Author: bugman
Date: Fri Feb 18 14:20:06 2011
New Revision: 12556
URL: http://svn.gna.org/viewcvs/relax?rev=12556&view=rev
Log:
Added a relax script and R1 data file for relax's optimisation and MC sims
using the PDC file errors.
Added:
1.3/test_suite/shared_data/pdc_files/r1_pdc_err
1.3/test_suite/shared_data/pdc_files/relax_fit_pdc_err.py
- copied, changed from r12554,
1.3/test_suite/shared_data/pdc_files/relax_fit.py
Added: 1.3/test_suite/shared_data/pdc_files/r1_pdc_err
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/pdc_files/r1_pdc_err?rev=12556&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/pdc_files/r1_pdc_err (added)
+++ 1.3/test_suite/shared_data/pdc_files/r1_pdc_err Fri Feb 18 14:20:06 2011
@@ -1,0 +1,72 @@
+
+# mol_name res_num res_name spin_num spin_name value
error
+None 2 Gln None N 2.19316068443
0.0264822775112
+None 3 Ile None N 2.33150942395
0.0218282475286
+None 4 Phe None N 2.34809773828
0.0393993956573
+None 5 Val None N 2.24905317514
0.0190416227806
+None 6 Lys None N 2.27991249993
0.0073387122964
+None 7 Thr None N 2.21988325334
0.0289980021014
+None 8 Leu None N 2.23992585719
0.0394637142884
+None 9 Thr None N 1.96827404586
0.0285585555608
+None 10 Gly None N 2.08825352037
0.00856203608884
+None 11 Lys None N 1.99766965295
0.0154821098023
+None 12 Thr None N 2.16418266589
0.0589894950385
+None 13 Ile None N 2.27249997894
0.0323797055027
+None 14 Thr None N 2.19913359459
0.0261282530191
+None 15 Leu None N 2.27947735732
0.0804008170395
+None 16 Glu None N 2.08663871613
0.0742976416989
+None 17 Val None N 2.28454679926
0.0319478148557
+None 18 Glu None N 2.10794161516
0.0491390514111
+None 20 Ser None N 2.2432376545
0.0174075720472
+None 21 Asp None N 2.34905882789
0.00896916086091
+None 22 Thr None N 2.27492782819
0.0283784241729
+None 23 Ile None N 2.46692508258
0.0512139594604
+None 25 Asn None N 2.39550908267
0.028141856637
+None 26 Val None N 2.13297271051
0.0738836932379
+None 27 Lys None N 2.36245343286
0.034473000886
+None 28 Ala None N 2.38481618154
0.0369276054641
+None 29 Lys None N 2.32688199592
0.0267154381038
+None 30 Thr None N 2.42020223098
0.0641345037416
+None 31 Gln None N 2.37198006924
0.0607157552927
+None 32 Asp None N 2.343030317
0.0287089229986
+None 33 Lys None N 2.19288519999
0.0322404521468
+None 34 Glu None N 2.23809730593
0.016155226898
+None 35 Gly None N 2.24610605696
0.0166231784999
+None 36 Ile None N 1.99097003714
0.018556395961
+None 39 Asp None N 2.29368308937
0.0107946336402
+None 40 Gln None N 2.25465715695
0.0219579437623
+None 41 Gln None N 2.22439489827
0.0246838738103
+None 42 Arg None N 2.27979894813
0.14609662846
+None 43 Leu None N 2.17239195077
0.0562093749792
+None 44 Ile None N 2.27944810393
0.0274015962376
+None 45 Phe None N 2.26621382042
0.0325598012054
+None 46 Ala None N 2.17327103743
0.0366263114163
+None 47 Gly None N 2.19159971705
0.0200974396044
+None 48 Lys None N 2.20125816954
0.0769594227925
+None 49 Gln None N 2.11409184343
0.0211565921351
+None 50 Leu None N 2.24441747047
0.0466054926297
+None 51 Glu None N 2.13351495913
0.0369010861993
+None 52 Asp None N 2.04583349976
