relax SVN archive

Bug fix for the frame order specific analysis API base_data_loop() method.

This was looping over non-existent PCS and RDC data. Now the alignment ID is checked for in the
interatomic data container 'rdc' data structure and the spin container 'pcs' data structure, as well
as values of None, before yielding the data.

Implemented the frame order analysis backend for the statistics.model and statistics.aic user functions.

This simply required aliasing the specific analysis API common _get_model_container_cdp() method to
get_model_container().

Modified the frame order system test check_chi2() method to test the statistics.model user function.

This causes all of the Frame_order.test_cam_* system tests to fail, as the user function backend is
not implemented for the frame order analysis.

Merged revisions 27606 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27606 | bugman | 2015-02-09 10:50:36 +0100 (Mon, 09 Feb 2015) | 10 lines

Fix for bug #23259 (https://gna.org/bugs/?23259).

This is the broken user functions in the prompt UI with the RelaxError: The user function 'X' has
been renamed to 'Y'. The problem was that the only the first part of the user function name, for
example 'minimise' from 'minimise.calculate' was being checked in the user function name translation
table. As the minimise user function has been renamed to minimise.execute, 'minimise' is in the
translation table and hence minimise.calculate was being identified as the minimise user function.
Now the full user function name is reconstructed before checking the translation table.
........

Merged revisions 27606 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27606 | bugman | 2015-02-09 10:50:36 +0100 (Mon, 09 Feb 2015) | 10 lines

Fix for bug #23259 (https://gna.org/bugs/?23259).

This is the broken user functions in the prompt UI with the RelaxError: The user function 'X' has
been renamed to 'Y'. The problem was that the only the first part of the user function name, for
example 'minimise' from 'minimise.calculate' was being checked in the user function name translation
table. As the minimise user function has been renamed to minimise.execute, 'minimise' is in the
translation table and hence minimise.calculate was being identified as the minimise user function.
Now the full user function name is reconstructed before checking the translation table.
........

Fix for bug #23259 (https://gna.org/bugs/?23259).

This is the broken user functions in the prompt UI with the RelaxError: The user function 'X' has
been renamed to 'Y'. The problem was that the only the first part of the user function name, for
example 'minimise' from 'minimise.calculate' was being checked in the user function name translation
table. As the minimise user function has been renamed to minimise.execute, 'minimise' is in the
translation table and hence minimise.calculate was being identified as the minimise user function.
Now the full user function name is reconstructed before checking the translation table.

Merged revisions 27540-27551,27553-27569,27592-27603 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27540 | bugman | 2015-02-05 12:03:31 +0100 (Thu, 05 Feb 2015) | 5 lines

Created the infrastructure for a Statistics system test class.

This will be used for checking statistics produced by relax.
........
r27541 | bugman | 2015-02-05 12:28:01 +0100 (Thu, 05 Feb 2015) | 20 lines

Reverted r27540, the Statistics system test class.

The command used was:
svn merge -r27540:r27539 .

Any statistics are specific to the different analysis types, therefore such tests would be better
in the respective specific analysis system test classes.

.....
r27540 | bugman | 2015-02-05 12:03:31 +0100 (Thu, 05 Feb 2015) | 5 lines
Changed paths:
M /trunk/test_suite/system_tests/__init__.py
A /trunk/test_suite/system_tests/statistics.py

Created the infrastructure for a Statistics system test class.

This will be used for checking statistics produced by relax.
.....
........
r27542 | bugman | 2015-02-05 14:06:39 +0100 (Thu, 05 Feb 2015) | 7 lines

Created the N_state_model.test_statistics system test.

This system test will be used to implement the new statistics user function class consisting of the
structure.model and structure.aic user functions for calculating and storing the [chi2, n, k]
parameters and Akaike's Information Criterion statistic respectively.
........
r27543 | bugman | 2015-02-05 14:27:43 +0100 (Thu, 05 Feb 2015) | 6 lines

Added the structure.align user function to the renaming translation table.

This is so relax identifies structure.align user functions in scripts to raise an error saying that
the structure.superimpose user function should be used instead.
........
r27544 | bugman | 2015-02-05 14:56:44 +0100 (Thu, 05 Feb 2015) | 3 lines

Added the office-chart-pie set of Oxygen icons for use in the new statistics user function class.
........
r27545 | bugman | 2015-02-05 14:59:36 +0100 (Thu, 05 Feb 2015) | 5 lines

Created the empty statistics user function class.

