Author: bugman
Date: Fri Jan 18 18:22:57 2013
New Revision: 18235
URL: http://svn.gna.org/viewcvs/relax?rev=18235&view=rev
Log:
Merged revisions 18224-18234 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18224 | bugman | 2013-01-18 14:19:34 +0100 (Fri, 18 Jan 2013) | 3 lines
The Pipes.test_change_type system test is skipped if the required scipy
module is not installed.
........
r18225 | bugman | 2013-01-18 14:20:36 +0100 (Fri, 18 Jan 2013) | 5 lines
Python 3 fix for the new pcs.structural_noise user function.
There was a string/unicode problem in the Grace plot creation code.
........
r18226 | bugman | 2013-01-18 16:10:14 +0100 (Fri, 18 Jan 2013) | 6 lines
Created the Pcs.test_load_multi_col_data system test to demonstrate a
failure of PCS data loading.
This is a problem when 15N data is in one column and 1H data is in another,
and the spin_id argument
is used to specify which is which.
........
r18227 | bugman | 2013-01-18 16:17:44 +0100 (Fri, 18 Jan 2013) | 3 lines
Added some printouts to the Pcs.test_load_multi_col_data system test.
........
r18228 | bugman | 2013-01-18 16:44:15 +0100 (Fri, 18 Jan 2013) | 5 lines
Bug fix for the loading of PCS data from a file with different spin types
in different columns.
This was caught by the Pcs.test_load_multi_col_data system test which now
passes.
........
r18229 | bugman | 2013-01-18 17:01:52 +0100 (Fri, 18 Jan 2013) | 3 lines
Created the Pcs.test_grace_plot system test to check the pcs.corr_plot user
function.
........
r18230 | bugman | 2013-01-18 17:39:09 +0100 (Fri, 18 Jan 2013) | 6 lines
Created the Pcs.test_load_multi_col_data2 system test to catch a bug with
the molecule name.
This is the same as the Pcs.test_load_multi_col_data system test but the
spins have the molecule
name set.
........
r18231 | bugman | 2013-01-18 17:50:16 +0100 (Fri, 18 Jan 2013) | 5 lines
Created the Mol_res_spin.test_prune_metadata system test to catch a bug in
the spin ID lookup table.
Spin IDs appear not to be correctly removed from the lookup table.
........
r18232 | bugman | 2013-01-18 17:58:27 +0100 (Fri, 18 Jan 2013) | 5 lines
Bug fix for generic_fns.mol_res_spin.metadata_prune().
Non-unique molecules and residues are now removed from the spin ID lookup
table.
........
r18233 | bugman | 2013-01-18 18:05:41 +0100 (Fri, 18 Jan 2013) | 3 lines
Added some more checks to the Mol_res_spin.test_prune_metadata system test
to demonstrate more bugs.
........
r18234 | bugman | 2013-01-18 18:19:03 +0100 (Fri, 18 Jan 2013) | 7 lines
Proper bug fix for the spin ID metadata lookup table pruning.
The Mol_res_spin.test_prune_metadata system test now passes. The previous
fix of r18232 was not
complete, and it should have been in the spin_id_variants_elim() function
rather than
metadata_prune().
........
Added:
branches/frame_order_testing/test_suite/shared_data/align_data/pcs_dy_200911.txt
- copied unchanged from r18234,
trunk/test_suite/shared_data/align_data/pcs_dy_200911.txt
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/generic_fns/mol_res_spin.py
branches/frame_order_testing/generic_fns/pcs.py
branches/frame_order_testing/test_suite/system_tests/mol_res_spin.py
branches/frame_order_testing/test_suite/system_tests/pcs.py
branches/frame_order_testing/test_suite/system_tests/pipes.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Jan 18 18:22:57 2013
@@ -1,1 +1,1 @@
-/trunk:1-18220
+/trunk:1-18234
Modified: branches/frame_order_testing/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/mol_res_spin.py?rev=18235&r1=18234&r2=18235&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/mol_res_spin.py (original)
+++ branches/frame_order_testing/generic_fns/mol_res_spin.py Fri Jan 18
18:22:57 2013
@@ -1964,6 +1964,7 @@
dp = pipes.get_pipe(pipe)
# Loop over the molecules.
+ to_remove = []
for i in range(len(dp.mol)):
# Molecule skipping.
if mol_index != None and mol_index != i:
@@ -1991,10 +1992,10 @@
spin = res.spin[k]
# The list of IDs to remove.
- spin_ids = spin_id_variants_elim(dp=dp, mol_index=i,
res_index=j, spin_index=k)
+ to_remove = spin_id_variants_elim(dp=dp, mol_index=i,
res_index=j, spin_index=k)
