Author: bugman
Date: Fri Oct 24 16:14:19 2008
New Revision: 7966
URL: http://svn.gna.org/viewcvs/relax?rev=7966&view=rev
Log:
Created a system test using Tyler Reddy's bug report - bug #12487
(https://gna.org/bugs/?12487).
Added:
1.3/test_suite/shared_data/results_files/tylers_peptide_trunc.bz2 (with
props)
1.3/test_suite/shared_data/structures/tylers_peptide_trunc.pdb
1.3/test_suite/system_tests/scripts/tylers_peptide.py
Modified:
1.3/test_suite/system_tests/model_free.py
Added: 1.3/test_suite/shared_data/results_files/tylers_peptide_trunc.bz2
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/results_files/tylers_peptide_trunc.bz2?rev=7966&view=auto
==============================================================================
Binary file - no diff available.
Propchange: 1.3/test_suite/shared_data/results_files/tylers_peptide_trunc.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added: 1.3/test_suite/shared_data/structures/tylers_peptide_trunc.pdb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/structures/tylers_peptide_trunc.pdb?rev=7966&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/structures/tylers_peptide_trunc.pdb (added)
+++ 1.3/test_suite/shared_data/structures/tylers_peptide_trunc.pdb Fri Oct 24
16:14:19 2008
@@ -1,0 +1,22 @@
+MODEL 11
+ATOM 58 N LEU A 111 49.590 -6.195 2.883 1.00 0.00
N
+ATOM 59 CA LEU A 111 50.800 -5.667 3.505 1.00 0.00
C
+ATOM 60 C LEU A 111 51.791 -5.186 2.447 1.00 0.00
C
+ATOM 61 O LEU A 111 52.781 -4.528 2.764 1.00 0.00
O
+ATOM 62 CB LEU A 111 51.457 -6.747 4.371 1.00 0.00
C
+ATOM 63 CG LEU A 111 52.007 -7.863 3.478 1.00 0.00
C
+ATOM 64 CD1 LEU A 111 53.529 -7.738 3.383 1.00 0.00
C
+ATOM 65 CD2 LEU A 111 51.649 -9.221 4.085 1.00 0.00
C
+ATOM 66 H LEU A 111 49.238 -7.063 3.174 1.00 0.00
H
+ATOM 67 HA LEU A 111 50.532 -4.834 4.136 1.00 0.00
H
+ATOM 68 HB2 LEU A 111 52.263 -6.309 4.940 1.00 0.00
H
+ATOM 69 HB3 LEU A 111 50.722 -7.159 5.047 1.00 0.00
H
+ATOM 70 HG LEU A 111 51.577 -7.782 2.491 1.00 0.00
H
+ATOM 71 HD11 LEU A 111 53.961 -7.843 4.367 1.00 0.00
H
+ATOM 72 HD12 LEU A 111 53.789 -6.772 2.978 1.00 0.00
H
+ATOM 73 HD13 LEU A 111 53.914 -8.514 2.738 1.00 0.00
H
+ATOM 74 HD21 LEU A 111 50.600 -9.420 3.926 1.00 0.00
H
+ATOM 75 HD22 LEU A 111 51.857 -9.210 5.144 1.00 0.00
H
+ATOM 76 HD23 LEU A 111 52.238 -9.993 3.611 1.00 0.00
H
+ENDMDL
+END
Modified: 1.3/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/model_free.py?rev=7966&r1=7965&r2=7966&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/model_free.py (original)
+++ 1.3/test_suite/system_tests/model_free.py Fri Oct 24 16:14:19 2008
@@ -989,6 +989,13 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].r, NH_BOND_LENGTH)
+ def test_tylers_peptide(self):
+ """Try a component of model-free analysis on Tyler Reddy's peptide
data (truncated)."""
+
+ # Execute the script.
+ self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/tylers_peptide.py')
+
+
def test_write_results(self):
"""Writing of model-free results using the user function
results.write()."""
Added: 1.3/test_suite/system_tests/scripts/tylers_peptide.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/tylers_peptide.py?rev=7966&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/tylers_peptide.py (added)
+++ 1.3/test_suite/system_tests/scripts/tylers_peptide.py Fri Oct 24 16:14:19
2008
@@ -1,0 +1,18 @@
+# System test constructed from Tyler Reddy's bug report at
https://gna.org/bugs/?12487.
+
+# Python module imports.
+import sys
+
+# Path of the relaxation data.
+DATA_PATH = sys.path[-1] + '/test_suite/shared_data/'
+
+# A set of user functions executed by the full_analysis.py script.
+pipe.create(pipe_name='ellipsoid', pipe_type='mf')
+results.read(file='tylers_peptide_trunc', dir=DATA_PATH+'results_files')
+model_free.remove_tm(spin_id=None)
+sequence.display()
+structure.read_pdb(file='tylers_peptide_trunc.pdb',
dir=DATA_PATH+'structures', model=None, parser='scientific')
+structure.vectors(attached='H', spin_id=None, struct_index=None,
verbosity=1, ave=True, unit=True)
+diffusion_tensor.init(params=(1e-08, 0, 0, 0, 0, 0), time_scale=1.0,
d_scale=1.0, angle_units='deg', param_types=0, spheroid_type=None,
fixed=False)
+fix(element='all_spins', fixed=True)
+grid_search(lower=None, upper=None, inc=6, constraints=True, verbosity=1)
r7966 - in /1.3/test_suite: shared_data/results_files/ shared_data/structures/ system_tests/ system_tests/scripts/