relax SVN archive

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.

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.

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.

Added an icon which will be used for a link to the PDF user manual from http://www.nmr-relax.com/manual

Added the Open Source Software Directory to the http://www.nmr-relax.com/links.html webpage.

The URL with the relax link is http://www.opensourcesoftwaredirectory.com/Scientific/Chemo-and-bio

Added 'spin_lock_nu1' as a dictionary type parameter of the relaxation dispersion specific analysis.

Deleted the .no_stats.html page at http://www.nmr-relax.com as it doesn't do anything.

Fix for the link to http://nmr-relax.com/api/1.0/ at http://nmr-relax.com/api/index.html.

Added http://www.nmr-relax.com/ to all of the http://www.nmr-relax.com/ links in the menu SSI element.

This is to allow the menu to be operational from http://www.nmr-relax.com/api/index.html.

Merged revisions 19401-19409,19428-19430,19433-19434 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r19401 | bugman | 2013-04-08 15:07:50 +0200 (Mon, 08 Apr 2013) | 7 lines

Created the pipe_control.plotting module.

This will be used as a base for the plotting of all types of data. This includes the current OpenDX
and Grace modules, as well as future modules. The determine_functions() function has been added and
is used to simplify the pipe_control.grace.get_data() function.
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r19402 | bugman | 2013-04-08 16:45:13 +0200 (Mon, 08 Apr 2013) | 6 lines

The grace.write user function data type argument sequence values have changed.

Instead of 'spin', this can now be 'res_num' or 'spin_num' to specify that either the residue number
or spin number should be plotted on the desired axis. The x_data_type now defaults to 'res_num'.
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r19403 | bugman | 2013-04-08 16:46:14 +0200 (Mon, 08 Apr 2013) | 5 lines

Created the pipe_control.mol_res_spin.count_max_spins_per_residue() function.

This will be used by the plotting module to determine if more than one spin per residue exists.
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r19404 | bugman | 2013-04-08 16:49:17 +0200 (Mon, 08 Apr 2013) | 3 lines

Fixes for the change of the grace.write user function data type 'spin' to 'res_num'.
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r19405 | bugman | 2013-04-08 16:55:19 +0200 (Mon, 08 Apr 2013) | 3 lines

Updated the pipe_control.plotting.determine_functions() function.
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r19406 | bugman | 2013-04-09 15:40:58 +0200 (Tue, 09 Apr 2013) | 7 lines

Added the skip_desel flag to the important pipe_control.mol_res_spin.spin_loop() generator function.

This is used to skip deselected spins within the loop. As must of the code in relax using the
spin_loop() does this anyway, this can be used to simplify many of the spin looping elements in
relax.
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r19407 | bugman | 2013-04-09 18:21:18 +0200 (Tue, 09 Apr 2013) | 5 lines

Fix for the new pipe_control.mol_res_spin.count_max_spins_per_residue() function.

The data pipe container was missing.
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r19408 | bugman | 2013-04-09 18:54:26 +0200 (Tue, 09 Apr 2013) | 5 lines

Fix for the analysis specific API common _return_value_general() method.

The value of None is now handled properly when a simulation value is asked for.
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r19409 | bugman | 2013-04-09 21:53:41 +0200 (Tue, 09 Apr 2013) | 5 lines

Restored the default behaviour of the spin_loop().

The skip_desel flag is now functional and defaults to False.
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r19428 | bugman | 2013-04-10 15:53:44 +0200 (Wed, 10 Apr 2013) | 5 lines

Fix for the relax_times and intensities parameter definitions for specific_analyses.relax_fit.

These are dictionaries, not lists.
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r19429 | bugman | 2013-04-10 16:21:16 +0200 (Wed, 10 Apr 2013) | 5 lines

Expanded the relax_fit system test script to produce all types of currently supported Grace graphs.

This is to more extensively test the grace.write user function.
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r19430 | bugman | 2013-04-10 16:28:27 +0200 (Wed, 10 Apr 2013) | 16 lines

Large redesign of the 2D graphing code in relax.

This currently affects only the grace.write user function, but the new infrastructure will make it
much easier to expand the graphing abilities and to support other 2D graphing software. The
plotting code has also been significantly simplified.

The pipe_control.grace.get_data() function has been shifted into the pipe_control.plotting module.
It has been split up into the base assemble_data() function with the data assembly shifted to
assemble_data_scatter(), assemble_data_seq_value() and assemble_data_series_series(). This split
massively simplifies the code by not packing all different graph and set combinations into one.

In addition the auxiliary functions classify_graph_2D(), fetch_1D_data(), get_functions(), and
get_data_type() have been created to maximise code sharing between the different assemble_*()
functions.
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r19433 | bugman | 2013-04-10 17:28:21 +0200 (Wed, 10 Apr 2013) | 6 lines

Modified the relax_fit system test script to generate a new type of graph.

This is the residue number sequence verses the peak intensity series data (and vice versa) via the
grace.write user function. This is to help in the implementation of this graph type.
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r19434 | bugman | 2013-04-10 17:29:36 +0200 (Wed, 10 Apr 2013) | 6 lines

Created the pipe_control.plotting.assemble_data_seq_series() function.

This is to allow the residue or spin numbering to be plotted against any series type data (lists or
dictionaries), or vice versa.
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