This adds the infrastructure for creating the statistics user functions.
........
r27546 | bugman | 2015-02-05 15:19:57 +0100 (Thu, 05 Feb 2015) | 3 lines

Small fix for the structure.add_model user function description.
........
r27547 | bugman | 2015-02-05 15:26:04 +0100 (Thu, 05 Feb 2015) | 3 lines

Created the frontend for the statistics.model user function.
........
r27548 | bugman | 2015-02-05 15:41:47 +0100 (Thu, 05 Feb 2015) | 5 lines

Created a wizard graphic for the statistics user functions.

This is based on a number of Oxygen icons, as labelled in the SVG layer names.
........
r27549 | bugman | 2015-02-05 15:43:11 +0100 (Thu, 05 Feb 2015) | 3 lines

The statistics.model user function now uses the new statistics wizard graphic.
........
r27550 | bugman | 2015-02-05 15:45:47 +0100 (Thu, 05 Feb 2015) | 5 lines

Created the empty pipe_control.statistics module.

This will be used for the backend of all of the statistics user functions.
........
r27551 | bugman | 2015-02-05 17:14:08 +0100 (Thu, 05 Feb 2015) | 8 lines

Fixes for the EPS versions of some Oxygen icons used in the relax manual.

This is the actions.document-preview-archive and actions.office-chart-pie Oxygen icons used for the
user function icons. The files were not created correctly in the Gimp. The export to EPS requires
the width and height to be both set to 6 mm, and the X and Y offsets to zero. This allows the icon
bounding boxes and sizes to match the other EPS icons.
........
r27553 | bugman | 2015-02-05 17:41:31 +0100 (Thu, 05 Feb 2015) | 7 lines

Implemented the backend of the statistics.model user function.

The implementation heavily uses the specific analysis API, calling the calculate(), model_loop(),
print_model_title(), model_statistics() and get_model_container() methods to do all of the work.
The last of these API methods is yet to be implemented.
........
r27554 | bugman | 2015-02-05 17:45:26 +0100 (Thu, 05 Feb 2015) | 6 lines

Fix for the statistics.model user function backend.

The API methods are now called with the model_info argument set to a keyword argument so that it is
always passed in as the correct argument.
........
r27555 | bugman | 2015-02-05 17:47:03 +0100 (Thu, 05 Feb 2015) | 6 lines

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

This method was horribly broken, as it was never used. The new statistics.model user function
together with the N-state model uncovers this breakage.
........
r27556 | bugman | 2015-02-05 18:24:03 +0100 (Thu, 05 Feb 2015) | 6 lines

Defined the get_model_container() specific analysis API method.

This base method raises a RelaxImplementError, therefore each analysis type must implement its own
method (or use an API common method).
........
r27557 | bugman | 2015-02-05 18:29:00 +0100 (Thu, 05 Feb 2015) | 7 lines

Implemented the specific analysis API _get_model_container_cdp() commmon method.

This is to be used for the get_model_container() for returning the current data pipe object as the
model container. This is for the global models where the model information is stored in the pipe
object rather than in spin containers.
........
r27558 | bugman | 2015-02-05 18:29:42 +0100 (Thu, 05 Feb 2015) | 5 lines

The N-state model now uses the _get_model_container_cdp() method.

This is aliased as the get_model_container() specific analysis API method.
........
r27559 | bugman | 2015-02-05 18:31:57 +0100 (Thu, 05 Feb 2015) | 3 lines

Fix for the N_state_model.test_statistics system test - the probabilities were missing from k.
........
r27560 | bugman | 2015-02-05 18:38:43 +0100 (Thu, 05 Feb 2015) | 3 lines

Expanded the printouts from the statistics.model user function to include the statistics.
........
r27561 | bugman | 2015-02-05 18:47:41 +0100 (Thu, 05 Feb 2015) | 9 lines

Big bug fix for the N-state model num_data_points() function.

This is from the specific_analyses.n_state_model.data module. This code was very much out of date.
It was expecting an ancient behaviour where the spin container 'pcs' variable and interatomic data
container 'rdc' where lists of floats. However these were converted many years ago to dictionaries
with keys set to the alignment IDs. The result was that no RDCs nor PCSs were counted as a base
data point, so the function would in most cases return a value of zero.
........
r27562 | bugman | 2015-02-05 18:51:10 +0100 (Thu, 05 Feb 2015) | 3 lines

Updated the N-state model num_data_points() function to use more modern integer incrementation.
........
r27563 | bugman | 2015-02-05 18:58:26 +0100 (Thu, 05 Feb 2015) | 6 lines

Fixes for the printout from the pipe_control.pcs.return_pcs_data() function.

