Author: bugman
Date: Tue Jun 26 11:09:31 2012
New Revision: 17059
URL: http://svn.gna.org/viewcvs/relax?rev=17059&view=rev
Log:
Updated all N-state model analysis references to RDCs and NOEs to use the
interatomic data containers.
This is mainly for the methods reliant on the base_data_loop() iterator.
Modified:
branches/interatomic/specific_fns/n_state_model.py
Modified: branches/interatomic/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/n_state_model.py?rev=17059&r1=17058&r2=17059&view=diff
==============================================================================
--- branches/interatomic/specific_fns/n_state_model.py (original)
+++ branches/interatomic/specific_fns/n_state_model.py Tue Jun 26 11:09:31
2012
@@ -943,14 +943,6 @@
# Skip spins without PCS data.
if not hasattr(spin, 'pcs'):
- # Add rows of None if other alignment data exists.
- if hasattr(spin, 'rdc'):
- pcs[-1].append(None)
- pcs_err[-1].append(None)
- pcs_weight[-1].append(None)
- j = j + 1
-
- # Jump to the next spin.
continue
# Append the PCSs to the list.
@@ -1261,18 +1253,20 @@
if not spin.select:
continue
- # RDC data (skipping array elements set to None).
- if 'rdc' in data_types:
- if hasattr(spin, 'rdc'):
- for rdc in spin.rdc:
- if isinstance(rdc, float):
- n = n + 1
-
# PCS data (skipping array elements set to None).
if 'pcs' in data_types:
if hasattr(spin, 'pcs'):
for pcs in spin.pcs:
if isinstance(pcs, float):
+ n = n + 1
+
+ # Interatomic data loop.
+ for interatom in interatomic_loop():
+ # RDC data (skipping array elements set to None).
+ if 'rdc' in data_types:
+ if hasattr(interatom, 'rdc'):
+ for rdc in interatom.rdc:
+ if isinstance(rdc, float):
n = n + 1
# Alignment tensors.
@@ -1620,56 +1614,57 @@
def base_data_loop(self):
"""Loop over the base data of the spins - RDCs, PCSs, and NOESY data.
- This loop iterates for each data point (RDC, PCS, NOESY) for each
spin, returning the identification information.
-
- @return: A list of the spin ID string, the data type
('rdc', 'pcs', 'noesy'), and the alignment ID if required.
- @rtype: list of str
- """
-
- # Loop over the spins.
- for spin, spin_id in spin_loop(return_id=True):
+ This loop iterates for each data point (RDC, PCS, NOESY) for each
spin or interatomic data container, returning the identification information.
+
+ @return: A list of the spin or interatomic data
container, the data type ('rdc', 'pcs', 'noesy'), and the alignment ID if
required.
+ @rtype: list of [SpinContainer instance, str, str] or
[InteratomContainer instance, str, str]
+ """
+
+ # Loop over the interatomic data containers.
+ for interatom in interatomic_loop():
# Re-initialise the data structure.
- base_ids = [spin_id, None, None]
-
- # Skip deselected spins.
- if not spin.select:
- continue
+ data = [interatom, None, None]
# RDC data.
- if hasattr(spin, 'rdc'):
- base_ids[1] = 'rdc'
+ if hasattr(interatom, 'rdc'):
+ data[1] = 'rdc'
# Loop over the alignment IDs.
for id in cdp.rdc_ids:
# Add the ID.
- base_ids[2] = id
+ data[2] = id
# Yield the set.
- yield base_ids
+ yield data
+
+ # NOESY data.
+ if hasattr(interatom, 'noesy'):
+ data[1] = 'noesy'
+
+ # Loop over the alignment IDs.
+ for id in cdp.noesy_ids:
+ # Add the ID.
+ data[2] = id
+
+ # Yield the set.
+ yield data
+
+ # Loop over the spins.
+ for spin in spin_loop():
+ # Re-initialise the data structure.