# ID removal.
- for spin_id in spin_ids:
+ for spin_id in to_remove:
# Blank IDs.
if spin_id == '':
continue
@@ -3271,13 +3272,18 @@
# The spin IDs without spin info.
if spin_count > 1:
spin_ids.append(generate_spin_id(mol_name=mol.name, res_num=res.num,
res_name=res.name))
+ spin_ids.append(generate_spin_id(res_num=res.num, res_name=res.name))
+ spin_ids.append(generate_spin_id(mol_name=mol.name))
# The spin IDs without residue info.
if res_count > 1:
spin_ids.append(generate_spin_id(mol_name=mol.name,
spin_num=spin.num, spin_name=spin.name))
+ spin_ids.append(generate_spin_id(spin_num=spin.num,
spin_name=spin.name))
+ spin_ids.append(generate_spin_id(mol_name=mol.name))
# The spin IDs without molecule info.
if mol_count > 1:
+ spin_ids.append(generate_spin_id(res_num=res.num, res_name=res.name))
spin_ids.append(generate_spin_id(res_num=res.num, res_name=res.name,
spin_num=spin.num, spin_name=spin.name))
# The spin IDs without spin or residue info.
Modified: branches/frame_order_testing/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/pcs.py?rev=18235&r1=18234&r2=18235&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/pcs.py (original)
+++ branches/frame_order_testing/generic_fns/pcs.py Fri Jan 18 18:22:57 2013
@@ -613,6 +613,8 @@
# Get the corresponding spin container.
id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=res_name, spin_num=spin_num, spin_name=spin_name)
spin = return_spin(id)
+ if spin == None and spin_id[0] == '@': # Allow spin IDs of atom
names to be used to specify multi column data.
+ spin = return_spin(id+spin_id)
if spin == None:
warn(RelaxNoSpinWarning(id))
continue
@@ -878,7 +880,7 @@
file = open_write_file(file, dir, force)
# The header.
- grace.write_xy_header(file=file, title="PCS structural noise",
subtitle="%s Angstrom structural noise"%rmsd, sets=len(align_ids),
set_names=align_ids, symbol_sizes=[0.5]*len(align_ids),
linetype=[0]*len(align_ids), data_type=['pcs_bc', 'pcs'],
axis_labels=["Ln\S3+\N to spin distance (Angstrom)", "PCS standard deviation
(ppm)"])
+ grace.write_xy_header(file=file, title="PCS structural noise",
subtitle="%s Angstrom structural noise"%rmsd, sets=len(align_ids),
set_names=align_ids, symbol_sizes=[0.5]*len(align_ids),
linetype=[0]*len(align_ids), data_type=['pcs_bc', 'pcs'],
axis_labels=["Ln\\S3+\\N to spin distance (Angstrom)", "PCS standard
deviation (ppm)"])
# The main data.
grace.write_xy_data(data=[grace_data], file=file, graph_type='xy')
Modified: branches/frame_order_testing/test_suite/system_tests/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/mol_res_spin.py?rev=18235&r1=18234&r2=18235&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/mol_res_spin.py
(original)
+++ branches/frame_order_testing/test_suite/system_tests/mol_res_spin.py Fri
Jan 18 18:22:57 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2012 Edward d'Auvergne
#
+# Copyright (C) 2012-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -42,6 +42,31 @@
self.interpreter.pipe.create('mf', 'mf')
+ def test_prune_metadata(self):
+ """Check the proper pruning of the spin ID metadata."""
+
+ # Create a data pipe for all the data.
+ self.interpreter.pipe.create('CaM N-dom', 'N-state')
+
+ # Create some spins.
+ self.interpreter.spin.create(spin_name='N', spin_num=1,
res_name='Gly', res_num=3, mol_name='CaM')
+ self.interpreter.spin.create(spin_name='H', spin_num=2,
res_name='Gly', res_num=3, mol_name='CaM')
+
+ # Make sure that certain spin IDs have been removed.
+ print("The spin ID lookup table:\n%s" % cdp.mol._spin_id_lookup)
+ self.assert_(':3' not in cdp.mol._spin_id_lookup)
+ self.assert_('#CaM' not in cdp.mol._spin_id_lookup)
+
+ # Create some more spins.
+ self.interpreter.spin.create(spin_name='N', spin_num=3,
res_name='Gly', res_num=4, mol_name='CaM')
+ self.interpreter.spin.create(spin_name='H', spin_num=4,
res_name='Gly', res_num=4, mol_name='CaM')
+
+ # Make sure that certain spin IDs have been removed.
