Author: bugman
Date: Tue Feb 22 15:08:50 2011
New Revision: 12608
URL: http://svn.gna.org/viewcvs/relax?rev=12608&view=rev
Log:
Updated the convert_data_r1.py to directly read the data out of the Bruker
PDC file.
Modified:
1.3/test_suite/shared_data/pdc_files/convert_data_r1.py
Modified: 1.3/test_suite/shared_data/pdc_files/convert_data_r1.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/pdc_files/convert_data_r1.py?rev=12608&r1=12607&r2=12608&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/pdc_files/convert_data_r1.py (original)
+++ 1.3/test_suite/shared_data/pdc_files/convert_data_r1.py Tue Feb 22
15:08:50 2011
@@ -1,77 +1,122 @@
#! /usr/bin/env python
+
+from string import split, strip
+
+
+# The file data.
+file = open('testT1.txt')
+lines = file.readlines()
+file.close()
# The data - PDC T2, PDC T2 err, PDC scale factor, relax R2, relax R2 err
(MC sim).
data = [
-['Gln', 2, 0.4560, 0.012326 , 2.22814 , 2.19316068443,
0.0264822775112],
-['Ile', 3, 0.4289, 0.0089800 , 2.22814 , 2.33150942395,
0.0218282475286],
-['Phe', 4, 0.4259, 0.015866 , 2.22814 , 2.34809773828,
0.0393993956573],
-['Val', 5, 0.4446, 0.0084807 , 2.22814 , 2.24905317514,
0.0190416227806],
-['Lys', 6, 0.4386, 0.0032737 , 2.22814 , 2.27991249993,
0.0073387122964],
-['Thr', 7, 0.4505, 0.012887 , 2.22814 , 2.21988325334,
0.0289980021014],
-['Leu', 8, 0.4464, 0.017357 , 2.22814, 2.23992585719,
0.0394637142884],
-['Thr', 9, 0.5081, 0.016893 , 2.22814, 1.96827404586,
0.0285585555608],
-['Gly', 10, 0.4789, 0.0045383 , 2.22814, 2.08825352037,
0.00856203608884],
-['Lys', 11, 0.5006, 0.0087386 , 2.22814, 1.99766965295,
0.0154821098023],
-['Thr', 12, 0.4621, 0.028354 , 2.22814, 2.16418266589,
0.0589894950385],
-['Ile', 13, 0.4400, 0.014724 , 2.22814 , 2.27249997894,
0.0323797055027],
-['Thr', 14, 0.4547, 0.011743 , 2.22814 , 2.19913359459,
0.0261282530191],
-['Leu', 15, 0.4387, 0.033559 , 2.22814 , 2.27947735732,
0.0804008170395],
-['Glu', 16, 0.4792, 0.038163 , 2.22814, 2.08663871613,
0.0742976416989],
-['Val', 17, 0.4377, 0.013371 , 2.22814 , 2.28454679926,
0.0319478148557],
-['Glu', 18, 0.4744, 0.025534 , 2.22814 , 2.10794161516,
0.0491390514111],
-['Ser', 20, 0.4458, 0.0075985 , 2.22814 , 2.2432376545,
0.0174075720472],
-['Asp', 21, 0.4257, 0.0036873 , 2.22814 , 2.34905882789,
0.00896916086091],
-['Thr', 22, 0.4396, 0.012438 , 2.22814 , 2.27492782819,
0.0283784241729],
-['Ile', 23, 0.4054, 0.018904 , 2.22814, 2.46692508258,
0.0512139594604],
-['Asn', 25, 0.4174, 0.010689 , 2.22814 , 2.39550908267,
0.028141856637],
-['Val', 26, 0.4688, 0.035345 , 2.22814, 2.13297271051,
0.0738836932379],
-['Lys', 27, 0.4233, 0.013666 , 2.22814 , 2.36245343286,
0.034473000886],
-['Ala', 28, 0.4193, 0.014360 , 2.22814 , 2.38481618154,
0.0369276054641],
-['Lys', 29, 0.4298, 0.011476 , 2.22814 , 2.32688199592,
0.0267154381038],
