Author: bugman
Date: Thu Apr 11 09:46:03 2013
New Revision: 19449
URL: http://svn.gna.org/viewcvs/relax?rev=19449&view=rev
Log:
Merged revisions 19442-19448 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r19442 | bugman | 2013-04-10 19:44:37 +0200 (Wed, 10 Apr 2013) | 6 lines
Added a link to the PDF user manual from the HTML user manual.
This will affect all pages at http://www.nmr-relax.com/manual/ by adding an
icon to the navigation
bar pointing to the PDF manual at
http://download.gna.org/relax/manual/relax.pdf.
........
r19443 | bugman | 2013-04-11 09:30:16 +0200 (Thu, 11 Apr 2013) | 5 lines
Bug fix for the new pipe_control.mol_res_spin.count_max_spins_per_residue()
function.
This function, introduced at r19403, was not returning the correct variable.
........
r19444 | bugman | 2013-04-11 09:31:49 +0200 (Thu, 11 Apr 2013) | 6 lines
The plotting of residue or spin numbers verses values now handles multiple
spin types properly.
This is in the pipe_control.plotting.assemble_data_seq_value() function.
The spin name is being
used to identify different spin types for the graph sets.
........
r19445 | bugman | 2013-04-11 09:32:57 +0200 (Thu, 11 Apr 2013) | 5 lines
Fix for the Noe.test_noe_analysis system test.
The set labels are now different in that they no longer end in '. '.
........
r19446 | bugman | 2013-04-11 09:40:53 +0200 (Thu, 11 Apr 2013) | 5 lines
The pipe_control.mol_res_spin.count_max_spins_per_residue() function now
accepts a spin ID argument.
This can be used to restrict the spins to count.
........
r19447 | bugman | 2013-04-11 09:42:37 +0200 (Thu, 11 Apr 2013) | 5 lines
The spin ID string is now being used by the plotting functions.
The spin ID was not being passed into the assemble_data_*() functions.
........
r19448 | bugman | 2013-04-11 09:42:58 +0200 (Thu, 11 Apr 2013) | 3 lines
Removed a debugging printout.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/docs/latex/relax.tex
branches/relax_disp/pipe_control/mol_res_spin.py
branches/relax_disp/pipe_control/plotting.py
branches/relax_disp/test_suite/system_tests/noe.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Apr 11 09:46:03 2013
@@ -1,1 +1,1 @@
-/trunk:1-19434
+/trunk:1-19448
Modified: branches/relax_disp/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/relax.tex?rev=19449&r1=19448&r2=19449&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/relax.tex (original)
+++ branches/relax_disp/docs/latex/relax.tex Thu Apr 11 09:46:03 2013
@@ -106,6 +106,7 @@
% latex2html stuff.
\usepackage{html}
+\htmladdtonavigation{\htmladdnormallink{\htmladdimg{http://www.nmr-relax.com/images/pdf_icon_nav.png}}{http://download.gna.org/relax/manual/relax.pdf}}
\htmladdtonavigation{\htmladdnormallink{\htmladdimg{http://www.nmr-relax.com/images/relax_logo_nav.png}}{http://www.nmr-relax.com}}
% Make the index.
Modified: branches/relax_disp/pipe_control/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/mol_res_spin.py?rev=19449&r1=19448&r2=19449&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/mol_res_spin.py (original)
+++ branches/relax_disp/pipe_control/mol_res_spin.py Thu Apr 11 09:46:03 2013
@@ -417,11 +417,13 @@
status.spin_lock.release(sys._getframe().f_code.co_name)
-def count_max_spins_per_residue(pipe=None, skip_desel=True):
+def count_max_spins_per_residue(pipe=None, spin_id=None, skip_desel=True):
"""Determine the maximum number of spins present per residue.
@keyword pipe: The data pipe containing the spin. Defaults to
the current data pipe.
@type pipe: str
+ @param spin_id: The molecule, residue, and spin identifier
string.
+ @type spin_id: str
@keyword skip_desel: A flag which if true will cause deselected spins
to be skipped in the count.
@type skip_desel: bool
@return: The number of non-empty spins.
@@ -444,6 +446,9 @@
# Get the data pipe.
dp = pipes.get_pipe(pipe)
+
+ # Parse the selection string.
+ select_obj = Selection(spin_id)
# Loop over the molecules.
for mol in dp.mol:
@@ -454,6 +459,10 @@
# Loop over the spins.
for spin in res.spin:
+ # Skip the spin if there is no match to the selection.
