Author: bugman
Date: Wed Mar 11 18:02:08 2009
New Revision: 8970
URL: http://svn.gna.org/viewcvs/relax?rev=8970&view=rev
Log:
Updated the order_parameters saveframe to match the new NMR-STAR design.
The new design is described in the document attached to the post
https://mail.gna.org/public/relax-devel/2009-03/msg00019.html (Message-id:
<49B7463E.7080109@xxxxxxxxxxxxx>).
Modified:
branches/bmrb/bmrblib/thermodynamics/order_parameters.py
branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/bmrblib/thermodynamics/order_parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/order_parameters.py?rev=8970&r1=8969&r2=8970&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters.py Wed Mar 11
18:02:08 2009
@@ -252,25 +252,25 @@
# Keys and objects.
info = [
- ['OrderParamID', 'data_ids'],
- ['CompIndexID', 'res_nums'],
- ['CompID', 'res_names'],
- ['AtomID', 'atom_names'],
- ['OrderParamVal', 's2'],
- ['OrderParamValErr', 's2_err'],
- ['TauEVal', 'te'],
- ['TauEValErr', 'te_err'],
- ['TauFVal', 'tf'],
- ['TauFValErr', 'tf_err'],
- ['TauSVal', 'ts'],
- ['TauSValErr', 'ts_err'],
- ['RexVal', 'rex'],
- ['RexValErr', 'rex_err'],
- ['Sf2Val', 's2f'],
- ['Sf2ValErr', 's2f_err'],
- ['Ss2Val', 's2s'],
- ['Ss2ValErr', 's2s_err'],
- ['ChiSquaredVal', 'chi2']
+ ['OrderParamID', 'data_ids'],
+ ['CompIndexID', 'res_nums'],
+ ['CompID', 'res_names'],
+ ['AtomID', 'atom_names'],
+ ['S2Val', 's2'],
+ ['S2ValErr', 's2_err'],
+ ['S2fVal', 's2f'],
+ ['S2fValErr', 's2f_err'],
+ ['S2sVal', 's2s'],
+ ['S2sValErr', 's2s_err'],
+ ['TauEVal', 'te'],
+ ['TauEValErr', 'te_err'],
+ ['TauFVal', 'tf'],
+ ['TauFValErr', 'tf_err'],
+ ['TauSVal', 'ts'],
+ ['TauSValErr', 'ts_err'],
+ ['RexVal', 'rex'],
+ ['RexValErr', 'rex_err'],
+ ['ChiSquaredVal', 'chi2']
]
# Get the TabTable.
@@ -297,8 +297,8 @@
self.tag_names['CompIndexID'] = 'Residue_seq_code'
self.tag_names['CompID'] = 'Residue_label'
self.tag_names['AtomID'] = 'Atom_name'
- self.tag_names['OrderParamVal'] = 'S2_value'
- self.tag_names['OrderParamValErr'] = 'S2_value_fit_error'
+ self.tag_names['S2Val'] = 'S2_value'
+ self.tag_names['S2ValErr'] = 'S2_value_fit_error'
self.tag_names['TauEVal'] = 'Tau_e_value'
self.tag_names['TauEValErr'] = 'Tau_e_value_fit_error'
self.tag_names['TauFVal'] = 'Tau_f_value'
@@ -307,7 +307,7 @@
self.tag_names['TauSValErr'] = 'Tau_s_value_fit_error'
self.tag_names['RexVal'] = None
self.tag_names['RexValErr'] = None
- self.tag_names['Sf2Val'] = 'S2f_value'
- self.tag_names['Sf2ValErr'] = 'S2f_value_fit_error'
- self.tag_names['Ss2Val'] = 'S2s_value'
- self.tag_names['Ss2ValErr'] = 'S2s_value_fit_error'
+ self.tag_names['S2fVal'] = 'S2f_value'
+ self.tag_names['S2fValErr'] = 'S2f_value_fit_error'
+ self.tag_names['S2sVal'] = 'S2s_value'
+ self.tag_names['S2sValErr'] = 'S2s_value_fit_error'
Modified: branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py?rev=8970&r1=8969&r2=8970&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py Wed Mar 11
18:02:08 2009
@@ -89,18 +89,18 @@
self.tag_names['CompIndexID'] = 'Comp_index_ID'
self.tag_names['CompID'] = 'Comp_ID'
self.tag_names['AtomID'] = 'Atom_ID'
- self.tag_names['OrderParamVal'] = 'Order_param_val'
- self.tag_names['OrderParamValErr'] = 'Order_param_val_fit_err'
+ self.tag_names['S2Val'] = 'S2_val'
+ self.tag_names['S2ValErr'] = 'S2_val_err'
+ self.tag_names['S2fVal'] = 'S2f_val'
+ self.tag_names['S2fValErr'] = 'S2f_val_err'
+ self.tag_names['S2sVal'] = 'S2s_val'
+ self.tag_names['S2sValErr'] = 'S2s_val_err'
self.tag_names['TauEVal'] = 'Tau_e_val'
- self.tag_names['TauEValErr'] = 'Tau_e_val_fit_err'
+ self.tag_names['TauEValErr'] = 'Tau_e_val_err'
self.tag_names['TauFVal'] = 'Tau_f_val'
