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Commit Date  
[r22037] by bugman

Merged revisions 22033 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22033 | bugman | 2014-01-21 10:24:22 +0100 (Tue, 21 Jan 2014) | 3 lines

Small bug fix for the new Structure.test_bug_21522_master_record_atom_count system test.
........

 2014-01-21 09:33:41 Tree
[r22036] by bugman

Merged revisions 22032 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r22032 | bugman | 2014-01-21 10:23:35 +0100 (Tue, 21 Jan 2014) | 6 lines

The structure.write_pdb user function can now handle a file instance for the file argument.

This is for the Structure.test_bug_21522_master_record_atom_count system test, to allow a dummy file
object to be used. This can also be useful for power users.
........

 2014-01-21 09:32:48 Tree
[r22035] by bugman

Merged revisions 22031 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22031 | bugman | 2014-01-21 10:15:22 +0100 (Tue, 21 Jan 2014) | 11 lines

Created the Structure.test_bug_21522_master_record_atom_count system test.

This is designed to catch bug #21522 (https://gna.org/bugs/?21522), the structure.write_pdb user
function creating an incorrect MASTER record. This hence also catches bug #21520
(https://gna.org/bugs/?21520), the failure of the structure.write_pdb user function when creating
the MASTER record due to too many ATOM and HETATM records being present.

The test simply creates to structural models, adds one atom, and writes out a PDB file, checking its
contents.
........

 2014-01-21 09:31:30 Tree
[r22034] by bugman

Fix for bug #21522 (https://gna.org/bugs/?21522) and bug #21520 (https://gna.org/bugs/?21520).

These bugs are the structure.write_pdb user function creating an incorrect MASTER record and the
failure of the structure.write_pdb user function when creating the MASTER record due to too many
ATOM and HETATM records being present.

The counts for the ATOM, HETATM, and TER records are now only for a single model, rather than being
the sum for all models together.

 2014-01-21 09:30:24 Tree
[r22033] by bugman

Small bug fix for the new Structure.test_bug_21522_master_record_atom_count system test.

 2014-01-21 09:24:22 Tree
[r22032] by bugman

The structure.write_pdb user function can now handle a file instance for the file argument.

This is for the Structure.test_bug_21522_master_record_atom_count system test, to allow a dummy file
object to be used. This can also be useful for power users.

 2014-01-21 09:23:35 Tree
[r22031] by bugman

Created the Structure.test_bug_21522_master_record_atom_count system test.

This is designed to catch bug #21522 (https://gna.org/bugs/?21522), the structure.write_pdb user
function creating an incorrect MASTER record. This hence also catches bug #21520
(https://gna.org/bugs/?21520), the failure of the structure.write_pdb user function when creating
the MASTER record due to too many ATOM and HETATM records being present.

The test simply creates to structural models, adds one atom, and writes out a PDB file, checking its
contents.

 2014-01-21 09:15:22 Tree
[r22030] by bugman

Merged revisions 22029 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r22029 | bugman | 2014-01-17 16:59:00 +0100 (Fri, 17 Jan 2014) | 3 lines

Removal of a debugging printout accidentally committed at r22025.
........

 2014-01-17 16:06:15 Tree
[r22029] by bugman

Removal of a debugging printout accidentally committed at r22025.

 2014-01-17 15:59:00 Tree
[r22028] by bugman

Merged revisions 21980,21983-22012,22016,22024-22027 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r21980 | bugman | 2014-01-15 10:40:53 +0100 (Wed, 15 Jan 2014) | 3 lines

Fix for the parameters listed for the IT99 dispersion model in the manual.
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r21983 | bugman | 2014-01-15 15:55:32 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.cr72 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.cr72-module.html.
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r21984 | bugman | 2014-01-15 15:57:31 +0100 (Wed, 15 Jan 2014) | 3 lines

Spacing fix for the lib.dispersion.cr72 module docstring.
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r21985 | bugman | 2014-01-15 16:00:51 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.dpl94 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.dpl94-module.html.
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r21986 | bugman | 2014-01-15 16:05:26 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.it99 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.it99-module.html.
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r21987 | bugman | 2014-01-15 16:10:19 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.lm63_3site API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63_3site-module.html.
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r21988 | bugman | 2014-01-15 16:15:23 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.lm63 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63-module.html.
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r21989 | bugman | 2014-01-15 16:20:07 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.m61b API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.m61b-module.html.
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r21990 | bugman | 2014-01-15 16:26:03 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.m61 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.m61-module.html.
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r21991 | bugman | 2014-01-15 16:31:41 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.mmq_cr72 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.mmq_cr72-module.html.
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r21992 | bugman | 2014-01-15 16:42:33 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.mp05 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.mp05-module.html.
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r21993 | bugman | 2014-01-15 16:50:56 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_3d API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_3d-module.html.
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r21994 | bugman | 2014-01-15 16:55:01 +0100 (Wed, 15 Jan 2014) | 3 lines

Epydoc URL simplifications.
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r21995 | bugman | 2014-01-15 16:59:09 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_expanded API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_expanded-module.html.
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r21996 | bugman | 2014-01-15 17:14:49 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.ns_cpmg_2site_star API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_star-module.html.
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r21997 | bugman | 2014-01-15 17:16:45 +0100 (Wed, 15 Jan 2014) | 3 lines

