relax SVN archive

Implemented the new frame order rotor model parameters in the target function.

The parameters {axis_theta, axis_phi} have been replaced by the single axis_alpha. To support the
new model construct, the CoM of the entire system is now passed into the target function.

Added support for the new axis_alpha frame order parameter to the specific_analyses.frame_order package.

Converted the Frame_order.test_cam_rotor system script test to use the new rotor model parameters.

The rotor frame order parameters {P_alpha, P_beta, P_gamma, T_x, T_y, T_z, E_theta, E_phi, p_x, p_y,
p_z}, where P_i are the Euler angles defining the average domain position, T_i are the translations
defining the average domain position, E_i are the Eigenframe angles defining the rotation axis, and
p_i are the pivot point coordinates, will be converted to {P_alpha, P_beta, P_gamma, T_x, T_y, T_z,
Ax_alpha, p_x, p_y, p_z}. Ax_alpha is the new parameter which defines the rotation axis together
with the pivot using the minimal parameter set {p_x, p_y, p_z, Ax_alpha}.

Fix for the user function intro flag.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i

It should be turned on for the script so you see the "relax>" messages, and then turned off again for the prompt so that
the user function text and "relax>" is not printed out twice.

Merged revisions 22181-22189 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22181 | tlinnet | 2014-02-14 10:32:15 +0100 (Fri, 14 Feb 2014) | 3 lines

Shifted the pedantic flag to escalate flag. The option -p would insted be used for the option --prompt.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i
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r22182 | tlinnet | 2014-02-14 10:32:17 +0100 (Fri, 14 Feb 2014) | 3 lines

Added the -p --prompt option for running a relax script and inspect interactively.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i
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r22183 | tlinnet | 2014-02-14 11:22:56 +0100 (Fri, 14 Feb 2014) | 1 line

Second
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r22184 | tlinnet | 2014-02-14 11:22:57 +0100 (Fri, 14 Feb 2014) | 6 lines

Modified the help text to explain that -p will launch relax in prompt mode after running any optionally supplied scripts.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i

This is to allow the -p --prompt option to be given without a script. relax should support this so that a user doesn't get too confused when
trying to start in prompt mode with the --prompt flag and support the --prompt argument without a script being supplied.
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r22185 | tlinnet | 2014-02-14 11:47:33 +0100 (Fri, 14 Feb 2014) | 22 lines

Manually reverted the temporary change of r22184 and 22183.

The command used was:

svn merge -r22184:r22182 .

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r22184 | tlinnet | 2014-02-14 11:22:57 +0100 (Fri, 14 Feb 2014) | 6 lines

Modified the help text to explain that -p will launch relax in prompt mode after running any optionally supplied scripts.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i

This is to allow the -p --prompt option to be given without a script. relax should support this so that a user doesn't get too confused when
trying to start in prompt mode with the --prompt flag and support the --prompt argument without a script being supplied.
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r22183 | tlinnet | 2014-02-14 11:22:56 +0100 (Fri, 14 Feb 2014) | 1 line

Second
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r22186 | tlinnet | 2014-02-14 11:54:44 +0100 (Fri, 14 Feb 2014) | 6 lines

Modified the help text to explain that -p will launch relax in prompt mode after running any optionally supplied scripts.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i

This is to allow the -p --prompt option to be given without a script. relax should support this so that a user doesn't get too confused when
trying to start in prompt mode with the --prompt flag and support the --prompt argument without a script being supplied.
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r22187 | tlinnet | 2014-02-14 12:13:05 +0100 (Fri, 14 Feb 2014) | 6 lines

Finished implementing the functionality of interacting with variables after executing a script.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i

For getting access to variables after executing a script, the variable should be saved under: cdp.X, where X define a container.
The name space issue is discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5012
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r22188 | tlinnet | 2014-02-14 12:28:25 +0100 (Fri, 14 Feb 2014) | 3 lines

Added Copyright info to modified file.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i
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r22189 | bugman | 2014-02-14 14:24:25 +0100 (Fri, 14 Feb 2014) | 8 lines

Organisation of the relax command line options into distinct groups.

This follows from the message at http://thread.gmane.org/gmane.science.nmr.relax.devel/5024.

The optparse.OptionGroup object is now used to cluster the arguments. This cleans up the output of
'relax -h' and explains the options to the user in a clearer way.
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Organisation of the relax command line options into distinct groups.

This follows from the message at http://thread.gmane.org/gmane.science.nmr.relax.devel/5024.

The optparse.OptionGroup object is now used to cluster the arguments. This cleans up the output of
'relax -h' and explains the options to the user in a clearer way.

Added Copyright info to modified file.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i

Finished implementing the functionality of interacting with variables after executing a script.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i

For getting access to variables after executing a script, the variable should be saved under: cdp.X, where X define a container.
The name space issue is discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5012

Modified the help text to explain that -p will launch relax in prompt mode after running any optionally supplied scripts.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i

This is to allow the -p --prompt option to be given without a script. relax should support this so that a user doesn't get too confused when
trying to start in prompt mode with the --prompt flag and support the --prompt argument without a script being supplied.

Manually reverted the temporary change of r22184 and 22183.

The command used was:

svn merge -r22184:r22182 .

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r22184 | tlinnet | 2014-02-14 11:22:57 +0100 (Fri, 14 Feb 2014) | 6 lines

Modified the help text to explain that -p will launch relax in prompt mode after running any optionally supplied scripts.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect interactively after running script - The equivalence to python -i

This is to allow the -p --prompt option to be given without a script. relax should support this so that a user doesn't get too confused when
trying to start in prompt mode with the --prompt flag and support the --prompt argument without a script being supplied.
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r22183 | tlinnet | 2014-02-14 11:22:56 +0100 (Fri, 14 Feb 2014) | 1 line

Second
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