns: pcs.py rdc.py