Author: bugman
Date: Mon Jul 23 15:46:43 2012
New Revision: 17296
URL: http://svn.gna.org/viewcvs/relax?rev=17296&view=rev
Log:
Updated the frame order base_data_loop() generator method and its
dependencies for the interatomic design.
This includes the create_mc_data(), return_error() and sim_pack_data()
methods.
Modified:
branches/frame_order_testing/specific_fns/frame_order.py
Modified: branches/frame_order_testing/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/frame_order.py?rev=17296&r1=17295&r2=17296&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Mon Jul 23
15:46:43 2012
@@ -38,7 +38,7 @@
from float import isNaN, isInf
from generic_fns import pipes
from generic_fns.angles import wrap_angles
-from generic_fns.interatomic import interatomic_loop
+from generic_fns.interatomic import interatomic_loop, return_interatom
from generic_fns.mol_res_spin import return_spin, spin_loop
from generic_fns.structure import geometric
from generic_fns.structure.cones import Iso_cone, Pseudo_elliptic
@@ -1539,39 +1539,38 @@
# First the tensors.
yield 'A'
- # Then the spin IDs for the moving domain.
+ # The moving domain ID.
id = cdp.domain[self._domain_moving()]
+
+ # Loop over the interatomic data containers for the moving domain
(for the RDC data).
+ for interatom in interatomic_loop(id):
+ # Skip deselected containers.
+ if not interatom.select:
+ continue
+
+ # No RDC, so skip.
+ if not hasattr(interatom, 'rdc'):
+ continue
+
+ # Loop over the alignment IDs.
+ for align_id in cdp.pcs_ids:
+ # Yield the info set.
+ yield ['rdc', interatom.spin_id1, interatom.spin_id2,
align_id]
+
+ # Loop over the spin containers for the moving domain (for the PCS
data).
for spin, spin_id in spin_loop(id, return_id=True):
- # Re-initialise the data structure.
- base_ids = [spin_id, None, None]
-
# Skip deselected spins.
if not spin.select:
continue
- # RDC data.
- if hasattr(spin, 'rdc'):
- base_ids[1] = 'rdc'
-
- # Loop over the alignment IDs.
- for id in cdp.rdc_ids:
- # Add the ID.
- base_ids[2] = id
-
- # Yield the set.
- yield base_ids
-
- # PCS data.
- if hasattr(spin, 'pcs'):
- base_ids[1] = 'pcs'
-
- # Loop over the alignment IDs.
- for id in cdp.pcs_ids:
- # Add the ID.
- base_ids[2] = id
-
- # Yield the set.
- yield base_ids
+ # No PCS, so skip.
+ if not hasattr(spin, 'pcs'):
+ continue
+
+ # Loop over the alignment IDs.
+ for align_id in cdp.pcs_ids:
+ # Yield the info set.
+ yield ['pcs', spin_id, align_id]
def calculate(self, spin_id=None, verbosity=1, sim_index=None):
@@ -1601,8 +1600,8 @@
def create_mc_data(self, data_id=None):
"""Create the Monte Carlo data by back calculating the reduced
tensor data.
- @keyword data_id: Unused.
- @type data_id: None
+ @keyword data_id: The data set as yielded by the base_data_loop()
generator method.
+ @type data_id: str or list of str
@return: The Monte Carlo simulation data.
@rtype: list of floats
"""
@@ -1621,40 +1620,47 @@
mc_data.append(tensor.Axz)
mc_data.append(tensor.Ayz)
- # The spin specific data.
- else:
+ # The RDC data.
+ elif data_id[0] == 'rdc':
+ # Unpack the set.
+ data_type, spin_id1, spin_id2, align_id = data_id
+
+ # Get the interatomic data container.
+ interatom = return_interatom(spin_id1, spin_id2)
+
+ # Does back-calculated data exist?
+ if not hasattr(interatom, 'rdc_bc'):
+ self.calculate()
+
+ # The data.
+ if not hasattr(interatom, 'rdc_bc') or not
interatom.rdc_bc.has_key(align_id):
+ data = None
+ else:
+ data = interatom.rdc_bc[align_id]
+
+ # Append the data.
+ mc_data.append(data)
+
+ # The PCS data.
+ elif data_id[0] == 'pcs':
+ # Unpack the set.
+ data_type, spin_id, align_id = data_id
+
# Get the spin container.
- spin = return_spin(data_id[0])
-
- # RDC data.
- if data_id[1] == 'rdc' and hasattr(spin, 'rdc'):
- # Does back-calculated data exist?
- if not hasattr(spin, 'rdc_bc'):
- self.calculate()
-
- # The data.
- if not hasattr(spin, 'rdc_bc') or not
spin.rdc_bc.has_key(data_id[2]):
- data = None
- else:
- data = spin.rdc_bc[data_id[2]]
-
- # Append the data.
- mc_data.append(data)
-
- # PCS data.
- elif data_id[1] == 'pcs' and hasattr(spin, 'pcs'):
- # Does back-calculated data exist?
- if not hasattr(spin, 'pcs_bc'):
- self.calculate()
-
- # The data.
- if not hasattr(spin, 'pcs_bc') or not
spin.pcs_bc.has_key(data_id[2]):
- data = None
- else:
- data = spin.pcs_bc[data_id[2]]
-
- # Append the data.
- mc_data.append(data)
+ spin = return_spin(spin_id)
+
+ # Does back-calculated data exist?
+ if not hasattr(spin, 'pcs_bc'):
+ self.calculate()
+
+ # The data.