-['Thr', 30, 0.4132, 0.026029 , 2.22814, 2.42020223098,
0.0641345037416],
-['Gln', 31, 0.4216, 0.023199 , 2.22814 , 2.37198006924,
0.0607157552927],
-['Asp', 32, 0.4268, 0.011464 , 2.22814 , 2.343030317,
0.0287089229986],
-['Lys', 33, 0.4560, 0.014005 , 2.22814 , 2.19288519999,
0.0322404521468],
-['Glu', 34, 0.4468, 0.0067758 , 2.22814 , 2.23809730593,
0.016155226898],
-['Gly', 35, 0.4452, 0.0072146 , 2.22814 , 2.24610605696,
0.0166231784999],
-['Ile', 36, 0.5023, 0.011122 , 2.22814 , 1.99097003714,
0.018556395961],
-['Asp', 39, 0.4360, 0.0041799 , 2.22814 , 2.29368308937,
0.0107946336402],
-['Gln', 40, 0.4435, 0.0097303 , 2.22814 , 2.25465715695,
0.0219579437623],
-['Gln', 41, 0.4496, 0.010974 , 2.22814 , 2.22439489827,
0.0246838738103],
-['Arg', 42, 0.4386, 0.060259 , 2.22814, 2.27979894813,
0.14609662846],
-['Leu', 43, 0.4603, 0.027054 , 2.22814 , 2.17239195077,
0.0562093749792],
-['Ile', 44, 0.4387, 0.012389 , 2.22814 , 2.27944810393,
0.0274015962376],
-['Phe', 45, 0.4413, 0.014084 , 2.22814 , 2.26621382042,
0.0325598012054],
-['Ala', 46, 0.4601, 0.017401 , 2.22814, 2.17327103743,
0.0366263114163],
-['Gly', 47, 0.4563, 0.0095167 , 2.22814, 2.19159971705,
0.0200974396044],
-['Lys', 48, 0.4543, 0.034380 , 2.22814, 2.20125816954,
0.0769594227925],
-['Gln', 49, 0.4730, 0.0099851 , 2.22814 , 2.11409184343,
0.0211565921351],
-['Leu', 50, 0.4455, 0.020395 , 2.22814 , 2.24441747047,
0.0466054926297],
-['Glu', 51, 0.4687, 0.018214 , 2.22814 , 2.13351495913,
0.0369010861993],
-['Asp', 52, 0.4888, 0.017327 , 2.22814 , 2.04583349976,
0.0309251585403],
-['Arg', 54, 0.4561, 0.0059463 , 2.22814 , 2.19228267695,
0.0125176652031],
-['Thr', 55, 0.4396, 0.013766 , 2.22814 , 2.27502074947,
0.0319568936121],
-['Leu', 56, 0.4221, 0.0064286 , 2.22814 , 2.36913113746,
0.0158844775147],
-['Ser', 57, 0.4351, 0.0057569 , 2.22814 , 2.29814478201,
0.0142640516301],
-['Asp', 58, 0.4207, 0.010105 , 2.22814 , 2.37720483191,
0.0272911357828],
-['Tyr', 59, 0.4493, 0.0055646 , 2.22814 , 2.22553611629,
0.0125933167265],
-['Asn', 60, 0.4377, 0.0058785 , 2.22814 , 2.28459962433,
0.013370924242],
-['Ile', 61, 0.4270, 0.010546 , 2.22814 , 2.34213728573,
0.0264153868176],
-['Gln', 62, 0.5067, 0.012662 , 2.22814 , 1.97367886288,
0.0217945020797],
-['Lys', 63, 0.4619, 0.0094808 , 2.22814 , 2.16500024708,
0.0195312534223],
-['Glu', 64, 0.4312, 0.0095453 , 2.22814 , 2.31913930394,
0.0223294049604],
-['Ser', 65, 0.4568, 0.0043694 , 2.22814 , 2.18918681844,
0.00908363177241],
-['Thr', 66, 0.4584, 0.0054046 , 2.22814 , 2.18167008464,
0.0112902195625],
-['Leu', 67, 0.4410, 0.018436 , 2.22814, 2.26772345178,
0.0444564014823],
-['His', 68, 0.4451, 0.0043067 , 2.22814 , 2.24680733455,
0.00926065649886],
-['Leu', 69, 0.4447, 0.015813 , 2.22814 , 2.24851949133,
0.0379125750722],
-['Val', 70, 0.4319, 0.011793 , 2.22814 , 2.31543911345,