+ print("The spin ID lookup table:\n%s" % cdp.mol._spin_id_lookup)
+ self.assert_('@N' not in cdp.mol._spin_id_lookup)
+ self.assert_('@H' not in cdp.mol._spin_id_lookup)
+
+
def test_residue_delete(self):
"""Test residue deletion."""
Modified: branches/frame_order_testing/test_suite/system_tests/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/pcs.py?rev=18235&r1=18234&r2=18235&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/pcs.py (original)
+++ branches/frame_order_testing/test_suite/system_tests/pcs.py Fri Jan 18
18:22:57 2013
@@ -25,6 +25,9 @@
# Python module imports.
from os import sep
+from re import search
+from string import split
+from tempfile import mkdtemp
# relax module imports.
from generic_fns.mol_res_spin import count_spins, spin_loop
@@ -34,6 +37,153 @@
class Pcs(SystemTestCase):
"""Class for testing PCS operations."""
+
+ def test_grace_plot(self):
+ """Test the creation of Grace plots of PCS data."""
+
+ # Create a data pipe for all the data.
+ self.interpreter.pipe.create('CaM N-dom', 'N-state')
+
+ # Create some spins.
+ self.interpreter.spin.create(spin_name='N', spin_num=1,
res_name='Gly', res_num=3)
+ self.interpreter.spin.create(spin_name='H', spin_num=2,
res_name='Gly', res_num=3)
+ self.interpreter.spin.create(spin_name='N', spin_num=3,
res_name='Gly', res_num=4)
+ self.interpreter.spin.create(spin_name='H', spin_num=4,
res_name='Gly', res_num=4)
+ self.interpreter.sequence.display()
+
+ # Set the element type.
+ self.interpreter.spin.element(element='N', spin_id='@N')
+ self.interpreter.spin.element(element='H', spin_id='@H')
+
+ # Data directory.
+ dir = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
+
+ # PCSs.
+ self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt',
dir=dir, res_num_col=1, data_col=2, error_col=4, spin_id='@N')
+ self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt',
dir=dir, res_num_col=1, data_col=3, error_col=4, spin_id='@H')
+
+ # Fudge the back-calculated PCS data.
+ for spin in spin_loop():
+ spin.pcs_bc = {}
+ spin.pcs_bc['dy'] = spin.pcs['dy'] + 0.1
+
+ # Create the grace plot.
+ self.tmpdir = mkdtemp()
+ self.interpreter.pcs.corr_plot(format='grace', file='pcs_corr.agr',
dir=self.tmpdir, force=True)
+
+ # Read the file data.
+ file = open(self.tmpdir+sep+'pcs_corr.agr')
+ lines = file.readlines()
+ file.close()
+
+ # Check the diagonal data.
+ for i in range(len(lines)):
+ if search('G0.S0', lines[i]):
+ point1 = split(lines[i+2])
+ point2 = split(lines[i+3])
+ self.assertAlmostEqual(float(point1[0]), -100.0)
+ self.assertAlmostEqual(float(point1[1]), -100.0)
+ self.assertAlmostEqual(float(point2[0]), 100.0)
+ self.assertAlmostEqual(float(point2[1]), 100.0)
+
+ # Check the 15N data.
+ for i in range(len(lines)):
+ if search('G0.S1', lines[i]):
+ point1 = split(lines[i+2])
+ point2 = split(lines[i+3])
+ self.assertAlmostEqual(float(point1[0]), 0.917+0.1)
+ self.assertAlmostEqual(float(point1[1]), 0.917)
+ self.assertAlmostEqual(float(point1[2]), 0.1)
+ self.assertAlmostEqual(float(point2[0]), 1.131+0.1)
+ self.assertAlmostEqual(float(point2[1]), 1.131)
+ self.assertAlmostEqual(float(point2[2]), 0.1)
+
+ # Check the 1H data.
+ for i in range(len(lines)):
+ if search('G0.S2', lines[i]):
+ point1 = split(lines[i+2])
+ point2 = split(lines[i+3])
+ self.assertAlmostEqual(float(point1[0]), 0.843+0.1)
+ self.assertAlmostEqual(float(point1[1]), 0.843)
+ self.assertAlmostEqual(float(point1[2]), 0.1)
+ self.assertAlmostEqual(float(point2[0]), 1.279+0.1)
+ self.assertAlmostEqual(float(point2[1]), 1.279)
+ self.assertAlmostEqual(float(point2[2]), 0.1)
+
+
+ def test_load_multi_col_data(self):
+ """Test the loading of PCS data from a file with different columns
for each spin type."""
+
+ # Create a data pipe for all the data.
