Author: bugman
Date: Tue Mar 3 17:50:29 2015
New Revision: 27768
URL: http://svn.gna.org/viewcvs/relax?rev=27768&view=rev
Log:
Merged revisions 27763-27767 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27763 | bugman | 2015-03-03 17:34:39 +0100 (Tue, 03 Mar 2015) | 5 lines
Created the Rdc.test_corr_plot system test to check the rdc.corr_plot user
function.
This shows that this poorly tested function works correctly.
........
r27764 | bugman | 2015-03-03 17:40:22 +0100 (Tue, 03 Mar 2015) | 5 lines
Created the Pcs.test_corr_plot system test to check the pcs.corr_plot user
function.
This user function is poorly tested, and this test triggers a series of
bugs.
........
r27765 | bugman | 2015-03-03 17:42:30 +0100 (Tue, 03 Mar 2015) | 6 lines
Added the 'title' and 'subtitle' arguments to the pcs.corr_plot user
function.
This problem was detected by the new Pcs.test_corr_plot system test. The
pcs.corr_plot user
function now matches the rdc.corr_plot user function in terms of arguments.
........
r27766 | bugman | 2015-03-03 17:46:21 +0100 (Tue, 03 Mar 2015) | 3 lines
Fix for the pcs.corr_plot user function when the spin containers have no
element information.
........
r27767 | bugman | 2015-03-03 17:50:02 +0100 (Tue, 03 Mar 2015) | 5 lines
Completed the Pcs.test_corr_plot system test.
The file contents are now known and have been carefully checking in Grace.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/pipe_control/pcs.py
branches/frame_order_cleanup/test_suite/system_tests/pcs.py
branches/frame_order_cleanup/test_suite/system_tests/rdc.py
branches/frame_order_cleanup/user_functions/pcs.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Mar 3 17:50:29 2015
@@ -1 +1 @@
-/trunk:1-27761
+/trunk:1-27767
Modified: branches/frame_order_cleanup/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pcs.py?rev=27768&r1=27767&r2=27768&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pcs.py (original)
+++ branches/frame_order_cleanup/pipe_control/pcs.py Tue Mar 3 17:50:29
2015
@@ -428,7 +428,10 @@
# The spin types.
types = []
for spin in spin_loop():
- if spin.element not in types:
+ if not hasattr(spin, 'element'):
+ if None not in types:
+ types.append(None)
+ elif spin.element not in types:
types.append(spin.element)
# Loop over the PCS data.
@@ -459,7 +462,7 @@
continue
# Incorrect spin type.
- if spin.element != types[i]:
+ if hasattr(spin, 'element') and spin.element != types[i]:
continue
# Skip if data is missing.
Modified: branches/frame_order_cleanup/test_suite/system_tests/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/pcs.py?rev=27768&r1=27767&r2=27768&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/pcs.py (original)
+++ branches/frame_order_cleanup/test_suite/system_tests/pcs.py Tue Mar 3
17:50:29 2015
@@ -26,7 +26,7 @@
# Python module imports.
from os import sep
from re import search
-from tempfile import mkdtemp
+from tempfile import mkdtemp, mktemp
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
@@ -37,6 +37,128 @@
class Pcs(SystemTestCase):
"""Class for testing PCS operations."""
+
+ def test_corr_plot(self):
+ """Test the operation of the pcs.corr_plot user function."""
+
+ # Create a data pipe.
+ self.interpreter.pipe.create('orig', 'N-state')
+
+ # Data directory.
+ dir = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
+
+ # Load the spins.
+ self.interpreter.sequence.read(file='pcs.txt', dir=dir,
spin_name_col=1)
+ self.interpreter.sequence.display()
+
+ # Load the PCSs.
+ self.interpreter.pcs.read(align_id='tb', file='pcs.txt', dir=dir,
spin_name_col=1, data_col=2)
+ self.interpreter.sequence.display()
+
+ # Create back-calculated PCS values from the real values.
