Author: semor
Date: Tue Dec 23 17:04:48 2008
New Revision: 8224
URL: http://svn.gna.org/viewcvs/relax?rev=8224&view=rev
Log:
Many corrections of formatting.
These were found using the relax 'code_validator' script (E. d'Auvergne) and
mainly include trailing
whitespaces and missing empty lines before functions.
Modified:
1.3/generic_fns/spectrum.py
1.3/physical_constants.py
1.3/prompt/align_tensor.py
1.3/prompt/dasha.py
1.3/prompt/help.py
1.3/prompt/interpreter.py
1.3/prompt/spectrum.py
1.3/relax_io.py
1.3/specific_fns/base_class.py
1.3/specific_fns/consistency_tests.py
1.3/specific_fns/model_free/main.py
1.3/specific_fns/n_state_model.py
1.3/specific_fns/noe.py
1.3/test_suite/system_tests/angles.py
1.3/test_suite/system_tests/diffusion_tensor.py
1.3/test_suite/system_tests/n_state_model.py
1.3/test_suite/system_tests/peak_lists.py
1.3/test_suite/system_tests/scripts/5_state_xz.py
1.3/test_suite/system_tests/unit_vectors.py
Modified: 1.3/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spectrum.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/generic_fns/spectrum.py (original)
+++ 1.3/generic_fns/spectrum.py Tue Dec 23 17:04:48 2008
@@ -465,7 +465,7 @@
print ''
print 'The following information was extracted from the intensity file
(res_num, h_name, x_name, intensities).'
- print ' ' + `res_num`, h_name, x_name, intensity
+ print ' ' + `res_num`, h_name, x_name, intensity
# Generate the spin identification string.
spin_id = generate_spin_id_data_array(data=line,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col)
Modified: 1.3/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/physical_constants.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/physical_constants.py (original)
+++ 1.3/physical_constants.py Tue Dec 23 17:04:48 2008
@@ -143,10 +143,10 @@
# Function for returning the desired gyromagnetic ratio.
def return_gyromagnetic_ratio(nucleus=None):
"""Return the gyromagnetic ratio for the given nucleus type.
-
+
@keyword nucleus: The nucleus type.
@type nucleus: str
- @raises RelaxError: If the nucleus type is unknown.
+ @raises RelaxError: If the nucleus type is unknown.
@returns: The desired gyromagnetic ratio.
@rtype: float
"""
@@ -194,7 +194,7 @@
@keyword element: The element type.
@type element: str
- @raises RelaxError: If the element type is unknown.
+ @raises RelaxError: If the element type is unknown.
@returns: The desired atomic mass.
@rtype: float
"""
Modified: 1.3/prompt/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/align_tensor.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/prompt/align_tensor.py (original)
+++ 1.3/prompt/align_tensor.py Tue Dec 23 17:04:48 2008
@@ -215,7 +215,7 @@
5: {Azz, Axx-yy, Axy, Axz, Ayz} (units of Hertz),
6: {Pxx, Pyy, Pxy, Pxz, Pyz} (unitless),
7: {Pzz, Pxx-yy, Pxy, Pxz, Pyz} (unitless),
-
+
Other formats may be added later. The relationship between the
Saupe order matrix S and the
alignment tensor A is
Modified: 1.3/prompt/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/dasha.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/prompt/dasha.py (original)
+++ 1.3/prompt/dasha.py Tue Dec 23 17:04:48 2008
@@ -162,7 +162,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- dir: The directory where the file 'dasha_results' is found.
+ dir: The directory where the file 'dasha_results' is found.
"""
# Function intro text.
Modified: 1.3/prompt/help.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/help.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/prompt/help.py (original)
+++ 1.3/prompt/help.py Tue Dec 23 17:04:48 2008
@@ -66,6 +66,7 @@
to the help function built into the normal python interpreter.
"""
+
def __repr__(self):
return self.text
Modified: 1.3/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/interpreter.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/prompt/interpreter.py (original)
+++ 1.3/prompt/interpreter.py Tue Dec 23 17:04:48 2008
@@ -116,7 +116,7 @@
self.__show_script = show_script
self.__quit_flag = quit
self.__raise_relax_error = raise_relax_error
-
+
# The prompts.
sys.ps1 = 'relax> '
sys.ps2 = 'relax| '
@@ -465,7 +465,7 @@
except:
raise
- # Add an empty line to make exiting relax look better.
+ # Add an empty line to make exiting relax look better.
if show_script:
sys.stdout.write("\n")
Modified: 1.3/prompt/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/spectrum.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/prompt/spectrum.py (original)
+++ 1.3/prompt/spectrum.py Tue Dec 23 17:04:48 2008
@@ -160,7 +160,7 @@
If there are in addition to the replicated spectra loaded peak
intensities which only
consist of a single spectrum, i.e. not all spectra are replicated,
then the variances of
replicated replicated spectra sets will be averaged. This will be
used for the entire
- experiment so that there will be only a single error value for all
spins and for all
+ experiment so that there will be only a single error value for all
spins and for all
spectra.
