Author: bugman
Date: Fri Oct 24 18:20:21 2008
New Revision: 7969
URL: http://svn.gna.org/viewcvs/relax?rev=7969&view=rev
Log:
Merged revisions 7952,7961-7963,7965-7968 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r7952 | bugman | 2008-10-23 17:39:25 +0200 (Thu, 23 Oct 2008) | 9 lines
Fix for bug #12487 (https://gna.org/bugs/index.php?12487).
This bug was reported by Tyler Reddy (TREDDY at dal dot ca).
The problem was that missing XH bond vector data was being manifested as
the spin.xh_vect object
being set to None. The overfit_deselect() function which is responsible
for deselecting unsuitable
spins prior to optimisation was only checking if the object existed, not if
it was None!
........
r7961 | bugman | 2008-10-24 13:44:28 +0200 (Fri, 24 Oct 2008) | 3 lines
Added a check to the atom_loop() to make sure structural data is loaded.
........
r7962 | bugman | 2008-10-24 13:56:38 +0200 (Fri, 24 Oct 2008) | 3 lines
Added a check for empty PDB files in the internal structural object.
........
r7963 | bugman | 2008-10-24 14:22:44 +0200 (Fri, 24 Oct 2008) | 3 lines
Added another spin to try to catch a program bug (unsuccessfully).
........
r7965 | semor | 2008-10-24 15:41:46 +0200 (Fri, 24 Oct 2008) | 5 lines
Introduced verifications for the '-t' and '-l' options not to erase the
python script used.
This should fix bug 12498 (http://gna.org/bugs/?12498).
........
r7966 | bugman | 2008-10-24 16:14:19 +0200 (Fri, 24 Oct 2008) | 3 lines
Created a system test using Tyler Reddy's bug report - bug #12487
(https://gna.org/bugs/?12487).
........
r7967 | semor | 2008-10-24 16:19:17 +0200 (Fri, 24 Oct 2008) | 7 lines
Modified the '-l' and '-t' options so they check for an existing file and
don't overwrite it.
This was proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2008-10/msg00087.html
(Message ID: 7f080ed10810240648p19b83da1x4c8990acf1834c5b@xxxxxxxxxxxxxx)
........
r7968 | semor | 2008-10-24 17:55:21 +0200 (Fri, 24 Oct 2008) | 7 lines
Still improved the detection of existing files not to be overwritten when
logging or teeing.
This follows a post by Edward at:
https://mail.gna.org/public/relax-devel/2008-10/msg00091.html
(Message ID: 7f080ed10810240816o30acc1ddlbaa131bc5a9ea1ff@xxxxxxxxxxxxxx)
........
Added:
branches/spectral_errors/test_suite/shared_data/results_files/tylers_peptide_trunc.bz2
- copied unchanged from r7968,
1.3/test_suite/shared_data/results_files/tylers_peptide_trunc.bz2
branches/spectral_errors/test_suite/shared_data/structures/tylers_peptide_trunc.pdb
- copied unchanged from r7968,
1.3/test_suite/shared_data/structures/tylers_peptide_trunc.pdb
branches/spectral_errors/test_suite/system_tests/scripts/tylers_peptide.py
- copied unchanged from r7968,
1.3/test_suite/system_tests/scripts/tylers_peptide.py
Modified:
branches/spectral_errors/ (props changed)
branches/spectral_errors/generic_fns/structure/internal.py
branches/spectral_errors/relax
branches/spectral_errors/specific_fns/model_free/main.py
branches/spectral_errors/test_suite/system_tests/model_free.py
branches/spectral_errors/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
Propchange: branches/spectral_errors/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Oct 24 18:20:21 2008
@@ -1,1 +1,1 @@
-/1.3:1-7948
+/1.3:1-7968
Modified: branches/spectral_errors/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/generic_fns/structure/internal.py?rev=7969&r1=7968&r2=7969&view=diff
==============================================================================
--- branches/spectral_errors/generic_fns/structure/internal.py (original)
+++ branches/spectral_errors/generic_fns/structure/internal.py Fri Oct 24
18:20:21 2008
@@ -35,7 +35,7 @@
from api_base import Base_struct_API
from generic_fns import pipes, relax_re
from generic_fns.mol_res_spin import Selection
-from relax_errors import RelaxError
+from relax_errors import RelaxError, RelaxNoPdbError
from relax_io import open_read_file
from relax_warnings import RelaxWarning
@@ -321,6 +321,10 @@
file = open_read_file(file_path)
lines = file.readlines()
file.close()
+
+ # Check for empty files.
+ if lines == []:
+ raise RelaxError, "The PDB file is empty."
# Init.
model = None
@@ -645,6 +649,10 @@
element name (str), and atomic position
(array of len 3).
"""
+ # Check that the structure is loaded.