+ for spin in spin_loop():
+ if hasattr(spin, 'pcs'):
+ if not hasattr(spin, 'pcs_bc'):
+ spin.pcs_bc = {}
+ spin.pcs_bc['tb'] = spin.pcs['tb']
+ if spin.pcs_bc['tb'] != None:
+ spin.pcs_bc['tb'] += 1.0
+
+ # Correlation plot.
+ ds.tmpfile = mktemp()
+ self.interpreter.pcs.corr_plot(format='grace', title='Test',
subtitle='Test2', file=ds.tmpfile, dir=None, force=True)
+
+ # The expected file contents.
+ real_contents = [
+ "@version 50121",
+ "@page size 842, 595",
+ "@with g0",
+ "@ world 0.0, 0.0, 2.0, 2.0",
+ "@ view 0.15, 0.15, 1.28, 0.85",
+ "@ title \"Test\"",
+ "@ subtitle \"Test2\"",
+ "@ xaxis label \"Back-calculated PCS (ppm)\"",
+ "@ xaxis label char size 1.00",
+ "@ xaxis tick major 1",
+ "@ xaxis tick major size 0.50",
+ "@ xaxis tick major linewidth 0.5",
+ "@ xaxis tick minor ticks 9",
+ "@ xaxis tick minor linewidth 0.5",
+ "@ xaxis tick minor size 0.25",
+ "@ xaxis ticklabel char size 0.70",
+ "@ yaxis label \"Measured PCS (ppm)\"",
+ "@ yaxis label char size 1.00",
+ "@ yaxis tick major 1",
+ "@ yaxis tick major size 0.50",
+ "@ yaxis tick major linewidth 0.5",
+ "@ yaxis tick minor ticks 9",
+ "@ yaxis tick minor linewidth 0.5",
+ "@ yaxis tick minor size 0.25",
+ "@ yaxis ticklabel char size 0.70",
+ "@ legend on",
+ "@ legend 1, 0.5",
+ "@ legend box fill pattern 1",
+ "@ legend char size 1.0",
+ "@ frame linewidth 0.5",
+ "@ s0 symbol 1",
+ "@ s0 symbol size 0.45",
+ "@ s0 symbol linewidth 0.5",
+ "@ s0 errorbar size 0.5",
+ "@ s0 errorbar linewidth 0.5",
+ "@ s0 errorbar riser linewidth 0.5",
+ "@ s0 line linestyle 2",
+ "@ s1 symbol 2",
+ "@ s1 symbol size 0.45",
+ "@ s1 symbol linewidth 0.5",
+ "@ s1 errorbar size 0.5",
+ "@ s1 errorbar linewidth 0.5",
+ "@ s1 errorbar riser linewidth 0.5",
+ "@ s1 line linestyle 0",
+ "@ s1 legend \"tb (None)\"",
+ "@target G0.S0",
+ "@type xy",
+ "-100 -100.000000000000000
\"# 0\"",
+ "100 100.000000000000000
\"# 0\"",
+ "&",
+ "@target G0.S1",
+ "@type xy",
+ "1.004 0.004000000000000
\"# @C1\"",
+ "1.008 0.008000000000000
\"# @C2\"",
+ "1.021 0.021000000000000
\"# @C3\"",
+ "1.029 0.029000000000000
\"# @C4\"",
+ "1.016 0.016000000000000
\"# @C5\"",
+ "1.01 0.010000000000000
\"# @C6\"",
+ "1.008 0.008000000000000
\"# @H1\"",
+ "1.003 0.003000000000000
\"# @H2\"",
+ "1.006 0.006000000000000
\"# @H3\"",
+ "1.003 0.003000000000000
\"# @H4\"",
+ "1.007 0.007000000000000
\"# @H5\"",
+ "1.005 0.005000000000000
\"# @H6\"",
+ "1.001 0.001000000000000
\"# @H7\"",
+ "1.07 0.070000000000000
\"# @C7\"",
+ "1.025 0.025000000000000
\"# @C9\"",
+ "1.098 0.098000000000000
\"# @C10\"",
+ "1.054 0.054000000000000
\"# @C11\"",
+ "1.075 0.075000000000000
\"# @C12\"",
+ "1.065 0.065000000000000
\"# @H12\"",
+ "1.07 0.070000000000000
\"# @H14\"",
+ "1.015 0.015000000000000
\"# @H15\"",
+ "1.098 0.098000000000000
\"# @H16\"",
+ "1.06 0.060000000000000
\"# @H17\"",
+ "1.12 0.120000000000000
\"# @H18\"",
+ "&"
+ ]
+
+ # Check the data.
