Author: bugman
Date: Thu Nov 6 11:06:42 2008
New Revision: 7970
URL: http://svn.gna.org/viewcvs/relax?rev=7970&view=rev
Log:
Merged revisions 7942-7948,7952,7961-7963,7965-7968 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r7942 | bugman | 2008-10-23 16:44:53 +0200 (Thu, 23 Oct 2008) | 6 lines
Fix for the relax IO logging with the -l command line argument.
This is a partial fix for bug #12489 (https://gna.org/bugs/?12489). The
teeing problem still has
to be fixed.
........
r7943 | bugman | 2008-10-23 16:54:43 +0200 (Thu, 23 Oct 2008) | 3 lines
Converted the tee class method into a module function.
........
r7944 | bugman | 2008-10-23 16:56:12 +0200 (Thu, 23 Oct 2008) | 3 lines
Epydoc'd the tee function docstring.
........
r7945 | bugman | 2008-10-23 16:57:45 +0200 (Thu, 23 Oct 2008) | 3 lines
Docstring improvements for the log() function.
........
r7946 | bugman | 2008-10-23 16:58:04 +0200 (Thu, 23 Oct 2008) | 3 lines
Removed a line of redundant code.
........
r7947 | bugman | 2008-10-23 16:58:56 +0200 (Thu, 23 Oct 2008) | 3 lines
Added the missing import of relax_io.tee.
........
r7948 | bugman | 2008-10-23 17:01:18 +0200 (Thu, 23 Oct 2008) | 5 lines
Final fixes for bug #12489 (https://gna.org/bugs/?12489).
The log() and tee() functions are now operational.
........
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/multi_processor_merge/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/multi_processor_merge/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/multi_processor_merge/test_suite/system_tests/scripts/tylers_peptide.py
- copied unchanged from r7968,
1.3/test_suite/system_tests/scripts/tylers_peptide.py
Modified:
branches/multi_processor_merge/ (props changed)
branches/multi_processor_merge/generic_fns/structure/internal.py
branches/multi_processor_merge/relax
branches/multi_processor_merge/relax_io.py
branches/multi_processor_merge/specific_fns/model_free/main.py
branches/multi_processor_merge/test_suite/system_tests/model_free.py
branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
Propchange: branches/multi_processor_merge/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Nov 6 11:06:42 2008
@@ -1,1 +1,1 @@
-/1.3:1-7940
+/1.3:1-7969
Modified: branches/multi_processor_merge/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/structure/internal.py?rev=7970&r1=7969&r2=7970&view=diff
==============================================================================
--- branches/multi_processor_merge/generic_fns/structure/internal.py
(original)
+++ branches/multi_processor_merge/generic_fns/structure/internal.py Thu Nov
6 11:06:42 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/multi_processor_merge/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/relax?rev=7970&r1=7969&r2=7970&view=diff
==============================================================================
--- branches/multi_processor_merge/relax (original)
+++ branches/multi_processor_merge/relax Thu Nov 6 11:06:42 2008
@@ -53,7 +53,7 @@
from prompt.gpl import gpl
from prompt import interpreter
import relax_errors
-from relax_io import log
+from relax_io import log, tee
import relax_warnings
from test_suite.test_suite_runner import Test_suite_runner
import version
@@ -206,6 +206,10 @@
# The log file.
self.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:
self.log_file = None
@@ -217,6 +221,10 @@
# The tee file.
self.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:
self.tee_file = None
Modified: branches/multi_processor_merge/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/relax_io.py?rev=7970&r1=7969&r2=7970&view=diff
==============================================================================
--- branches/multi_processor_merge/relax_io.py (original)
+++ branches/multi_processor_merge/relax_io.py Thu Nov 6 11:06:42 2008
@@ -170,7 +170,7 @@
def log(file_name=None, dir=None, verbosity=1):
- """Function for turning logging on.
+ """Turn on logging, sending both STDOUT and STDERR streams to a file.
@param file_name: The name of the file to extract the data from.
@type file_name: str
@@ -184,6 +184,11 @@
# Log file.
log_file, file_path = open_write_file(file_name=file_name, dir=dir,
force=True, verbosity=verbosity, return_path=True)
+ # Logging IO streams.
+ log_stdin = stdin
+ log_stdout = None
+ log_stderr = SplitIO()
+
# Print out.
if verbosity:
print "Redirecting the sys.stdin IO stream to the python stdin IO
stream."