The number of PCSs printed out was including values of None when data was missing for one alignment.
These values of None are no longer counted.
........
r27564 | bugman | 2015-02-05 18:58:43 +0100 (Thu, 05 Feb 2015) | 6 lines

Fixes for the printout from the pipe_control.rdc.return_rdc_data() function.

The number of RDCs printed out was including values of None when data was missing for one alignment.
These values of None are no longer counted.
........
r27565 | bugman | 2015-02-05 19:04:32 +0100 (Thu, 05 Feb 2015) | 6 lines

More fixes for the RDC and PCS count printouts from the corresponding data assembly functions.

Sometimes the RDC or PCS value could be present as None. This is now detected and the count is not
incremented.
........
r27566 | bugman | 2015-02-05 19:10:44 +0100 (Thu, 05 Feb 2015) | 5 lines

More fixes for the PCS count printout from the pipe_control.pcs.return_pcs_data() function.

The check for None values was incorrect.
........
r27567 | bugman | 2015-02-05 19:12:57 +0100 (Thu, 05 Feb 2015) | 6 lines

Fixes for the N-state model num_data_points() function.

The deselected interatomic data containers are no longer used for counting RDC data. And the
skipping of deselected spin containers for the PCS is now via the spin_loop() skip_desel argument.
........
r27568 | bugman | 2015-02-05 19:14:41 +0100 (Thu, 05 Feb 2015) | 6 lines

Fix for the N_state_model.test_statistics system test.

The deselected spins and interatomic data containers are now taken into account for the RDC and PCS
data point counts.
........
r27569 | bugman | 2015-02-05 19:26:32 +0100 (Thu, 05 Feb 2015) | 8 lines

Implementation of the statistics.aic user function.

This is very similar to the statistics.model user function - the code was copied and only slightly
modified. The new user function will calculate the current chi-squared value per model, obtain the
model statistics, calculate the AIC value per model, and store the AIC value, chi-squared value and
number of parameters in the appropriate location for the model in the relax data store.
........
r27592 | bugman | 2015-02-06 12:05:31 +0100 (Fri, 06 Feb 2015) | 3 lines

Created the empty lib.plotting.veusz module for graphing using Veusz (http://home.gna.org/veusz/).
........
r27593 | bugman | 2015-02-06 14:29:35 +0100 (Fri, 06 Feb 2015) | 6 lines

Shifted the lib.software.grace module to lib.plotting.grace.

This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/7532 and
http://thread.gmane.org/gmane.science.nmr.relax.devel/7536.
........
r27594 | bugman | 2015-02-06 14:40:04 +0100 (Fri, 06 Feb 2015) | 3 lines

Copyright update.
........
r27595 | bugman | 2015-02-06 14:42:20 +0100 (Fri, 06 Feb 2015) | 7 lines

Created XY-data functions for the plotting API of the relax library.

These are currently copies of the heads of the lib.plotting.grace functions write_xy_data() and
write_xy_header(). These lib.plotting.api functions (write_xy_data() and write_xy_header()) are set
up to use the grace functions.
........
r27596 | bugman | 2015-02-06 14:47:10 +0100 (Fri, 06 Feb 2015) | 3 lines

Converted all of the Grace plotting in relax to use the plotting API of the relax library.
........
r27597 | bugman | 2015-02-06 14:58:01 +0100 (Fri, 06 Feb 2015) | 7 lines

Shifted the pipe_control.grace.write() function.

This is now the format independent pipe_control.plotting.write_xy() function. The format argument
has been added and this defaults to 'grace'. The grace.write user function has been updated to use
the new backend.
........
r27598 | bugman | 2015-02-06 15:01:00 +0100 (Fri, 06 Feb 2015) | 3 lines

Updated the pcs.structural_noise user function to use the relax library plotting API.
........
r27599 | bugman | 2015-02-06 15:05:30 +0100 (Fri, 06 Feb 2015) | 6 lines

Fixes for the new pipe_control.plotting.write_xy() function.