+ print("\nChecking the Grace file contents.")
+ file = open(ds.tmpfile)
+ lines = file.readlines()
+ file.close()
+ self.assertEqual(len(real_contents), len(lines))
+ for i in range(len(lines)):
+ print(lines[i][:-1])
+ self.assertEqual(real_contents[i], lines[i][:-1])
+
def test_grace_plot(self):
"""Test the creation of Grace plots of PCS data."""
Modified: branches/frame_order_cleanup/test_suite/system_tests/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/rdc.py?rev=27768&r1=27767&r2=27768&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/rdc.py (original)
+++ branches/frame_order_cleanup/test_suite/system_tests/rdc.py Tue Mar 3
17:50:29 2015
@@ -25,6 +25,7 @@
# Python module imports.
from os import sep
+from tempfile import mktemp
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
@@ -64,6 +65,111 @@
# Q factors.
self.interpreter.rdc.calc_q_factors()
+
+
+ def test_corr_plot(self):
+ """Test the operation of the rdc.corr_plot user function."""
+
+ # Create a data pipe.
+ self.interpreter.pipe.create('orig', 'N-state')
+
+ # Data directory.
+ dir = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
+
+ # Load the spins.
+ self.interpreter.sequence.read(file='tb.txt', dir=dir, spin_id_col=1)
+ self.interpreter.sequence.attach_protons()
+ self.interpreter.sequence.display()
+
+ # Load the RDCs.
+ self.interpreter.rdc.read(align_id='tb', file='tb.txt', dir=dir,
spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
+ self.interpreter.sequence.display()
+
+ # Create back-calculated RDC values from the real values.
+ for interatom in interatomic_loop():
+ if hasattr(interatom, 'rdc'):
+ if not hasattr(interatom, 'rdc_bc'):
+ interatom.rdc_bc = {}
+ interatom.rdc_bc['tb'] = interatom.rdc['tb'] + 1.0
+
+ # Correlation plot.
+ ds.tmpfile = mktemp()
+ self.interpreter.rdc.corr_plot(format='grace', title='Test',
subtitle='Test2', file=ds.tmpfile, dir=None, force=True)
+
+ # The expected file contents.