+ if not hasattr(spin, 'pcs_bc') or not
spin.pcs_bc.has_key(align_id):
+ data = None
+ else:
+ data = spin.pcs_bc[align_id]
+
+ # Append the data.
+ mc_data.append(data)
# Return the data.
return mc_data
@@ -1997,10 +2003,10 @@
def return_error(self, data_id):
"""Return the alignment tensor error structure.
- @param data_id: The information yielded by the base_data_loop()
generator method.
- @type data_id: None
- @return: The array of tensor error values.
- @rtype: list of float
+ @param data_id: The data set as yielded by the base_data_loop()
generator method.
+ @type data_id: str or list of str
+ @return: The array of tensor error values.
+ @rtype: list of float
"""
# Initialise the MC data structure.
@@ -2017,28 +2023,35 @@
mc_errors.append(tensor.Axz_err)
mc_errors.append(tensor.Ayz_err)
- # The spin specific data.
- else:
+ # The RDC data.
+ elif data_id[0] == 'rdc':
+ # Unpack the set.
+ data_type, spin_id1, spin_id2, align_id = data_id
+
+ # Get the interatomic data container.
+ interatom = return_interatom(spin_id1, spin_id2)
+
+ # Do errors exist?
+ if not hasattr(interatom, 'rdc_err'):
+ raise RelaxError("The RDC errors are missing for interatomic
data container between spins '%s' and '%s'." % (spin_id1, spin_id2))
+
+ # Append the data.
+ mc_errors.append(interatom.rdc_err[align_id])
+
+ # The PCS data.
+ elif data_id[0] == 'pcs':
+ # Unpack the set.
+ data_type, spin_id, align_id = data_id
+
# Get the spin container.
- spin = return_spin(data_id[0])
-
- # RDC data.
- if data_id[1] == 'rdc' and hasattr(spin, 'rdc'):
- # Do errors exist?
- if not hasattr(spin, 'rdc_err'):
- raise RelaxError("The RDC errors are missing for spin
'%s'." % data_id[0])
-
- # Append the data.
- mc_errors.append(spin.rdc_err[data_id[2]])
-
- # PCS data.
- elif data_id[1] == 'pcs' and hasattr(spin, 'pcs'):
- # Do errors exist?
- if not hasattr(spin, '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]])
+ spin = return_spin(spin_id)
+
+ # Do errors exist?
+ if not hasattr(spin, 'pcs_err'):
+ raise RelaxError("The PCS errors are missing for spin '%s'."
% spin_id)
+
+ # Append the data.
+ mc_errors.append(spin.pcs_err[align_id])
# Return the errors.
return mc_errors
@@ -2178,8 +2191,8 @@
def sim_pack_data(self, data_id, sim_data):
"""Pack the Monte Carlo simulation data.
- @param data_id: The identification data as yielded by the
base_data_loop() generator method.
- @type data_id: string or list of str
+ @param data_id: The data set as yielded by the base_data_loop()
generator method.
+ @type data_id: str or list of str
@param sim_data: The Monte Carlo simulation data.
@type sim_data: list of float
"""
@@ -2204,32 +2217,40 @@
tensor.Axz_sim.append(sim_data[i][5*j + 3])
tensor.Ayz_sim.append(sim_data[i][5*j + 4])
- # The spin specific data.
- else:
+ # The RDC data.
+ elif data_id[0] == 'rdc':
+ # Unpack the set.
+ data_type, spin_id1, spin_id2, align_id = data_id
+
+ # Get the interatomic data container.
+ interatom = return_interatom(spin_id1, spin_id2)
+
+ # Initialise.
+ if not hasattr(interatom, 'rdc_sim'):
+ interatom.rdc_sim = {}
+
+ # Store the data structure.
+ interatom.rdc_sim[align_id] = []
+ for i in range(cdp.sim_number):
+ print sim_data[i]
+ interatom.rdc_sim[align_id].append(sim_data[i][0])
+
+ # The PCS data.
+ elif data_id[0] == 'pcs':
+ # Unpack the set.
+ data_type, spin_id, align_id = data_id
+
# Get the spin container.
- spin = return_spin(data_id[0])
-
- # RDC data.
- if data_id[1] == 'rdc' and hasattr(spin, 'rdc'):
- # Initialise.
- if not hasattr(spin, 'rdc_sim'):
- spin.rdc_sim = {}
-
- # Store the data structure.
- spin.rdc_sim[data_id[2]] = []
- for i in range(cdp.sim_number):
- spin.rdc_sim[data_id[2]].append(sim_data[i][0])
-
- # PCS data.
- if data_id[1] == 'pcs' and hasattr(spin, 'pcs'):
- # Initialise.
- if not hasattr(spin, 'pcs_sim'):
- spin.pcs_sim = {}
-
- # Store the data structure.
- spin.pcs_sim[data_id[2]] = []
- for i in range(cdp.sim_number):
- spin.pcs_sim[data_id[2]].append(sim_data[i][0])
+ spin = return_spin(spin_id)
+
+ # Initialise.
+ if not hasattr(spin, 'pcs_sim'):
+ spin.pcs_sim = {}
+
+ # Store the data structure.
+ spin.pcs_sim[data_id[2]] = []
+ for i in range(cdp.sim_number):
+ spin.pcs_sim[data_id[2]].append(sim_data[i][0])
def sim_return_param(self, model_info, index):
r17296 - /branches/frame_order_testing/specific_fns/frame_order.py