This includes missing imports which should have moved from pipe_control.grace, as well as shifting
the axis_setup() function from the pipe_control.grace module into the pipe_control.plotting module.
........
r27600 | bugman | 2015-02-06 15:14:15 +0100 (Fri, 06 Feb 2015) | 6 lines

The rdc.corr_plot user function backend now uses the relax library plotting API.

The write_xy_data() and write_xy_header() functions from lib.plotting.api are now uses instead of
the equivalent pipe_control.grace functions which no longer exist.
........
r27601 | bugman | 2015-02-06 15:16:05 +0100 (Fri, 06 Feb 2015) | 3 lines

More import fixes for the new pipe_control.plotting.write_xy() function.
........
r27602 | bugman | 2015-02-06 15:17:51 +0100 (Fri, 06 Feb 2015) | 5 lines

Fix for the backend of the relax_disp.plot_disp_curves user function.

The lib.plotting.api functions write_xy_data() and write_xy_header() require the format argument.
........
r27603 | bugman | 2015-02-06 15:32:12 +0100 (Fri, 06 Feb 2015) | 3 lines

Updated the relative stereochemistry auto-analysis to use the relax library plotting API.
........

Merged revisions 27540-27551,27553-27569,27592-27603 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r27540 | bugman | 2015-02-05 12:03:31 +0100 (Thu, 05 Feb 2015) | 5 lines

Created the infrastructure for a Statistics system test class.

This will be used for checking statistics produced by relax.
........
r27541 | bugman | 2015-02-05 12:28:01 +0100 (Thu, 05 Feb 2015) | 20 lines

Reverted r27540, the Statistics system test class.

The command used was:
svn merge -r27540:r27539 .

Any statistics are specific to the different analysis types, therefore such tests would be better
in the respective specific analysis system test classes.

.....
r27540 | bugman | 2015-02-05 12:03:31 +0100 (Thu, 05 Feb 2015) | 5 lines
Changed paths:
M /trunk/test_suite/system_tests/__init__.py
A /trunk/test_suite/system_tests/statistics.py

Created the infrastructure for a Statistics system test class.

This will be used for checking statistics produced by relax.
.....
........
r27542 | bugman | 2015-02-05 14:06:39 +0100 (Thu, 05 Feb 2015) | 7 lines

Created the N_state_model.test_statistics system test.

This system test will be used to implement the new statistics user function class consisting of the
structure.model and structure.aic user functions for calculating and storing the [chi2, n, k]
parameters and Akaike's Information Criterion statistic respectively.
........
r27543 | bugman | 2015-02-05 14:27:43 +0100 (Thu, 05 Feb 2015) | 6 lines

Added the structure.align user function to the renaming translation table.

This is so relax identifies structure.align user functions in scripts to raise an error saying that
the structure.superimpose user function should be used instead.
........
r27544 | bugman | 2015-02-05 14:56:44 +0100 (Thu, 05 Feb 2015) | 3 lines

Added the office-chart-pie set of Oxygen icons for use in the new statistics user function class.
........
r27545 | bugman | 2015-02-05 14:59:36 +0100 (Thu, 05 Feb 2015) | 5 lines

Created the empty statistics user function class.

This adds the infrastructure for creating the statistics user functions.
........
r27546 | bugman | 2015-02-05 15:19:57 +0100 (Thu, 05 Feb 2015) | 3 lines

Small fix for the structure.add_model user function description.
........
r27547 | bugman | 2015-02-05 15:26:04 +0100 (Thu, 05 Feb 2015) | 3 lines

Created the frontend for the statistics.model user function.
........
r27548 | bugman | 2015-02-05 15:41:47 +0100 (Thu, 05 Feb 2015) | 5 lines

Created a wizard graphic for the statistics user functions.

This is based on a number of Oxygen icons, as labelled in the SVG layer names.
........
r27549 | bugman | 2015-02-05 15:43:11 +0100 (Thu, 05 Feb 2015) | 3 lines

The statistics.model user function now uses the new statistics wizard graphic.
........
r27550 | bugman | 2015-02-05 15:45:47 +0100 (Thu, 05 Feb 2015) | 5 lines

Created the empty pipe_control.statistics module.

This will be used for the backend of all of the statistics user functions.
........
r27551 | bugman | 2015-02-05 17:14:08 +0100 (Thu, 05 Feb 2015) | 8 lines

Fixes for the EPS versions of some Oxygen icons used in the relax manual.