Modified: 1.3/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax_io.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/relax_io.py (original)
+++ 1.3/relax_io.py Tue Dec 23 17:04:48 2008
@@ -521,7 +521,7 @@
def readlines(self):
"""Mimic the file object readlines() method.
-
+
This method works even if this dummy file object is closed!
Modified: 1.3/specific_fns/base_class.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/base_class.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/specific_fns/base_class.py (original)
+++ 1.3/specific_fns/base_class.py Tue Dec 23 17:04:48 2008
@@ -209,7 +209,7 @@
@type param: str
@param sim: The Monte Carlo simulation index.
@type sim: None or int
- @return: The value and error corresponding to
+ @return: The value and error corresponding to
@rtype: tuple of length 2 of floats or None
"""
@@ -442,7 +442,7 @@
def sim_return_param(self, spin, index):
"""Return the array of simulation parameter values.
-
+
@param spin: The spin container.
@type spin: SpinContainer instance
@param index: The index of the parameter to return the array
of values for.
Modified: 1.3/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/consistency_tests.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/specific_fns/consistency_tests.py (original)
+++ 1.3/specific_fns/consistency_tests.py Tue Dec 23 17:04:48 2008
@@ -251,7 +251,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
These default values are found in the file 'physical_constants.py'.
-
______________________________________________________________________________________
+
______________________________________________________________________________________
| | |
|
| Data type | Object name | Value
|
|_______________________________________|____________________|_________________________|
Modified: 1.3/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/main.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/main.py (original)
+++ 1.3/specific_fns/model_free/main.py Tue Dec 23 17:04:48 2008
@@ -3054,7 +3054,7 @@
def sim_return_param(self, model_index, index):
"""Return the array of simulation parameter values.
-
+
@param model_index: The model index. This is zero for the global
models or equal to the
global spin index (which covers the molecule,
residue, and spin
indices).
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Tue Dec 23 17:04:48 2008
@@ -191,7 +191,7 @@
# No data is present.
if not list:
- raise RelaxError, "Neither RDC, PCS, nor alignment tensor data
is present."
+ raise RelaxError, "Neither RDC, PCS, nor alignment tensor data
is present."
# Return the list.
return list
@@ -319,7 +319,7 @@
As::
N-1
- \
+ \
pN = 1 - > pc,
/__
c=1
@@ -1066,6 +1066,7 @@
Note that setting the probability for state N will do nothing as it
is equal to one minus
all the other probabilities.
"""
+
__docformat__ = "plaintext"
# Get the current data pipe.
@@ -1398,7 +1399,7 @@
for rdc in spin.rdc:
if type(rdc) == float:
n = n + 1
-
+
# PCS data (skipping array elements set to None).
if 'pcs' in data_types:
if hasattr(spin, 'pcs'):
@@ -1466,7 +1467,7 @@
exists = True
if not exists:
raise RelaxError, "The reference domain cannot be found within
any of the loaded tensors."
-
+
# Set the reference domain.
cdp.ref_domain = ref
@@ -1534,6 +1535,7 @@
The objects corresponding to the object names are lists (or arrays)
with each element
corrsponding to each state.
"""
+
__docformat__ = "plaintext"
# Probability.
@@ -1662,6 +1664,7 @@
To set the parameters for a specific state c (ranging from 0 for the
first to N-1 for the
last, the number c should be added to the end of the parameter name.
So the Euler angle
gamma of the third state is specified using the string 'gamma2'.
+
"""
__docformat__ = "plaintext"
Modified: 1.3/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe.py Tue Dec 23 17:04:48 2008
@@ -105,12 +105,12 @@
if cdp.spectrum_type[i] == 'sat':
sat = sat + spin.intensities[i]
sat_err = sat_err + spin.intensity_err[i]
-
+
# Ref spectra.
if cdp.spectrum_type[i] == 'ref':
ref = ref + spin.intensities[i]
ref_err = ref_err + spin.intensity_err[i]
-
+
# Calculate the NOE.
spin.noe = sat / ref
Modified: 1.3/test_suite/system_tests/angles.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/angles.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/angles.py (original)
+++ 1.3/test_suite/system_tests/angles.py Tue Dec 23 17:04:48 2008
@@ -48,7 +48,7 @@
cdp = pipes.get_pipe()
