Author: bugman
Date: Thu Feb 24 12:48:03 2011
New Revision: 12620
URL: http://svn.gna.org/viewcvs/relax?rev=12620&view=rev
Log:
The PDC NOE conversion script is now taking the data directly from the PDC
file.
Modified:
1.3/test_suite/shared_data/pdc_files/convert_data_noe.py
Modified: 1.3/test_suite/shared_data/pdc_files/convert_data_noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/pdc_files/convert_data_noe.py?rev=12620&r1=12619&r2=12620&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/pdc_files/convert_data_noe.py (original)
+++ 1.3/test_suite/shared_data/pdc_files/convert_data_noe.py Thu Feb 24
12:48:03 2011
@@ -1,84 +1,60 @@
#! /usr/bin/env python
-# The PDC data.
-data = [
-['Gln', 2, 122.508, 8.898, 0.694, 0.00027],
-['Ile', 3, 114.800, 8.280, 0.706, 0.00030],
-['Phe', 4, 118.172, 8.565, 0.755, 0.00032],
-['Val', 5, 120.902, 9.256, 0.736, 0.00029],
-['Lys', 6, 127.647, 8.914, 0.726, 0.00029],
-['Thr', 7, 115.121, 8.703, 0.739, 0.00027],
-['Leu', 8, 120.902, 9.061, 0.690, 0.00032],
-['Thr', 9, 105.486, 7.596, 0.607, 0.00031],
-['Gly', 10, 108.858, 7.784, 0.582, 0.00019],
-['Lys', 11, 121.545, 7.230, 0.548, 0.00022],
-['Thr', 12, 120.260, 8.589, 0.660, 0.00022],
-['Ile', 13, 127.326, 9.508, 0.746, 0.00033],
-['Thr', 14, 121.223, 8.679, 0.759, 0.00025],
-['Leu', 15, 124.756, 8.695, 0.776, 0.00031],
-['Glu', 16, 122.131, 8.081, 0.763, 0.00019],
-['Val', 17, 117.209, 8.898, 0.716, 0.00028],
-['Glu', 18, 118.975, 8.630, 0.695, 0.00025],
-['Ser', 20, 103.077, 6.994, 0.720, 0.00026],
-['Asp', 21, 123.472, 8.003, 0.756, 0.00020],
-['Thr', 22, 108.697, 7.832, 0.704, 0.00029],
-['Ile', 23, 120.902, 8.483, 0.695, 0.00039],
-['Asn', 25, 121.063, 7.889, 0.737, 0.00035],
-['Val', 26, 122.026, 8.076, 0.667, 0.00016],
-['Lys', 27, 118.654, 8.516, 0.760, 0.00036],
-['Ala', 28, 123.151, 7.946, 0.752, 0.00034],
-['Lys', 29, 119.778, 7.824, 0.746, 0.00040],
-['Thr', 30, 120.902, 8.247, 0.734, 0.00030],
-['Gln', 31, 123.151, 8.516, 0.740, 0.00022],
-['Asp', 32, 119.457, 7.979, 0.736, 0.00028],
-['Lys', 33, 115.121, 7.393, 0.766, 0.00031],
-['Glu', 34, 113.997, 8.687, 0.731, 0.00026],
-['Gly', 35, 108.537, 8.459, 0.778, 0.00025],
-['Ile', 36, 119.939, 6.124, 0.791, 0.00026],
-['Asp', 39, 113.194, 8.483, 0.769, 0.00027],
-['Gln', 40, 116.566, 7.784, 0.758, 0.00029],
-['Gln', 41, 117.690, 7.434, 0.769, 0.00033],
-['Arg', 42, 122.669, 8.467, 0.755, 0.00034],
-['Leu', 43, 124.114, 8.776, 0.761, 0.00037],
-['Ile', 44, 122.026, 9.085, 0.750, 0.00038],
-['Phe', 45, 124.756, 8.809, 0.777, 0.00039],
-['Ala', 46, 132.465, 8.931, 0.749, 0.00055],
-['Gly', 47, 102.113, 8.052, 0.752, 0.00029],
-['Lys', 48, 121.705, 7.946, 0.709, 0.00030],
-['Gln', 49, 122.669, 8.589, 0.619, 0.00025],
-['Leu', 50, 125.399, 8.516, 0.727, 0.00041],
-['Glu', 51, 122.829, 8.337, 0.724, 0.00038],
-['Asp', 52, 119.939, 8.109, 0.779, 0.00033],
-['Arg', 54, 118.975, 7.426, 0.781, 0.00038],
-['Thr', 55, 108.537, 8.792, 0.762, 0.00034],
-['Leu', 56, 117.690, 8.109, 0.769, 0.00033],
-['Ser', 57, 113.194, 8.434, 0.787, 0.00028],
-['Asp', 58, 124.114, 7.897, 0.735, 0.00028],
-['Tyr', 59, 115.442, 7.222, 0.742, 0.00028],
-['Asn', 60, 115.603, 8.109, 0.768, 0.00024],
-['Ile', 61, 118.493, 7.206, 0.737, 0.00036],
-['Gln', 62, 124.596, 7.572, 0.605, 0.00029],
-['Lys', 63, 120.260, 8.434, 0.796, 0.00027],
-['Glu', 64, 114.318, 9.272, 0.717, 0.00034],
-['Ser', 65, 114.639, 7.629, 0.722, 0.00029],
-['Thr', 66, 117.048, 8.670, 0.695, 0.00024],
-['Leu', 67, 127.486, 9.378, 0.758, 0.00033],
-['His', 68, 119.136, 9.191, 0.729, 0.00040],
-['Leu', 69, 123.632, 8.255, 0.666, 0.00027],
-['Val', 70, 126.362, 9.134, 0.734, 0.00038],
-['Leu', 71, 122.829, 8.052, 0.727, 0.00027],
-['Arg', 72, 123.472, 8.557, 0.620, 0.00021],
-['Leu', 73, 124.114, 8.288, 0.340, 0.00017],
-['Arg', 74, 121.545, 8.378, 0.165, 0.00020],
-['Gly', 75, 110.624, 8.426, -0.432, 0.00028],
-['Gly', 76, 114.639, 7.889, -1.30, 0.00032]]
+from string import split, strip
+
+# The file data.
+file = open('testNOE.txt')
+lines = file.readlines()
+file.close()
+
+# Get the data.
+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 residue name and number.
+ res_name, res_num = split(row[0])
+
+ # The values.
+ data.append([])
+ data[index].append(res_name)
+ data[index].append(int(res_num[1:-1]))
+ data[index].append(float(row[3]))
+ data[index].append(float(row[4]))
+
+ # Increment the residue index.
+ index += 1
noe = []
noe_err = []
for i in range(len(data)):
- noe.append(data[i][4])
- noe_err.append(data[i][5])
+ noe.append(data[i][2])
+ noe_err.append(data[i][3])
print("\nnoe = %s" % noe)
print("\nnoe_err = %s" % noe_err)
r12620 - /1.3/test_suite/shared_data/pdc_files/convert_data_noe.py