+ data = [spin, None, None]
# PCS data.
if hasattr(spin, 'pcs'):
- base_ids[1] = 'pcs'
+ data[1] = 'pcs'
# Loop over the alignment IDs.
for id in cdp.pcs_ids:
# Add the ID.
- base_ids[2] = id
+ data[2] = id
# Yield the set.
- yield base_ids
-
- # NOESY data.
- if hasattr(spin, 'noesy'):
- base_ids[1] = 'noesy'
-
- # Loop over the alignment IDs.
- for id in cdp.noesy_ids:
- # Add the ID.
- base_ids[2] = id
-
- # Yield the set.
- yield base_ids
+ yield data
def calculate(self, spin_id=None, verbosity=1, sim_index=None):
@@ -1749,47 +1744,47 @@
# Initialise the MC data structure.
mc_data = []
- # Get the spin container and global spin index.
- spin = return_spin(data_id[0])
+ # Alias the spin or interatomic data container.
+ container = data_id[0]
# RDC data.
- if data_id[1] == 'rdc' and hasattr(spin, 'rdc'):
+ if data_id[1] == 'rdc' and hasattr(container, 'rdc'):
# Does back-calculated data exist?
- if not hasattr(spin, 'rdc_bc'):
+ if not hasattr(container, 'rdc_bc'):
self.calculate()
# The data.
- if not hasattr(spin, 'rdc_bc') or not
spin.rdc_bc.has_key(data_id[2]):
+ if not hasattr(container, 'rdc_bc') or not
container.rdc_bc.has_key(data_id[2]):
data = None
else:
- data = spin.rdc_bc[data_id[2]]
+ data = container.rdc_bc[data_id[2]]
# Append the data.
mc_data.append(data)
+ # NOESY data.
+ elif data_id[1] == 'noesy' and hasattr(container, 'noesy'):
+ # Does back-calculated data exist?
+ if not hasattr(container, 'noesy_bc'):
+ self.calculate()
+
+ # Append the data.
+ mc_data.append(container.noesy_bc)
+
# PCS data.
- elif data_id[1] == 'pcs' and hasattr(spin, 'pcs'):
+ elif data_id[1] == 'pcs' and hasattr(container, 'pcs'):
# Does back-calculated data exist?
- if not hasattr(spin, 'pcs_bc'):
+ if not hasattr(container, 'pcs_bc'):
self.calculate()
# The data.
- if not hasattr(spin, 'pcs_bc') or not
spin.pcs_bc.has_key(data_id[2]):
+ if not hasattr(container, 'pcs_bc') or not
container.pcs_bc.has_key(data_id[2]):
data = None
else:
- data = spin.pcs_bc[data_id[2]]
+ data = container.pcs_bc[data_id[2]]
# Append the data.
mc_data.append(data)
-
- # NOESY data.
- elif data_id[1] == 'noesy' and hasattr(spin, 'noesy'):
- # Does back-calculated data exist?
- if not hasattr(spin, 'noesy_bc'):
- self.calculate()
-
- # Append the data.
- mc_data.append(spin.noesy_bc)
# Return the data.
return mc_data
@@ -2190,39 +2185,39 @@
# Initialise the MC data structure.
mc_errors = []
- # Get the spin container and global spin index.
- spin = return_spin(data_id[0])
+ # Alias the spin or interatomic data container.
+ container = data_id[0]
# Skip deselected spins.
- if not spin.select:
+ if data_id[1] == 'pcs' and not container.select:
return
# RDC data.
- if data_id[1] == 'rdc' and hasattr(spin, 'rdc'):
+ if data_id[1] == 'rdc' and hasattr(container, 'rdc'):
# Do errors exist?
- if not hasattr(spin, 'rdc_err'):
- raise RelaxError("The RDC errors are missing for spin '%s'."