This is the actions.document-preview-archive and actions.office-chart-pie Oxygen icons used for the
user function icons. The files were not created correctly in the Gimp. The export to EPS requires
the width and height to be both set to 6 mm, and the X and Y offsets to zero. This allows the icon
bounding boxes and sizes to match the other EPS icons.
........
r27553 | bugman | 2015-02-05 17:41:31 +0100 (Thu, 05 Feb 2015) | 7 lines

Implemented the backend of the statistics.model user function.

The implementation heavily uses the specific analysis API, calling the calculate(), model_loop(),
print_model_title(), model_statistics() and get_model_container() methods to do all of the work.
The last of these API methods is yet to be implemented.
........
r27554 | bugman | 2015-02-05 17:45:26 +0100 (Thu, 05 Feb 2015) | 6 lines

Fix for the statistics.model user function backend.

The API methods are now called with the model_info argument set to a keyword argument so that it is
always passed in as the correct argument.
........
r27555 | bugman | 2015-02-05 17:47:03 +0100 (Thu, 05 Feb 2015) | 6 lines

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

This method was horribly broken, as it was never used. The new statistics.model user function
together with the N-state model uncovers this breakage.
........
r27556 | bugman | 2015-02-05 18:24:03 +0100 (Thu, 05 Feb 2015) | 6 lines

Defined the get_model_container() specific analysis API method.

This base method raises a RelaxImplementError, therefore each analysis type must implement its own
method (or use an API common method).
........
r27557 | bugman | 2015-02-05 18:29:00 +0100 (Thu, 05 Feb 2015) | 7 lines

Implemented the specific analysis API _get_model_container_cdp() commmon method.

This is to be used for the get_model_container() for returning the current data pipe object as the
model container. This is for the global models where the model information is stored in the pipe
object rather than in spin containers.
........
r27558 | bugman | 2015-02-05 18:29:42 +0100 (Thu, 05 Feb 2015) | 5 lines

The N-state model now uses the _get_model_container_cdp() method.

This is aliased as the get_model_container() specific analysis API method.
........
r27559 | bugman | 2015-02-05 18:31:57 +0100 (Thu, 05 Feb 2015) | 3 lines

Fix for the N_state_model.test_statistics system test - the probabilities were missing from k.
........
r27560 | bugman | 2015-02-05 18:38:43 +0100 (Thu, 05 Feb 2015) | 3 lines

Expanded the printouts from the statistics.model user function to include the statistics.
........
r27561 | bugman | 2015-02-05 18:47:41 +0100 (Thu, 05 Feb 2015) | 9 lines

Big bug fix for the N-state model num_data_points() function.

This is from the specific_analyses.n_state_model.data module. This code was very much out of date.
It was expecting an ancient behaviour where the spin container 'pcs' variable and interatomic data
container 'rdc' where lists of floats. However these were converted many years ago to dictionaries
with keys set to the alignment IDs. The result was that no RDCs nor PCSs were counted as a base
data point, so the function would in most cases return a value of zero.
........
r27562 | bugman | 2015-02-05 18:51:10 +0100 (Thu, 05 Feb 2015) | 3 lines

Updated the N-state model num_data_points() function to use more modern integer incrementation.
........
r27563 | bugman | 2015-02-05 18:58:26 +0100 (Thu, 05 Feb 2015) | 6 lines

Fixes for the printout from the pipe_control.pcs.return_pcs_data() function.

The number of PCSs printed out was including values of None when data was missing for one alignment.
These values of None are no longer counted.
........
r27564 | bugman | 2015-02-05 18:58:43 +0100 (Thu, 05 Feb 2015) | 6 lines

Fixes for the printout from the pipe_control.rdc.return_rdc_data() function.

The number of RDCs printed out was including values of None when data was missing for one alignment.
These values of None are no longer counted.
........
r27565 | bugman | 2015-02-05 19:04:32 +0100 (Thu, 05 Feb 2015) | 6 lines

More fixes for the RDC and PCS count printouts from the corresponding data assembly functions.

Sometimes the RDC or PCS value could be present as None. This is now detected and the count is not
incremented.
........
r27566 | bugman | 2015-02-05 19:10:44 +0100 (Thu, 05 Feb 2015) | 5 lines

More fixes for the PCS count printout from the pipe_control.pcs.return_pcs_data() function.

