Author: semor
Date: Thu Apr 3 18:56:44 2008
New Revision: 5266
URL: http://svn.gna.org/viewcvs/relax?rev=5266&view=rev
Log:
Fixed a few bugs introduced while modifying the code to the new design.
These bugs were noticed by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00011.html (Message-id:
<7f080ed10804030921h2703a004o65501fbd89cb08ed@xxxxxxxxxxxxxx>)
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=5266&r1=5265&r2=5266&view=diff
==============================================================================
--- 1.3/specific_fns/jw_mapping.py (original)
+++ 1.3/specific_fns/jw_mapping.py Thu Apr 3 18:56:44 2008
@@ -575,34 +575,35 @@
frq = `None`
# Loop over the sequence.
- for i in xrange(len(cdp.res)):
+ for spin in spin_loop(spin_id):
+
# Reassign data structure.
data = cdp.res[i]
# J(0).
j0 = None
- if hasattr(data, 'j0'):
- j0 = data.j0
+ if hasattr(spin, 'j0'):
+ j0 = spin.j0
# J(wX).
jwx = None
- if hasattr(data, 'jwx'):
- jwx = data.jwx
+ if hasattr(spin, 'jwx'):
+ jwx = spin.jwx
# J(wH).
jwh = None
- if hasattr(data, 'jwh'):
- jwh = data.jwh
+ if hasattr(spin, 'jwh'):
+ jwh = spin.jwh
# Bond length.
r = None
- if hasattr(data, 'r') and data.r != None:
- r = data.r / 1e-10
+ if hasattr(spin, 'r') and spin.r != None:
+ r = spin.r / 1e-10
# CSA.
csa = None
- if hasattr(data, 'csa') and data.csa != None:
- csa = data.csa / 1e-6
+ if hasattr(spin, 'csa') and spin.csa != None:
+ csa = spin.csa / 1e-6
# Relaxation data and errors.
ri = []
@@ -612,13 +613,13 @@
try:
# Find the residue specific data corresponding to i.
index = None
- for j in xrange(data.num_ri):
- if data.ri_labels[j] == cdp.ri_labels[i] and
data.frq_labels[data.remap_table[j]] == cdp.frq_labels[cdp.remap_table[i]]:
+ for j in xrange(spin.num_ri):
+ if spin.ri_labels[j] == cdp.ri_labels[i] and
spin.frq_labels[spin.remap_table[j]] == cdp.frq_labels[cdp.remap_table[i]]:
index = j
# Data exists for this data type.
- ri.append(spin)
- ri_error.append(spin)
+ ri.append(spin.relax_data[index])
+ ri_error.append(spin.relax_error[index])
# No data exists for this data type.
except:
@@ -626,7 +627,7 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='value', nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=spin.num,
name=spin.name, select=spin.select, spin_set='value', nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
# Errors.
@@ -639,34 +640,32 @@
return
# Loop over the sequence.
- for i in xrange(len(cdp.res)):
- # Reassign data structure.
- data = cdp.res[i]
+ for spin in spin_loop(spin_id):
# J(0).
j0 = None
- if hasattr(data, 'j0_err'):
- j0 = data.j0_err
+ if hasattr(spin, 'j0_err'):
+ j0 = spin.j0_err
# J(wX).
jwx = None
- if hasattr(data, 'jwx_err'):
- jwx = data.jwx_err
+ if hasattr(spin, 'jwx_err'):
+ jwx = spin.jwx_err
# J(wH).
jwh = None
- if hasattr(data, 'jwh_err'):
- jwh = data.jwh_err
+ if hasattr(spin, 'jwh_err'):
+ jwh = spin.jwh_err
# Bond length.
r = None
- if hasattr(data, 'r_err') and data.r_err != None:
- r = data.r_err / 1e-10
+ if hasattr(spin, 'r_err') and spin.r_err != None:
+ r = spin.r_err / 1e-10
# CSA.
csa = None
- if hasattr(data, 'csa_err') and data.csa_err != None:
- csa = data.csa_err / 1e-6
+ if hasattr(spin, 'csa_err') and spin.csa_err != None:
+ csa = spin.csa_err / 1e-6
# Relaxation data and errors.
ri = []
@@ -676,7 +675,7 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='error', nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=spin.num,
name=spin.name, select=spin.select, spin_set='error', nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
# Simulation values.
@@ -685,34 +684,32 @@
# Loop over the simulations.
for i in xrange(cdp.sim_number):
# Loop over the sequence.
- for j in xrange(len(cdp.res)):
- # Reassign data structure.
- data = cdp.res[j]
+ for spin in spin_loop(spin_id):
# J(0).
j0 = None
- if hasattr(data, 'j0_sim'):
- j0 = data.j0_sim[i]
+ if hasattr(spin, 'j0_sim'):
+ j0 = spin.j0_sim[i]
# J(wX).
jwx = None
- if hasattr(data, 'jwx_sim'):
- jwx = data.jwx_sim[i]
+ if hasattr(spin, 'jwx_sim'):
+ jwx = spin.jwx_sim[i]
# J(wH).
jwh = None
- if hasattr(data, 'jwh_sim'):
- jwh = data.jwh_sim[i]
+ if hasattr(spin, 'jwh_sim'):
+ jwh = spin.jwh_sim[i]
# Bond length.
r = None
- if hasattr(data, 'r_sim') and data.r_sim != None and
data.r_sim[i] != None:
- r = data.r_sim[i] / 1e-10
+ if hasattr(spin, 'r_sim') and spin.r_sim != None and
spin.r_sim[i] != None:
+ r = spin.r_sim[i] / 1e-10
# CSA.
csa = None
- if hasattr(data, 'csa_sim') and data.csa_sim != None and
data.csa_sim[i] != None:
- csa = data.csa_sim[i] / 1e-6
+ if hasattr(spin, 'csa_sim') and spin.csa_sim != None and
spin.csa_sim[i] != None:
+ csa = spin.csa_sim[i] / 1e-6
# Relaxation data and errors.
ri = []
@@ -722,13 +719,13 @@
try:
# Find the residue specific data corresponding
to k.
index = None
- for l in xrange(data.num_ri):
- if data.ri_labels[l] == cdp.ri_labels[k] and
data.frq_labels[data.remap_table[l]] == cdp.frq_labels[cdp.remap_table[k]]:
+ for l in xrange(spin.num_ri):
+ if spin.ri_labels[l] == cdp.ri_labels[k] and
spin.frq_labels[spin.remap_table[l]] == cdp.frq_labels[cdp.remap_table[k]]:
index = l
# Data exists for this data type.
- ri.append(spin)
- ri_error.append(spin)
+ ri.append(`spin.relax_sim_data[i][index]`)
+ ri_error.append(`spin.relax_error[index]`)
# No data exists for this data type.
except:
@@ -736,4 +733,4 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='sim_'+`i`, nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=spin.num,
name=spin.name, select=spin.select, spin_set='sim_'+`i`, nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
r5266 - /1.3/specific_fns/jw_mapping.py