+ if not select_obj.contains_spin(spin_num=spin.num,
spin_name=spin.name, res_num=res.num, res_name=res.name, mol=mol.name):
+ continue
+
# Skip deselected spins.
if skip_desel and not spin.select:
continue
@@ -465,7 +474,7 @@
max_num = max(max_num, spin_num)
# Return the maximum number of spins.
- return spin_num
+ return max_num
def count_molecules(selection=None, pipe=None):
Modified: branches/relax_disp/pipe_control/plotting.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/plotting.py?rev=19449&r1=19448&r2=19449&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/plotting.py (original)
+++ branches/relax_disp/pipe_control/plotting.py Thu Apr 11 09:46:03 2013
@@ -61,13 +61,13 @@
# Assemble the different graph data structures.
if graph_type == 'seq-value':
- data, set_labels, x_err_flag, y_err_flag =
assemble_data_seq_value(x_data_name=x_data_name, y_data_name=y_data_name,
plot_data=plot_data)
+ data, set_labels, x_err_flag, y_err_flag =
assemble_data_seq_value(spin_id=spin_id, x_data_name=x_data_name,
y_data_name=y_data_name, plot_data=plot_data)
elif graph_type == 'value-value':
- data, set_labels, x_err_flag, y_err_flag =
assemble_data_scatter(x_data_name=x_data_name, y_data_name=y_data_name,
plot_data=plot_data)
+ data, set_labels, x_err_flag, y_err_flag =
assemble_data_scatter(spin_id=spin_id, x_data_name=x_data_name,
y_data_name=y_data_name, plot_data=plot_data)
elif graph_type == 'seq-series':
- data, set_labels, x_err_flag, y_err_flag =
assemble_data_seq_series(x_data_name=x_data_name, y_data_name=y_data_name,
plot_data=plot_data, x_type=x_type, y_type=y_type)
+ data, set_labels, x_err_flag, y_err_flag =
assemble_data_seq_series(spin_id=spin_id, x_data_name=x_data_name,
y_data_name=y_data_name, plot_data=plot_data, x_type=x_type, y_type=y_type)
elif graph_type == 'series-series':
- data, set_labels, x_err_flag, y_err_flag =
assemble_data_series_series(x_data_name=x_data_name, y_data_name=y_data_name,
plot_data=plot_data, x_type=x_type, y_type=y_type)
+ data, set_labels, x_err_flag, y_err_flag =
assemble_data_series_series(spin_id=spin_id, x_data_name=x_data_name,
y_data_name=y_data_name, plot_data=plot_data, x_type=x_type, y_type=y_type)
else:
raise RelaxError("Unknown graph type '%s'." % graph_type)
@@ -257,7 +257,7 @@
# The number of data sets.
set_count = 1
if x_data_name == 'res_num' or y_data_name == 'res_num':
- set_count = count_max_spins_per_residue()
+ set_count = count_max_spins_per_residue(spin_id=spin_id)
# Expand the data structures for the number of sets.
if set_count > 1:
@@ -278,7 +278,15 @@
points = 1
# Loop over the spins.
+ spin_names = []
for spin, mol_name, res_num, res_name, id in spin_loop(full_info=True,
selection=spin_id, return_id=True, skip_desel=True):
+ # A new spin name.
+ if spin.name not in spin_names:
+ spin_names.append(spin.name)
+
+ # The set index.
+ set_index = spin_names.index(spin.name)
+
# Loop over the data points (for simulations).
for i in range(points):
# The X and Y data.
@@ -296,11 +304,11 @@
y_err_flag = True
# Append the data.
- data[0][0].append([x_val, y_val])
+ data[0][set_index].append([x_val, y_val])
if x_err_flag:
- data[0][0][-1].append(x_err)
+ data[0][set_index][-1].append(x_err)
if y_err_flag:
- data[0][0][-1].append(y_err)
+ data[0][set_index][-1].append(y_err)
# Return the data.
return data, set_labels, x_err_flag, y_err_flag
Modified: branches/relax_disp/test_suite/system_tests/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/noe.py?rev=19449&r1=19448&r2=19449&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/noe.py (original)
+++ branches/relax_disp/test_suite/system_tests/noe.py Thu Apr 11 09:46:03
2013
@@ -102,14 +102,14 @@
'@ s0 errorbar size 0.5\n',
'@ s0 errorbar linewidth 0.5\n',
'@ s0 errorbar riser linewidth 0.5\n',
- '@ s0 legend "N spins. "\n',
+ '@ s0 legend "N spins"\n',
'@ s1 symbol 2\n',
'@ s1 symbol size 0.45\n',
'@ s1 symbol linewidth 0.5\n',
'@ s1 errorbar size 0.5\n',
'@ s1 errorbar linewidth 0.5\n',
'@ s1 errorbar riser linewidth 0.5\n',
- '@ s1 legend "NE1 spins. "\n',
+ '@ s1 legend "NE1 spins"\n',
'@target G0.S0\n',
'@type xydy\n',
'4 0.033980647852827
0.020203299032766 \n',
r19449 - in /branches/relax_disp: ./ docs/latex/ pipe_control/ test_suite/system_tests/