0.0279226422469],
-['Leu', 71, 0.4596, 0.0046414 , 2.22814 , 2.1756894166,
0.00987045835498],
-['Arg', 72, 0.4622, 0.012209 , 2.22814 , 2.16361975928,
0.0253849160526],
-['Leu', 73, 0.5386, 0.016241 , 2.22814, 1.85657597782,
0.0255460422485],
-['Arg', 74, 0.6202, 0.020482 , 2.22814, 1.6122677679,
0.0231001217925],
-['Gly', 75, 0.8603, 0.038094 , 2.22814, 1.16243924266,
0.023448186193],
-['Gly', 76, 1.311, 0.011609 , 2.22814, 0.763064480891,
0.0030557315479]]
+['Gln', 2, None, None, None, 2.19316068443, 0.0264822775112],
+['Ile', 3, None, None, None, 2.33150942395, 0.0218282475286],
+['Phe', 4, None, None, None, 2.34809773828, 0.0393993956573],
+['Val', 5, None, None, None, 2.24905317514, 0.0190416227806],
+['Lys', 6, None, None, None, 2.27991249993, 0.0073387122964],
+['Thr', 7, None, None, None, 2.21988325334, 0.0289980021014],
+['Leu', 8, None, None, None, 2.23992585719, 0.0394637142884],
+['Thr', 9, None, None, None, 1.96827404586, 0.0285585555608],
+['Gly', 10, None, None, None, 2.08825352037, 0.00856203608884],
+['Lys', 11, None, None, None, 1.99766965295, 0.0154821098023],
+['Thr', 12, None, None, None, 2.16418266589, 0.0589894950385],
+['Ile', 13, None, None, None, 2.27249997894, 0.0323797055027],
+['Thr', 14, None, None, None, 2.19913359459, 0.0261282530191],
+['Leu', 15, None, None, None, 2.27947735732, 0.0804008170395],
+['Glu', 16, None, None, None, 2.08663871613, 0.0742976416989],
+['Val', 17, None, None, None, 2.28454679926, 0.0319478148557],
+['Glu', 18, None, None, None, 2.10794161516, 0.0491390514111],
+['Ser', 20, None, None, None, 2.2432376545, 0.0174075720472],
+['Asp', 21, None, None, None, 2.34905882789, 0.00896916086091],
+['Thr', 22, None, None, None, 2.27492782819, 0.0283784241729],
+['Ile', 23, None, None, None, 2.46692508258, 0.0512139594604],
+['Asn', 25, None, None, None, 2.39550908267, 0.028141856637],
+['Val', 26, None, None, None, 2.13297271051, 0.0738836932379],
+['Lys', 27, None, None, None, 2.36245343286, 0.034473000886],
+['Ala', 28, None, None, None, 2.38481618154, 0.0369276054641],
+['Lys', 29, None, None, None, 2.32688199592, 0.0267154381038],
+['Thr', 30, None, None, None, 2.42020223098, 0.0641345037416],
+['Gln', 31, None, None, None, 2.37198006924, 0.0607157552927],
+['Asp', 32, None, None, None, 2.343030317, 0.0287089229986],
+['Lys', 33, None, None, None, 2.19288519999, 0.0322404521468],
+['Glu', 34, None, None, None, 2.23809730593, 0.016155226898],
+['Gly', 35, None, None, None, 2.24610605696, 0.0166231784999],
+['Ile', 36, None, None, None, 1.99097003714, 0.018556395961],
+['Asp', 39, None, None, None, 2.29368308937, 0.0107946336402],
+['Gln', 40, None, None, None, 2.25465715695, 0.0219579437623],
+['Gln', 41, None, None, None, 2.22439489827, 0.0246838738103],
+['Arg', 42, None, None, None, 2.27979894813, 0.14609662846],