@@ -192,7 +197,7 @@
# Set the logging IO streams.
log_stdout = log_file
- log_stderr.split(python_stderr, log_file)
+ log_stderr.split(stderr, log_file)
# IO stream redirection.
sys.stdin = log_stdin
@@ -399,6 +404,45 @@
return new
+def tee(file_name=None, dir=None, compress_type=0, verbosity=1):
+ """Turn on teeing to split both STDOUT and STDERR streams and sending
second part to a file.
+
+ @param file_name: The name of the file to extract the data from.
+ @type file_name: str
+ @param dir: The path where the file is located. If None,
then the current directory
+ is assumed.
+ @type dir: str
+ @param compress_type: The compression type. The integer values
correspond to the compression
+ type: 0, no compression; 1, Bzip2 compression;
2, Gzip compression.
+ @type compress_type: int
+ @param verbosity: The verbosity level.
+ @type verbosity: int
+ """
+
+ # Tee file.
+ tee_file, file_path = open_write_file(file_name=file_name, dir=dir,
force=True, compress_type=compress_type, verbosity=verbosity, return_path=1)
+
+ # Tee IO streams.
+ tee_stdin = stdin
+ tee_stdout = SplitIO()
+ tee_stderr = SplitIO()
+
+ # Print out.
+ if verbosity:
+ print "Redirecting the sys.stdin IO stream to the python stdin IO
stream."
+ print "Redirecting the sys.stdout IO stream to both the python
stdout IO stream and the log file '%s'." % file_path
+ print "Redirecting the sys.stderr IO stream to both the python
stderr IO stream and the log file '%s'." % file_path
+
+ # Set the tee IO streams.
+ tee_stdout.split(stdout, tee_file)
+ tee_stderr.split(stderr, tee_file)
+
+ # IO stream redirection.
+ sys.stdin = tee_stdin
+ sys.stdout = tee_stdout
+ sys.stderr = tee_stderr
+
+
def test_binary(binary):
"""Function for testing that the binary string corresponds to a valid
executable file.
@@ -576,28 +620,6 @@
sys.stderr = self.python_stderr
- def tee(self, file_name=None, dir=None, compress_type=0, verbosity=1):
- """Function for turning logging on."""
-
- # Tee file.
- self.tee_file, file_path = self.open_write_file(file_name=file_name,
dir=dir, force=True, compress_type=compress_type, verbosity=verbosity,
return_path=1)
-
- # Print out.
- if verbosity:
- print "Redirecting the sys.stdin IO stream to the python stdin
IO stream."
- print "Redirecting the sys.stdout IO stream to both the python
stdout IO stream and the log file '%s'." % file_path
- print "Redirecting the sys.stderr IO stream to both the python
stderr IO stream and the log file '%s'." % file_path
-
- # Set the tee IO streams.
- self.tee_stdout.split(self.python_stdout, self.tee_file)
- self.tee_stderr.split(self.python_stderr, self.tee_file)
-
- # IO stream redirection.
- sys.stdin = self.tee_stdin
- sys.stdout = self.tee_stdout
- sys.stderr = self.tee_stderr
-
-
class SplitIO:
def __init__(self):
"""Class for splitting an IO stream to two outputs."""
Modified: branches/multi_processor_merge/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/model_free/main.py?rev=7970&r1=7969&r2=7970&view=diff
==============================================================================
--- branches/multi_processor_merge/specific_fns/model_free/main.py (original)
+++ branches/multi_processor_merge/specific_fns/model_free/main.py Thu Nov 6
11:06:42 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/multi_processor_merge/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/model_free.py?rev=7970&r1=7969&r2=7970&view=diff
==============================================================================
--- branches/multi_processor_merge/test_suite/system_tests/model_free.py
(original)
+++ branches/multi_processor_merge/test_suite/system_tests/model_free.py Thu
Nov 6 11:06:42 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/multi_processor_merge/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py?rev=7970&r1=7969&r2=7970&view=diff
==============================================================================
---
branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
(original)
+++
branches/multi_processor_merge/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
Thu Nov 6 11:06:42 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):
r7970 - in /branches/multi_processor_merge: ./ generic_fns/structure/ specific_fns/model_free/ test_suite/shared_data/result...