0.0309251585403
+None 54 Arg None N 2.19228267695
0.0125176652031
+None 55 Thr None N 2.27502074947
0.0319568936121
+None 56 Leu None N 2.36913113746
0.0158844775147
+None 57 Ser None N 2.29814478201
0.0142640516301
+None 58 Asp None N 2.37720483191
0.0272911357828
+None 59 Tyr None N 2.22553611629
0.0125933167265
+None 60 Asn None N 2.28459962433
0.013370924242
+None 61 Ile None N 2.34213728573
0.0264153868176
+None 62 Gln None N 1.97367886288
0.0217945020797
+None 63 Lys None N 2.16500024708
0.0195312534223
+None 64 Glu None N 2.31913930394
0.0223294049604
+None 65 Ser None N 2.18918681844
0.00908363177241
+None 66 Thr None N 2.18167008464
0.0112902195625
+None 67 Leu None N 2.26772345178
0.0444564014823
+None 68 His None N 2.24680733455
0.00926065649886
+None 69 Leu None N 2.24851949133
0.0379125750722
+None 70 Val None N 2.31543911345
0.0279226422469
+None 71 Leu None N 2.1756894166
0.00987045835498
+None 72 Arg None N 2.16361975928
0.0253849160526
+None 73 Leu None N 1.85657597782
0.0255460422485
+None 74 Arg None N 1.6122677679
0.0231001217925
+None 75 Gly None N 1.16243924266
0.023448186193
+None 76 Gly None N 0.763064480891
0.0030557315479
Copied: 1.3/test_suite/shared_data/pdc_files/relax_fit_pdc_err.py (from
r12554, 1.3/test_suite/shared_data/pdc_files/relax_fit.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/pdc_files/relax_fit_pdc_err.py?p2=1.3/test_suite/shared_data/pdc_files/relax_fit_pdc_err.py&p1=1.3/test_suite/shared_data/pdc_files/relax_fit.py&r1=12554&r2=12556&rev=12556&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/pdc_files/relax_fit.py (original)
+++ 1.3/test_suite/shared_data/pdc_files/relax_fit_pdc_err.py Fri Feb 18
14:20:06 2011
@@ -1,4 +1,9 @@
# Script for relaxation curve fitting.
+
+# relax module imports.
+from generic_fns.mol_res_spin import return_spin
+from relax_io import extract_data
+
# Create the data pipe.
pipe.create('rx', 'relax_fit')
@@ -41,6 +46,9 @@
1.50000000
]
+# The error file.
+err_lines = extract_data('errors_R1.txt')
+
# Loop over the spectra.
for i in xrange(len(times)):
# Load the peak intensities.
@@ -49,12 +57,20 @@
# Set the relaxation times.
relax_fit.relax_time(time=times[i], spectrum_id=names[i])
-# Specify the duplicated spectra.
-spectrum.replicated(spectrum_ids=['0.10', '0.10b'])
-spectrum.replicated(spectrum_ids=['0.50', '0.50b'])
+ # The errors.
+ for j in range(len(err_lines)):
+ # Skip comments.
+ if err_lines[j][0][0] == '#':
+ continue
-# Peak intensity error analysis.
-spectrum.error_analysis()
+ # The spin ID.
+ spin_id = ':%s' % err_lines[j][1]
+ spin = return_spin(spin_id)
+
+ # Set the error.
+ if not hasattr(spin, 'intensity_err'):
+ spin.intensity_err = {}
+ spin.intensity_err[names[i]] = float(err_lines[j][i+2])
# Set the relaxation curve type.
relax_fit.select_model('exp')
@@ -73,4 +89,7 @@
monte_carlo.error_analysis()
# Save the relaxation rates.
-value.write(param='rx', file='r1', force=True)
+value.write(param='rx', file='r1_pdc_err', force=True)
+
+# Save the program state.
+state.save('state', force=True)
r12556 - in /1.3/test_suite/shared_data/pdc_files: r1_pdc_err relax_fit_pdc_err.py