+['Leu', 43, None, None, None, 2.17239195077, 0.0562093749792],
+['Ile', 44, None, None, None, 2.27944810393, 0.0274015962376],
+['Phe', 45, None, None, None, 2.26621382042, 0.0325598012054],
+['Ala', 46, None, None, None, 2.17327103743, 0.0366263114163],
+['Gly', 47, None, None, None, 2.19159971705, 0.0200974396044],
+['Lys', 48, None, None, None, 2.20125816954, 0.0769594227925],
+['Gln', 49, None, None, None, 2.11409184343, 0.0211565921351],
+['Leu', 50, None, None, None, 2.24441747047, 0.0466054926297],
+['Glu', 51, None, None, None, 2.13351495913, 0.0369010861993],
+['Asp', 52, None, None, None, 2.04583349976, 0.0309251585403],
+['Arg', 54, None, None, None, 2.19228267695, 0.0125176652031],
+['Thr', 55, None, None, None, 2.27502074947, 0.0319568936121],
+['Leu', 56, None, None, None, 2.36913113746, 0.0158844775147],
+['Ser', 57, None, None, None, 2.29814478201, 0.0142640516301],
+['Asp', 58, None, None, None, 2.37720483191, 0.0272911357828],
+['Tyr', 59, None, None, None, 2.22553611629, 0.0125933167265],
+['Asn', 60, None, None, None, 2.28459962433, 0.013370924242],
+['Ile', 61, None, None, None, 2.34213728573, 0.0264153868176],
+['Gln', 62, None, None, None, 1.97367886288, 0.0217945020797],
+['Lys', 63, None, None, None, 2.16500024708, 0.0195312534223],
+['Glu', 64, None, None, None, 2.31913930394, 0.0223294049604],
+['Ser', 65, None, None, None, 2.18918681844, 0.00908363177241],
+['Thr', 66, None, None, None, 2.18167008464, 0.0112902195625],
+['Leu', 67, None, None, None, 2.26772345178, 0.0444564014823],
+['His', 68, None, None, None, 2.24680733455, 0.00926065649886],
+['Leu', 69, None, None, None, 2.24851949133, 0.0379125750722],
+['Val', 70, None, None, None, 2.31543911345, 0.0279226422469],
+['Leu', 71, None, None, None, 2.1756894166, 0.00987045835498],
+['Arg', 72, None, None, None, 2.16361975928, 0.0253849160526],
+['Leu', 73, None, None, None, 1.85657597782, 0.0255460422485],
+['Arg', 74, None, None, None, 1.6122677679, 0.0231001217925],
+['Gly', 75, None, None, None, 1.16243924266, 0.023448186193],
+['Gly', 76, None, None, None, 0.763064480891, 0.0030557315479]]
+
+# Get the data.
+in_data = False
+index = 0
+for line in lines:
+ # Split the line.
+ row = split(line, "\t")
+
+ # Strip the rubbish.
+ for j in range(len(row)):
+ row[j] = strip(row[j])
+
+ # Empty line.
+ if len(row) == 0:
+ continue
+
+ # The section.
+ if row[0] == 'SECTION:' and row[1] == 'results':
+ in_data = True
+ continue
+
+ # Not in the data section.
+ if not in_data:
+ continue
+
+ # The header line.
+ if row[0] == 'Peak name':
+ continue
+
+ # The values.
+ print `row`
+ data[index][2] = float(row[3])
+ data[index][3] = float(row[4])
+ data[index][4] = float(row[5])
+
+ # Increment the residue index.
+ index += 1
r1 = []
r1_err = []
r12608 - /1.3/test_suite/shared_data/pdc_files/convert_data_r1.py