# Res info.
- res_name = ['GLY', 'PRO', 'LEU', 'GLY', 'SER', 'MET', 'ASP', 'SER',
'PRO', 'PRO', 'GLU', 'GLY', 'TYR', 'ARG', 'ARG']
+ res_name = ['GLY', 'PRO', 'LEU', 'GLY', 'SER', 'MET', 'ASP', 'SER',
'PRO', 'PRO', 'GLU', 'GLY', 'TYR', 'ARG', 'ARG']
spin_num = [1, 11, 28, 51, 59, 71, 91, 104, 116, 133, 150, 167,
None, None, None]
spin_name = ['N']*12 + [None]*3
attached_atoms = [None, None, 'H', 'H', 'H', 'H', 'H', 'H', None,
None, 'H', 'H', None, None, None]
Modified: 1.3/test_suite/system_tests/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/diffusion_tensor.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/diffusion_tensor.py (original)
+++ 1.3/test_suite/system_tests/diffusion_tensor.py Tue Dec 23 17:04:48 2008
@@ -47,7 +47,7 @@
self.relax.interpreter._Sequence.read(file='Ap4Aase.seq',
dir=sys.path[-1] + '/test_suite/shared_data/')
self.relax.interpreter._Diffusion_tensor.init(10e-9, fixed=True)
self.tmpfile_sphere = mktemp()
-
+
# Spheroid tensor initialization.
self.relax.interpreter._Pipe.switch('spheroid')
self.relax.interpreter._Structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir=sys.path[-1] + '/test_suite/shared_data/structures', model=1)
Modified: 1.3/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/n_state_model.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/n_state_model.py (original)
+++ 1.3/test_suite/system_tests/n_state_model.py Tue Dec 23 17:04:48 2008
@@ -37,7 +37,6 @@
"""Reset the relax data storage object."""
ds.__reset__()
-
def test_5_state_xz(self):
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=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/peak_lists.py (original)
+++ 1.3/test_suite/system_tests/peak_lists.py Tue Dec 23 17:04:48 2008
@@ -33,23 +33,23 @@
class Peak_lists(TestCase):
"""TestCase class for the functional tests for the support of different
peak intensity files."""
-
+
def setUp(self):
"""Set up for all the functional tests."""
-
+
# Create a data pipe.
self.relax.interpreter._Pipe.create('mf', 'mf')
-
-
+
+
def tearDown(self):
"""Reset the relax data storage object."""
-
+
ds.__reset__()
-
-
+
+
def test_read_peak_list_generic(self):
"""Test the reading of a generic peak intensity list."""
-
+
# Get the current data pipe.
cdp = pipes.get_pipe()
@@ -60,7 +60,7 @@
self.relax.interpreter._Residue.create(35)
self.relax.interpreter._Residue.create(36)
self.relax.interpreter._Spin.name(name='N')
-
+
# Read the peak list.
self.relax.interpreter._Spectrum.read_intensities(file="generic_intensity.txt",
dir=sys.path[-1] + "/test_suite/shared_data/peak_lists", spectrum_id='test',
int_method='height')
@@ -79,7 +79,7 @@
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()
@@ -90,9 +90,9 @@
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']
+ 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',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None)
Modified: 1.3/test_suite/system_tests/scripts/5_state_xz.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/5_state_xz.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/5_state_xz.py (original)
+++ 1.3/test_suite/system_tests/scripts/5_state_xz.py Tue Dec 23 17:04:48 2008
@@ -30,7 +30,7 @@
n_state_model.set_domain(tensor='chi4 C-dom', domain='C')
n_state_model.set_domain(tensor='chi5 C-dom', domain='C')
-# Set that they are non-reduced tensors.
+# Set that they are non-reduced tensors.
n_state_model.set_type(tensor='chi1 C-dom', red=False)
n_state_model.set_type(tensor='chi2 C-dom', red=False)
n_state_model.set_type(tensor='chi3 C-dom', red=False)
@@ -60,7 +60,7 @@
n_state_model.set_domain(tensor='chi4 N-dom', domain='N')
n_state_model.set_domain(tensor='chi5 N-dom', domain='N')
-# Set that they are non-reduced tensors.
+# Set that they are non-reduced tensors.
n_state_model.set_type(tensor='chi1 N-dom', red=True)
n_state_model.set_type(tensor='chi2 N-dom', red=True)
n_state_model.set_type(tensor='chi3 N-dom', red=True)
Modified: 1.3/test_suite/system_tests/unit_vectors.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/unit_vectors.py?rev=8224&r1=8223&r2=8224&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/unit_vectors.py (original)
+++ 1.3/test_suite/system_tests/unit_vectors.py Tue Dec 23 17:04:48 2008
@@ -78,7 +78,7 @@
# Load the spins.
self.relax.interpreter._Structure.load_spins(spin_id='@N')
-
+
# Remove the spin numbers.
self.relax.interpreter._Spin.number()
@@ -106,7 +106,7 @@
# Load the spins.
self.relax.interpreter._Structure.load_spins(spin_id='@N')
-
+
# Calculate the unit vectors.
self.relax.interpreter._Structure.vectors(attached='H')
@@ -131,7 +131,7 @@
# Load the spins.
self.relax.interpreter._Structure.load_spins(spin_id='@N')
-
+
# Remove the spin numbers.
self.relax.interpreter._Spin.number()
r8224 - in /1.3: ./ generic_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/system_tests/ test_suite/system_t...