Author: bugman
Date: Thu Dec 4 13:23:18 2008
New Revision: 8125
URL: http://svn.gna.org/viewcvs/relax?rev=8125&view=rev
Log:
Seb, here is a challenge for the generic peak list reading code!
This includes a new valid peak intensity file and associated system test. In
this case the spectrum
ids are given, along with an array specifying the intensity columns. This
should cover much of what
I talked about in my post at
https://mail.gna.org/public/relax-devel/2008-12/msg00016.html.
Added:
1.3/test_suite/shared_data/peak_lists/generic_intensity2.txt
- copied, changed from r8124,
1.3/test_suite/shared_data/peak_lists/generic_intensity.txt
Modified:
1.3/test_suite/system_tests/peak_lists.py
Copied: 1.3/test_suite/shared_data/peak_lists/generic_intensity2.txt (from
r8124, 1.3/test_suite/shared_data/peak_lists/generic_intensity.txt)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/generic_intensity2.txt?p2=1.3/test_suite/shared_data/peak_lists/generic_intensity2.txt&p1=1.3/test_suite/shared_data/peak_lists/generic_intensity.txt&r1=8124&r2=8125&rev=8125&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/generic_intensity.txt (original)
+++ 1.3/test_suite/shared_data/peak_lists/generic_intensity2.txt Thu Dec 4
13:23:18 2008
@@ -1,7 +1,6 @@
-mol_name res_num res_name spin_num spin_name proton
intensity_1 intensity_2 intensity_3 intensity_4 intensity_5
intensity_6 intensity_7 intensity_8 intensity_9 intensity_10
-
-None 20 GLY None N HN 1.0000
0.9714 0.9602 0.9626 0.8839 0.8327
0.7088 0.5098 0.2410 0.1116
-None 23 ALA None N HN 1.0000
0.9789 0.9751 0.9762 0.9074 0.8532
0.7089 0.5170 0.2444 0.1537
-None 34 CYS None N HN 1.0000
0.9659 0.9580 0.9559 0.9325 0.8460
0.7187 0.5303 0.2954 0.1683
-None 35 MET None N HN 1.0000
0.9657 0.9389 0.9366 0.9331 0.8683
0.7169 0.5357 0.2769 0.1625
-None 36 LYS None N HN 1.0000
1.0060 0.9556 0.9456 0.9077 0.8411
0.6788 0.4558 0.2448 0.1569
+Num Name A B C D
E F G H I
J
+20 GLY 1.0000 0.9714 0.9602 0.9626
0.8839 0.8327 0.7088 0.5098 0.2410
0.1116
+23 ALA 1.0000 0.9789 0.9751 0.9762
0.9074 0.8532 0.7089 0.5170 0.2444
0.1537
+34 CYS 1.0000 0.9659 0.9580 0.9559
0.9325 0.8460 0.7187 0.5303 0.2954
0.1683
+35 MET 1.0000 0.9657 0.9389 0.9366
0.9331 0.8683 0.7169 0.5357 0.2769
0.1625
+36 LYS 1.0000 1.0060 0.9556 0.9456
0.9077 0.8411 0.6788 0.4558 0.2448
0.1569
Modified: 1.3/test_suite/system_tests/peak_lists.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/peak_lists.py?rev=8125&r1=8124&r2=8125&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/peak_lists.py (original)
+++ 1.3/test_suite/system_tests/peak_lists.py Thu Dec 4 13:23:18 2008
@@ -28,6 +28,7 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
from generic_fns import pipes
+from generic_fns.mol_res_spin import spin_loop
class Peak_lists(TestCase):
@@ -74,6 +75,47 @@
self.assertEqual(cdp.mol[0].res[0].spin[0].intensities[7], 0.5098)
self.assertEqual(cdp.mol[0].res[0].spin[0].intensities[8], 0.2410)
self.assertEqual(cdp.mol[0].res[0].spin[0].intensities[9], 0.1116)
+
+
+ def test_read_peak_list_generic2(self):
+ """Test the reading of a generic peak intensity list (test number
2)."""
+
+ # Get the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Create the sequence data, and name the spins.
+ self.relax.interpreter._Residue.create(20)
+ self.relax.interpreter._Residue.create(23)
+ self.relax.interpreter._Residue.create(34)
+ self.relax.interpreter._Residue.create(35)
+ self.relax.interpreter._Residue.create(36)
+ self.relax.interpreter._Spin.name(name='N')
+
+ # Spectrum ids.
+ spectrum_ids=['0.0109016', '0.0218032', '0.0436064', '0.0436064',
'0.0872128', '0.1744260', '0.3488510', '0.6977020', '1.3954000', '1.9949900']
+
+ # Read the peak list.
+
self.relax.interpreter._Spectrum.read_intensities(file="generic_intensity2.txt",
dir=sys.path[-1] + "/test_suite/shared_data/peak_lists",
spectrum_id=spectrum_ids, int_col=range(2, 12), int_method='volume')
+
+ # The intensities.
+ intensities = []
+ intensities.append([1.0000, 0.9714, 0.9602, 0.9626, 0.8839, 0.8327,
0.7088, 0.5098, 0.2410, 0.1116])
+ intensities.append([1.0000, 0.9789, 0.9751, 0.9762, 0.9074, 0.8532,
0.7089, 0.5170, 0.2444, 0.1537])
+ intensities.append([1.0000, 0.9659, 0.9580, 0.9559, 0.9325, 0.8460,
0.7187, 0.5303, 0.2954, 0.1683])
+ intensities.append([1.0000, 0.9657, 0.9389, 0.9366, 0.9331, 0.8683,
0.7169, 0.5357, 0.2769, 0.1625])
+ intensities.append([1.0000, 1.0060, 0.9556, 0.9456, 0.9077, 0.8411,
0.6788, 0.4558, 0.2448, 0.1569])
+
+ # Test the spectrum ids.
+ self.assertEqual(cdp.spectrum_ids, spectrum_ids)
+
+ # Test the data.
+ index = 0
+ for spin in spin_loop():
+ for j in xrange(len(spin.intensities)):
+ self.assertEqual(spin.intensities[j], intensities[index][j])
+
+ # Increment the index.
+ index = index + 1
def test_read_peak_list_nmrview(self):
r8125 - in /1.3/test_suite: shared_data/peak_lists/generic_intensity2.txt system_tests/peak_lists.py