+ self.interpreter.pipe.create('CaM N-dom', 'N-state')
+
+ # Create some spins.
+ self.interpreter.spin.create(spin_name='N', spin_num=1,
res_name='Gly', res_num=3)
+ self.interpreter.spin.create(spin_name='H', spin_num=2,
res_name='Gly', res_num=3)
+ self.interpreter.spin.create(spin_name='N', spin_num=3,
res_name='Gly', res_num=4)
+ self.interpreter.spin.create(spin_name='H', spin_num=4,
res_name='Gly', res_num=4)
+ self.interpreter.sequence.display()
+
+ # Data directory.
+ dir = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
+
+ # PCSs.
+ self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt',
dir=dir, res_num_col=1, data_col=2, error_col=4, spin_id='@N')
+ self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt',
dir=dir, res_num_col=1, data_col=3, error_col=4, spin_id='@H')
+
+ # The data.
+ pcs_data = {
+ ':3@N': 0.917,
+ ':3@H': 0.843,
+ ':4@N': 1.131,
+ ':4@H': 1.279,
+ }
+
+ # Check the PCS data.
+ print("\n")
+ for spin, spin_id in spin_loop(return_id=True):
+ print("Checking the PCS data of spin '%s'." % spin_id)
+ self.assert_(hasattr(spin, 'pcs'))
+ self.assertEqual(spin.pcs['dy'], pcs_data[spin_id])
+ self.assertEqual(spin.pcs_err['dy'], 0.1)
+
+
+ def test_load_multi_col_data2(self):
+ """Test the loading of PCS data from a file with different columns
for each spin type."""
+
+ # Create a data pipe for all the data.
+ self.interpreter.pipe.create('CaM N-dom', 'N-state')
+
+ # Create some spins.
+ self.interpreter.spin.create(spin_name='N', spin_num=1,
res_name='Gly', res_num=3, mol_name='CaM')
+ self.interpreter.spin.create(spin_name='H', spin_num=2,
res_name='Gly', res_num=3, mol_name='CaM')
+ self.interpreter.spin.create(spin_name='N', spin_num=3,
res_name='Gly', res_num=4, mol_name='CaM')
+ self.interpreter.spin.create(spin_name='H', spin_num=4,
res_name='Gly', res_num=4, mol_name='CaM')
+ self.interpreter.sequence.display()
+
+ # Data directory.
+ dir = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
+
+ # PCSs.
+ self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt',
dir=dir, res_num_col=1, data_col=2, error_col=4, spin_id='@N')
+ self.interpreter.pcs.read(align_id='dy', file='pcs_dy_200911.txt',
dir=dir, res_num_col=1, data_col=3, error_col=4, spin_id='@H')
+
+ # The data.
+ pcs_data = {
+ '#CaM:3@N': 0.917,
+ '#CaM:3@H': 0.843,
+ '#CaM:4@N': 1.131,
+ '#CaM:4@H': 1.279,
+ }
+
+ # Check the PCS data.
+ print("\n")
+ for spin, spin_id in spin_loop(return_id=True):
+ print("Checking the PCS data of spin '%s'." % spin_id)
+ self.assert_(hasattr(spin, 'pcs'))
+ self.assertEqual(spin.pcs['dy'], pcs_data[spin_id])
+ self.assertEqual(spin.pcs_err['dy'], 0.1)
+
def test_pcs_copy(self):
"""Test the operation of the pcs.copy user function."""
Modified: branches/frame_order_testing/test_suite/system_tests/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/pipes.py?rev=18235&r1=18234&r2=18235&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/pipes.py (original)
+++ branches/frame_order_testing/test_suite/system_tests/pipes.py Fri Jan 18
18:22:57 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2012 Edward d'Auvergne
#
+# Copyright (C) 2006-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -24,6 +24,7 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
+import dep_check
from generic_fns import pipes
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -31,6 +32,22 @@
class Pipes(SystemTestCase):
"""TestCase class for the functional tests of relax data pipes."""
+
+ def __init__(self, methodName='runTest'):
+ """Skip some tests if scipy is not installed.
+
+ @keyword methodName: The name of the test.
+ @type methodName: str
+ """
+
+ # Execute the base class method.
+ super(Pipes, self).__init__(methodName)
+
+ # Missing module.
+ if not dep_check.scipy_module and methodName in ['test_change_type']:
+ # Store in the status object.
+ status.skipped_tests.append([methodName, 'Scipy',
self._skip_type])
+
def test_change_type(self):
"""Test the pipe.change_type user function."""
r18235 - in /branches/frame_order_testing: ./ generic_fns/ test_suite/shared_data/align_data/ test_suite/system_tests/