The check for None values was incorrect.
........
r27567 | bugman | 2015-02-05 19:12:57 +0100 (Thu, 05 Feb 2015) | 6 lines

Fixes for the N-state model num_data_points() function.

The deselected interatomic data containers are no longer used for counting RDC data. And the
skipping of deselected spin containers for the PCS is now via the spin_loop() skip_desel argument.
........
r27568 | bugman | 2015-02-05 19:14:41 +0100 (Thu, 05 Feb 2015) | 6 lines

Fix for the N_state_model.test_statistics system test.

The deselected spins and interatomic data containers are now taken into account for the RDC and PCS
data point counts.
........
r27569 | bugman | 2015-02-05 19:26:32 +0100 (Thu, 05 Feb 2015) | 8 lines

Implementation of the statistics.aic user function.

This is very similar to the statistics.model user function - the code was copied and only slightly
modified. The new user function will calculate the current chi-squared value per model, obtain the
model statistics, calculate the AIC value per model, and store the AIC value, chi-squared value and
number of parameters in the appropriate location for the model in the relax data store.
........
r27592 | bugman | 2015-02-06 12:05:31 +0100 (Fri, 06 Feb 2015) | 3 lines

Created the empty lib.plotting.veusz module for graphing using Veusz (http://home.gna.org/veusz/).
........
r27593 | bugman | 2015-02-06 14:29:35 +0100 (Fri, 06 Feb 2015) | 6 lines

Shifted the lib.software.grace module to lib.plotting.grace.

This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/7532 and
http://thread.gmane.org/gmane.science.nmr.relax.devel/7536.
........
r27594 | bugman | 2015-02-06 14:40:04 +0100 (Fri, 06 Feb 2015) | 3 lines

Copyright update.
........
r27595 | bugman | 2015-02-06 14:42:20 +0100 (Fri, 06 Feb 2015) | 7 lines

Created XY-data functions for the plotting API of the relax library.

These are currently copies of the heads of the lib.plotting.grace functions write_xy_data() and
write_xy_header(). These lib.plotting.api functions (write_xy_data() and write_xy_header()) are set
up to use the grace functions.
........
r27596 | bugman | 2015-02-06 14:47:10 +0100 (Fri, 06 Feb 2015) | 3 lines

Converted all of the Grace plotting in relax to use the plotting API of the relax library.
........
r27597 | bugman | 2015-02-06 14:58:01 +0100 (Fri, 06 Feb 2015) | 7 lines

Shifted the pipe_control.grace.write() function.

This is now the format independent pipe_control.plotting.write_xy() function. The format argument
has been added and this defaults to 'grace'. The grace.write user function has been updated to use
the new backend.
........
r27598 | bugman | 2015-02-06 15:01:00 +0100 (Fri, 06 Feb 2015) | 3 lines

Updated the pcs.structural_noise user function to use the relax library plotting API.
........
r27599 | bugman | 2015-02-06 15:05:30 +0100 (Fri, 06 Feb 2015) | 6 lines

Fixes for the new pipe_control.plotting.write_xy() function.

This includes missing imports which should have moved from pipe_control.grace, as well as shifting
the axis_setup() function from the pipe_control.grace module into the pipe_control.plotting module.
........
r27600 | bugman | 2015-02-06 15:14:15 +0100 (Fri, 06 Feb 2015) | 6 lines

The rdc.corr_plot user function backend now uses the relax library plotting API.

The write_xy_data() and write_xy_header() functions from lib.plotting.api are now uses instead of
the equivalent pipe_control.grace functions which no longer exist.
........
r27601 | bugman | 2015-02-06 15:16:05 +0100 (Fri, 06 Feb 2015) | 3 lines

More import fixes for the new pipe_control.plotting.write_xy() function.
........
r27602 | bugman | 2015-02-06 15:17:51 +0100 (Fri, 06 Feb 2015) | 5 lines

Fix for the backend of the relax_disp.plot_disp_curves user function.

The lib.plotting.api functions write_xy_data() and write_xy_header() require the format argument.
........
r27603 | bugman | 2015-02-06 15:32:12 +0100 (Fri, 06 Feb 2015) | 3 lines

Updated the relative stereochemistry auto-analysis to use the relax library plotting API.
........

Updated the relative stereochemistry auto-analysis to use the relax library plotting API.

Fix for the backend of the relax_disp.plot_disp_curves user function.

The lib.plotting.api functions write_xy_data() and write_xy_header() require the format argument.