+ if not len(self.structural_data):
+ raise RelaxNoPdbError
+
# Generate the selection object.
sel_obj = Selection(atom_id)
Modified: branches/spectral_errors/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/relax?rev=7969&r1=7968&r2=7969&view=diff
==============================================================================
--- branches/spectral_errors/relax (original)
+++ branches/spectral_errors/relax Fri Oct 24 18:20:21 2008
@@ -202,6 +202,10 @@
# The log file.
log_file = options.log
+
+ # Fail if the file already exists.
+ if access(log_file, F_OK):
+ parser.error("the log file " + `log_file` + " already
exists")
else:
log_file = None
@@ -213,6 +217,10 @@
# The tee file.
tee_file = options.tee
+
+ # Fail if the file already exists.
+ if access(tee_file, F_OK):
+ parser.error("the tee file " + `tee_file` + " already
exists")
else:
tee_file = None
Modified: branches/spectral_errors/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/specific_fns/model_free/main.py?rev=7969&r1=7968&r2=7969&view=diff
==============================================================================
--- branches/spectral_errors/specific_fns/model_free/main.py (original)
+++ branches/spectral_errors/specific_fns/model_free/main.py Fri Oct 24
18:20:21 2008
@@ -1969,6 +1969,8 @@
# Test for structural data if required.
elif need_vect and not hasattr(spin, 'xh_vect'):
+ spin.select = False
+ elif need_vect and spin.xh_vect == None:
spin.select = False
Modified: branches/spectral_errors/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/test_suite/system_tests/model_free.py?rev=7969&r1=7968&r2=7969&view=diff
==============================================================================
--- branches/spectral_errors/test_suite/system_tests/model_free.py (original)
+++ branches/spectral_errors/test_suite/system_tests/model_free.py Fri Oct 24
18:20:21 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()."""
Modified:
branches/spectral_errors/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py?rev=7969&r1=7968&r2=7969&view=diff
==============================================================================
---
branches/spectral_errors/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
(original)
+++
branches/spectral_errors/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
Fri Oct 24 18:20:21 2008
@@ -67,6 +67,7 @@
cdp.mol[1].res[1].spin[0].name = 'C8'
cdp.mol[1].res[0].spin.add_item(spin_name='N5')
cdp.mol[1].res[1].spin.add_item(spin_name='N5')
+ cdp.mol[1].res[1].spin.add_item(spin_name='2H', spin_num=132)
# Deselect a number of spins.
cdp.mol[0].res[0].spin[0].select = 0
@@ -487,8 +488,8 @@
"""
# Test the number of spins counted.
- self.assertEqual(mol_res_spin.count_spins(), 3)
- self.assertEqual(mol_res_spin.count_spins(skip_desel=False), 7)
+ self.assertEqual(mol_res_spin.count_spins(), 4)
+ self.assertEqual(mol_res_spin.count_spins(skip_desel=False), 8)
self.assertEqual(mol_res_spin.count_spins(selection='@N5'), 1)
self.assertEqual(mol_res_spin.count_spins(selection='@N5',
skip_desel=False), 2)
@@ -1194,6 +1195,7 @@
spin2 = mol_res_spin.return_spin(selection=':2&:Glu')
spin3 = mol_res_spin.return_spin(selection=':4&:Pro', pipe='orig')
spin4 = mol_res_spin.return_spin(selection='#RNA:-5@N5', pipe='orig')
+ spin5 = mol_res_spin.return_spin(selection=':-4@2H', pipe='orig')
# Test the data of spin 1.
self.assertNotEqual(spin1, None)
@@ -1214,6 +1216,11 @@
self.assertNotEqual(spin4, None)
self.assertEqual(spin4.num, None)
self.assertEqual(spin4.name, 'N5')
+
+ # Test the data of the RNA res -4, spin 2H.
+ self.assertNotEqual(spin5, None)
+ self.assertEqual(spin5.num, 132)
+ self.assertEqual(spin5.name, '2H')
def test_return_spin_pipe_fail(self):
@@ -1347,8 +1354,8 @@
"""
# Spin data.
- select = [0, 1, 0, 0, 1, 1, 0]
- name = ['NH', 'NH', None, 'C8', 'N5', 'C8', 'N5']
+ select = [0, 1, 0, 0, 1, 1, 0, 1]
+ name = ['NH', 'NH', None, 'C8', 'N5', 'C8', 'N5', '2H']
# Loop over the spins.
i = 0
@@ -1363,7 +1370,7 @@
i = i + 1
# Test loop length.
- self.assertEqual(i, 7)
+ self.assertEqual(i, 8)
def test_spin_loop_single_spin(self):
r7969 - in /branches/spectral_errors: ./ generic_fns/structure/ specific_fns/model_free/ test_suite/shared_data/results_file...