% data_id[0])
+ if not hasattr(container, 'rdc_err'):
+ raise RelaxError("The RDC errors are missing for the spin
pair '%s' and '%s'." % (container.spin_id1, container.spin_id2))
# Append the data.
- mc_errors.append(spin.rdc_err[data_id[2]])
+ mc_errors.append(container.rdc_err[data_id[2]])
+
+ # NOESY data.
+ elif data_id[1] == 'noesy' and hasattr(container, 'noesy'):
+ # Do errors exist?
+ if not hasattr(container, 'noesy_err'):
+ raise RelaxError("The NOESY errors are missing for the spin
pair '%s' and '%s'." % (container.spin_id1, container.spin_id2))
+
+ # Append the data.
+ mc_errors.append(container.noesy_err)
# PCS data.
- elif data_id[1] == 'pcs' and hasattr(spin, 'pcs'):
+ elif data_id[1] == 'pcs' and hasattr(container, 'pcs'):
# Do errors exist?
- if not hasattr(spin, 'pcs_err'):
+ if not hasattr(container, 'pcs_err'):
raise RelaxError("The PCS errors are missing for spin '%s'."
% data_id[0])
# Append the data.
- mc_errors.append(spin.pcs_err[data_id[2]])
-
- # NOESY data.
- elif hasattr(spin, 'noesy'):
- # Do errors exist?
- if not hasattr(spin, 'noesy_err'):
- raise RelaxError("The NOESY errors are missing for spin
'%s'." % data_id[0])
-
- # Append the data.
- mc_errors.append(spin.noesy_err)
+ mc_errors.append(container.pcs_err[data_id[2]])
# Return the errors.
return mc_errors
@@ -2419,37 +2414,37 @@
@type sim_data: list of float
"""
- # Get the spin container.
- spin = return_spin(data_id[0])
+ # Alias the spin or interatomic data container.
+ container = data_id[0]
# RDC data.
- if data_id[1] == 'rdc' and hasattr(spin, 'rdc'):
+ if data_id[1] == 'rdc' and hasattr(container, 'rdc'):
# Initialise.
- if not hasattr(spin, 'rdc_sim'):
- spin.rdc_sim = {}
+ if not hasattr(container, 'rdc_sim'):
+ container.rdc_sim = {}
# Store the data structure.
- spin.rdc_sim[data_id[2]] = []
+ container.rdc_sim[data_id[2]] = []
for i in range(cdp.sim_number):
- spin.rdc_sim[data_id[2]].append(sim_data[i][0])
+ container.rdc_sim[data_id[2]].append(sim_data[i][0])
+
+ # NOESY data.
+ elif data_id[1] == 'noesy' and hasattr(container, 'noesy'):
+ # Store the data structure.
+ container.noesy_sim = []
+ for i in range(cdp.sim_number):
+ container.noesy_sim[data_id[2]].append(sim_data[i][0])
# PCS data.
- if data_id[1] == 'pcs' and hasattr(spin, 'pcs'):
+ elif data_id[1] == 'pcs' and hasattr(container, 'pcs'):
# Initialise.
- if not hasattr(spin, 'pcs_sim'):
- spin.pcs_sim = {}
+ if not hasattr(container, 'pcs_sim'):
+ container.pcs_sim = {}
# Store the data structure.
- spin.pcs_sim[data_id[2]] = []
+ container.pcs_sim[data_id[2]] = []
for i in range(cdp.sim_number):
- spin.pcs_sim[data_id[2]].append(sim_data[i][0])
-
- # NOESY data.
- if data_id[1] == 'noesy' and hasattr(spin, 'noesy'):
- # Store the data structure.
- spin.noesy_sim = []
- for i in range(cdp.sim_number):
- spin.noesy_sim[data_id[2]].append(sim_data[i][0])
+ container.pcs_sim[data_id[2]].append(sim_data[i][0])
def sim_return_param(self, model_info, index):
r17059 - /branches/interatomic/specific_fns/n_state_model.py