+ real_contents = [
+ "@version 50121",
+ "@page size 842, 595",
+ "@with g0",
+ "@ world -27.0, -27.0, 16.0, 16.0",
+ "@ view 0.15, 0.15, 1.28, 0.85",
+ "@ title \"Test\"",
+ "@ subtitle \"Test2\"",
+ "@ xaxis label \"Back-calculated RDC (Hz)\"",
+ "@ xaxis label char size 1.00",
+ "@ xaxis tick major 10",
+ "@ xaxis tick major size 0.50",
+ "@ xaxis tick major linewidth 0.5",
+ "@ xaxis tick minor ticks 9",
+ "@ xaxis tick minor linewidth 0.5",
+ "@ xaxis tick minor size 0.25",
+ "@ xaxis ticklabel char size 0.70",
+ "@ yaxis label \"Measured RDC (Hz)\"",
+ "@ yaxis label char size 1.00",
+ "@ yaxis tick major 10",
+ "@ yaxis tick major size 0.50",
+ "@ yaxis tick major linewidth 0.5",
+ "@ yaxis tick minor ticks 9",
+ "@ yaxis tick minor linewidth 0.5",
+ "@ yaxis tick minor size 0.25",
+ "@ yaxis ticklabel char size 0.70",
+ "@ legend on",
+ "@ legend 1, 0.5",
+ "@ legend box fill pattern 1",
+ "@ legend char size 1.0",
+ "@ frame linewidth 0.5",
+ "@ s0 symbol 1",
+ "@ s0 symbol size 0.45",
+ "@ s0 symbol linewidth 0.5",
+ "@ s0 errorbar size 0.5",
+ "@ s0 errorbar linewidth 0.5",
+ "@ s0 errorbar riser linewidth 0.5",
+ "@ s0 line linestyle 2",
+ "@ s1 symbol 2",
+ "@ s1 symbol size 0.45",
+ "@ s1 symbol linewidth 0.5",
+ "@ s1 errorbar size 0.5",
+ "@ s1 errorbar linewidth 0.5",
+ "@ s1 errorbar riser linewidth 0.5",
+ "@ s1 line linestyle 0",
+ "@ s1 legend \"tb\"",
+ "@target G0.S0",
+ "@type xydy",
+ "-100 -100.000000000000000
0.000000000000000 ",
+ "100 100.000000000000000
0.000000000000000 ",
+ "&",
+ "@target G0.S1",
+ "@type xydy",
+ "-25.2501958629 -26.250195862900000
1.000000000000000 \"#
#CaM:5@N-#CaM:5@H\"",
+ "10.9308176694 9.930817669420000
1.000000000000000 \"#
#CaM:6@N-#CaM:6@H\"",
+ "8.26317614156 7.263176141560000
1.000000000000000 \"#
#CaM:7@N-#CaM:7@H\"",
+ "-0.24840526981 -1.248405269810000
0.000000000000000 \"#
#CaM:8@N-#CaM:8@H\"",
+ "6.31803314334 5.318033143340000
1.000000000000000 \"#
#CaM:9@N-#CaM:9@H\"",
+ "15.0362909456 14.036290945599999
1.000000000000000 \"#
#CaM:10@N-#CaM:10@H\"",
+ "2.33652530397 1.336525303970000
0.000000000000000 \"#
#CaM:11@N-#CaM:11@H\"",
+ "-0.6021670281 -1.602167028100000
0.000000000000000 \"#
#CaM:12@N-#CaM:12@H\"",
+ "&",
+ ]
+
+ # Check the data.
+ print("\nChecking the Grace file contents.")
+ file = open(ds.tmpfile)
+ lines = file.readlines()
+ file.close()
+ self.assertEqual(len(real_contents), len(lines))
+ for i in range(len(lines)):
+ print(lines[i][:-1])
+ self.assertEqual(real_contents[i], lines[i][:-1])
def test_rdc_copy(self):
Modified: branches/frame_order_cleanup/user_functions/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/pcs.py?rev=27768&r1=27767&r2=27768&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/pcs.py (original)
+++ branches/frame_order_cleanup/user_functions/pcs.py Tue Mar 3 17:50:29
2015
@@ -179,6 +179,20 @@
can_be_none = True
)
uf.add_keyarg(
+ name = "title",
+ py_type = "str",
+ desc_short = "alternative plot title",
+ desc = "The title for the plot, overriding the default.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "subtitle",
+ py_type = "str",
+ desc_short = "alternative plot subtitle",
+ desc = "The subtitle for the plot, overriding the default.",
+ can_be_none = True
+)
+uf.add_keyarg(
name = "file",
default = "pcs_corr_plot.agr",
py_type = "str",
r27768 - in /branches/frame_order_cleanup: ./ pipe_control/ test_suite/system_tests/ user_functions/