Author: semor
Date: Thu Apr 3 04:35:30 2008
New Revision: 5250
URL: http://svn.gna.org/viewcvs/relax?rev=5250&view=rev
Log:
Modified the calculate() function from specific_fns.jw_mapping to the new
design.
Modified:
1.3/specific_fns/jw_mapping.py
Modified: 1.3/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=5250&r1=5249&r2=5250&view=diff
==============================================================================
--- 1.3/specific_fns/jw_mapping.py (original)
+++ 1.3/specific_fns/jw_mapping.py Thu Apr 3 04:35:30 2008
@@ -37,55 +37,50 @@
"""Class containing functions specific to reduced spectral density
mapping."""
- def calculate(self, run=None, verbosity=1, sim_index=None):
+ def calculate(self, verbosity=1, sim_index=None):
"""Calculation of the spectral density values."""
- # Run argument.
- self.run = run
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
# Test if the frequency has been set.
- if not hasattr(relax_data_store, 'jw_frq') or not
relax_data_store.jw_frq.has_key(self.run) or
type(relax_data_store.jw_frq[self.run]) != float:
- raise RelaxError, "The frequency for the run " + `self.run` + "
has not been set up."
-
- # Test if the nucleus type has been set.
- if not hasattr(relax_data_store, 'gx'):
- raise RelaxNucleusError
+ if not hasattr(cdp, 'jw_frq') or type(cdp.jw_frq) != float:
+ raise RelaxError, "The frequency has not been set up."
# Test if the sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
# Test if the CSA and bond length values have been set.
- for i in xrange(len(relax_data_store.res[self.run])):
+ for spin in spin_loop(spin_id):
+
# Skip unselected residues.
- if not relax_data_store.res[self.run][i].select:
+ if not spin.select:
continue
# CSA value.
- if not hasattr(relax_data_store.res[self.run][i], 'csa') or
relax_data_store.res[self.run][i].csa == None:
+ if not hasattr(spin, 'csa') or spin.csa == None:
raise RelaxNoValueError, "CSA"
# Bond length value.
- if not hasattr(relax_data_store.res[self.run][i], 'r') or
relax_data_store.res[self.run][i].r == None:
+ if not hasattr(spin, 'r') or spin.r == None:
raise RelaxNoValueError, "bond length"
# Frequency index.
- if relax_data_store.jw_frq[self.run] not in
relax_data_store.frq[self.run]:
- raise RelaxError, "No relaxation data corresponding to the
frequency " + `relax_data_store.jw_frq[self.run]` + " has been loaded."
+ if cdp.jw_frq not in cdp.frq:
+ raise RelaxError, "No relaxation data corresponding to the
frequency " + `cdp.jw_frq` + " has been loaded."
# Reduced spectral density mapping.
- for i in xrange(len(relax_data_store.res[self.run])):
- # Reassign data structure.
- data = relax_data_store.res[self.run][i]
+ for spin in spin_loop(spin_id):
# Skip unselected residues.
- if not data.select:
+ if not spin.select:
continue
# Residue specific frequency index.
frq_index = None
- for j in xrange(data.num_frq):
- if data.frq[j] == relax_data_store.jw_frq[self.run]:
+ for j in xrange(spin.num_frq):
+ if spin.frq[j] == cdp.jw_frq:
frq_index = j
if frq_index == None:
continue
@@ -96,57 +91,57 @@
noe = None
# Get the R1, R2, and NOE values corresponding to the set
frequency.
- for j in xrange(data.num_ri):
+ for j in xrange(spin.num_ri):
# R1.
- if data.remap_table[j] == frq_index and data.ri_labels[j] ==
'R1':
+ if spin.remap_table[j] == frq_index and spin.ri_labels[j] ==
'R1':
if sim_index == None:
- r1 = data.relax_data[j]
+ r1 = spin.relax_data[j]
else:
- r1 = data.relax_sim_data[sim_index][j]
+ r1 = spin.relax_sim_data[sim_index][j]
# R2.
- if data.remap_table[j] == frq_index and data.ri_labels[j] ==
'R2':
+ if spin.remap_table[j] == frq_index and spin.ri_labels[j] ==
'R2':
if sim_index == None:
- r2 = data.relax_data[j]
+ r2 = spin.relax_data[j]
else:
- r2 = data.relax_sim_data[sim_index][j]
+ r2 = spin.relax_sim_data[sim_index][j]
# NOE.
- if data.remap_table[j] == frq_index and data.ri_labels[j] ==
'NOE':
+ if spin.remap_table[j] == frq_index and spin.ri_labels[j] ==
'NOE':
if sim_index == None:
- noe = data.relax_data[j]
+ noe = spin.relax_data[j]
else:
- noe = data.relax_sim_data[sim_index][j]
+ noe = spin.relax_sim_data[sim_index][j]
# Skip the residue if not all of the three value exist.
if r1 == None or r2 == None or noe == None:
continue
# Initialise the function to calculate.
- self.jw = Mapping(frq=relax_data_store.jw_frq[self.run],
gx=relax_data_store.gx, gh=relax_data_store.gh, mu0=relax_data_store.mu0,
h_bar=relax_data_store.h_bar)
+ self.jw = Mapping(frq=cdp.jw_frq, gx=spin.gx, gh=spin.gh,
mu0=spin.mu0, h_bar=spin.h_bar)
# Calculate the spectral density values.
- j0, jwx, jwh = self.jw.func(r=data.r, csa=data.csa, r1=r1,
r2=r2, noe=noe)
+ j0, jwx, jwh = self.jw.func(r=spin.r, csa=spin.csa, r1=r1,
r2=r2, noe=noe)
# Reduced spectral density values.
if sim_index == None:
- data.j0 = j0
- data.jwx = jwx
- data.jwh = jwh
+ spin.j0 = j0
+ spin.jwx = jwx
+ spin.jwh = jwh
# Monte Carlo simulated reduced spectral density values.
else:
# Initialise the simulation data structures.
- self.data_init(data, sim=1)
- if data.j0_sim == None:
- data.j0_sim = []
- data.jwx_sim = []
- data.jwh_sim = []
+ self.spin_init(spin, sim=1)
+ if spin.j0_sim == None:
+ spin.j0_sim = []
+ spin.jwx_sim = []
+ spin.jwh_sim = []
# Reduced spectral density values.
- data.j0_sim.append(j0)
- data.jwx_sim.append(jwx)
- data.jwh_sim.append(jwh)
+ spin.j0_sim.append(j0)
+ spin.jwx_sim.append(jwx)
+ spin.jwh_sim.append(jwh)
def data_init(self, data, sim=0):
r5250 - /1.3/specific_fns/jw_mapping.py