- self.tag_names['TauFValErr'] = 'Tau_f_val_fit_err'
+ self.tag_names['TauFValErr'] = 'Tau_f_val_err'
self.tag_names['TauSVal'] = 'Tau_s_val'
- self.tag_names['TauSValErr'] = 'Tau_s_val_fit_err'
+ self.tag_names['TauSValErr'] = 'Tau_s_val_err'
self.tag_names['RexVal'] = 'Rex_val'
- self.tag_names['RexValErr'] = 'Rex_val_fit_err'
- self.tag_names['Sf2Val'] = 'S2f_val'
- self.tag_names['Sf2ValErr'] = 'S2f_val_fit_err'
- self.tag_names['Ss2Val'] = 'S2s_val'
- self.tag_names['Ss2ValErr'] = 'S2s_val_fit_err'
+ self.tag_names['RexValErr'] = 'Rex_val_err'
self.tag_names['ChiSquaredVal'] = 'Chi_squared_val'
Modified: branches/bmrb/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/bmrb.py?rev=8970&r1=8969&r2=8970&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Wed Mar 11 18:02:08 2009
@@ -21,11 +21,12 @@
###############################################################################
# Python module imports.
+from math import pi
import string
# relax module imports.
from bmrblib.nmr_star_dict_v3_1 import NMR_STAR_v3_1
-from generic_fns import mol_res_spin, relax_data
+from generic_fns import mol_res_spin, pipes, relax_data
from generic_fns.mol_res_spin import spin_loop
@@ -59,6 +60,9 @@
@type file_path: str
"""
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
# Initialise the NMR-STAR data object.
star = NMR_STAR_v3_1('relax_model_free_results', file_path)
@@ -67,6 +71,9 @@
# Generate the relaxation data saveframes.
relax_data.bmrb_write(star)
+
+ # Rex frq.
+ rex_frq = cdp.frq[0]
# Initialise the spin specific data lists.
res_num_list = []
@@ -92,6 +99,8 @@
tf_err_list = []
ts_err_list = []
rex_err_list = []
+
+ chi2_list = []
# Store the spin specific data in lists for later use.
for spin, mol_name, res_num, res_name, spin_id in
spin_loop(full_info=True, return_id=True):
@@ -119,7 +128,6 @@
r_list.append(spin.r)
isotope_list.append(int(string.strip(spin.heteronuc_type,
string.ascii_letters)))
-
# Model-free data.
s2_list.append(spin.s2)
s2f_list.append(spin.s2f)
@@ -127,7 +135,10 @@
te_list.append(spin.te)
tf_list.append(spin.tf)
ts_list.append(spin.ts)
- rex_list.append(spin.rex)
+ if spin.rex == None:
+ rex_list.append(None)
+ else:
+ rex_list.append(spin.rex / (2.0*pi*rex_frq**2))
s2_err_list.append(spin.s2_err)
s2f_err_list.append(spin.s2f_err)
@@ -135,13 +146,19 @@
te_err_list.append(spin.te_err)
tf_err_list.append(spin.tf_err)
ts_err_list.append(spin.ts_err)
- rex_err_list.append(spin.rex_err)
+ if spin.rex_err == None:
+ rex_err_list.append(None)
+ else:
+ rex_err_list.append(spin.rex_err / (2.0*pi*rex_frq**2))
+
+ # Opt stats.
+ chi2_list.append(spin.chi2)
# Generate the CSA saveframe.
star.chem_shift_anisotropy.add(res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, isotope=isotope_list,
csa=csa_list)
# Generate the model-free data saveframe.
- star.order_parameters.add(res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, s2=s2_list, s2f=s2f_list,
s2s=s2s_list, te=te_list, tf=tf_list, ts=ts_list, rex=rex_list,
s2_err=s2_err_list, s2f_err=s2f_err_list, s2s_err=s2s_err_list,
te_err=te_err_list, tf_err=tf_err_list, ts_err=ts_err_list,
rex_err=rex_err_list)
+ star.order_parameters.add(res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, s2=s2_list, s2f=s2f_list,
s2s=s2s_list, te=te_list, tf=tf_list, ts=ts_list, rex=rex_list,
s2_err=s2_err_list, s2f_err=s2f_err_list, s2s_err=s2s_err_list,
te_err=te_err_list, tf_err=tf_err_list, ts_err=ts_err_list,
rex_err=rex_err_list, rex_frq=rex_frq, chi2=chi2_list)
# Write the contents to the STAR formatted file.
star.write()
r8970 - in /branches/bmrb: bmrblib/thermodynamics/ specific_fns/model_free/