Added the 'NS CPMG 2-site 3D full' model to the lib.dispersion.ns_cpmg_2site_3d module docstring.
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r21998 | bugman | 2014-01-15 17:33:31 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.ns_mmq_2site API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_2site-module.html.
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r21999 | bugman | 2014-01-15 17:46:40 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.ns_mmq_3site API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_3site-module.html.
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r22000 | bugman | 2014-01-15 17:53:00 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.ns_r1rho_2site API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_2site-module.html.
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r22001 | bugman | 2014-01-15 17:58:09 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.ns_r1rho_3site API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_3site-module.html.
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r22002 | bugman | 2014-01-15 17:59:22 +0100 (Wed, 15 Jan 2014) | 3 lines

Small docstring edit for the lib.dispersion.mp05 module.
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r22003 | bugman | 2014-01-15 18:03:09 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.tap03 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.tap03-module.html.
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r22004 | bugman | 2014-01-15 18:20:18 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.tp02 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.tp02-module.html.
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r22005 | bugman | 2014-01-15 18:20:37 +0100 (Wed, 15 Jan 2014) | 3 lines

Epydoc URL simplifications in the lib.dispersion.mp05 module.
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r22006 | bugman | 2014-01-15 18:24:35 +0100 (Wed, 15 Jan 2014) | 3 lines

Epydoc docstring edit in the lib.dispersion.mmq_cr72 module.
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r22007 | bugman | 2014-01-15 18:30:44 +0100 (Wed, 15 Jan 2014) | 6 lines

Improvements and addition of many links to the lib.dispersion.tsmfk01 API documentation.

This is for the API documentation at:
http://www.nmr-relax.com/api/3.1/lib.dispersion.tsmfk01-module.html.
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r22008 | bugman | 2014-01-15 18:32:16 +0100 (Wed, 15 Jan 2014) | 3 lines

Copyright notice updates for the lib.dispersion modules changed today.
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r22009 | bugman | 2014-01-16 15:36:04 +0100 (Thu, 16 Jan 2014) | 85 lines

Added links to the relax wiki, API documentation, and relax website to all dispersion models in the manual.

This is to make it easier to find additional information about each of the models.

For reference, the relax wiki links are:
http://wiki.nmr-relax.com/R2eff
http://wiki.nmr-relax.com/No_Rex
http://wiki.nmr-relax.com/LM63
http://wiki.nmr-relax.com/LM63_3-site
http://wiki.nmr-relax.com/CR72_full
http://wiki.nmr-relax.com/CR72
http://wiki.nmr-relax.com/IT99
http://wiki.nmr-relax.com/TSMFK01
http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded
http://wiki.nmr-relax.com/NS_CPMG_2-site_3D_full
http://wiki.nmr-relax.com/NS_CPMG_2-site_3D
http://wiki.nmr-relax.com/NS_CPMG_2-site_star_full
http://wiki.nmr-relax.com/NS_CPMG_2-site_star
http://wiki.nmr-relax.com/MMQ_CR72
http://wiki.nmr-relax.com/NS_MMQ_2-site
http://wiki.nmr-relax.com/NS_MMQ_3-site_linear
http://wiki.nmr-relax.com/NS_MMQ_3-site
http://wiki.nmr-relax.com/M61
http://wiki.nmr-relax.com/M61_skew
http://wiki.nmr-relax.com/DPL94
http://wiki.nmr-relax.com/TP02
http://wiki.nmr-relax.com/TAP03
http://wiki.nmr-relax.com/MP05
http://wiki.nmr-relax.com/NS_R1rho_2-site
http://wiki.nmr-relax.com/NS_R1rho_3-site
http://wiki.nmr-relax.com/NS_R1rho_3-site_linear

The API documentation links are:
http://www.nmr-relax.com/api/3.1/specific_analyses.relax_disp.optimisation-module.html#back_calc_r2eff
http://www.nmr-relax.com/api/3.1/lib.dispersion.two_point-module.html#calc_two_point_r2eff
http://www.nmr-relax.com/api/3.1/target_functions.relax_disp.Dispersion-class.html#func_NOREX
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.lm63_3site-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.cr72-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.it99-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.tsmfk01-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_expanded-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_3d-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_star-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.mmq_cr72-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_2site-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_3site-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.m61-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.m61b-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.dpl94-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.tp02-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.tap03-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.mp05-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_2site-module.html
http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_r1rho_3site-module.html

The relax website links are:
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#R2eff
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#No_Rex
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#LM63
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#LM63_3-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#CR72_full
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#CR72
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#IT99
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#TSMFK01
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_expanded
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_3D_full
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_3D
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_star_full
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_star
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#MMQ_CR72
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_MMQ_2-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_MMQ_3-site_linear
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_MMQ_3-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#M61
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#M61_skew
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#DPL94
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#TP02
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#TAP03
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#MP05
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_R1rho_2-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_R1rho_3-site
http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_R1rho_3-site_linear
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r22010 | bugman | 2014-01-16 16:06:40 +0100 (Thu, 16 Jan 2014) | 3 lines

Updated the author list for the submitted paper for the relaxation dispersion analysis.
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r22011 | bugman | 2014-01-16 16:07:41 +0100 (Thu, 16 Jan 2014) | 5 lines

Added the primary reference for relaxation dispersion in relax to the dispersion chapter of the manual.

This is the paper which is not published yet.
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r22012 | bugman | 2014-01-16 16:09:49 +0100 (Thu, 16 Jan 2014) | 5 lines

Removed the single quantum R1rho-type data reference in the introduction of the dispersion chapter of the manual.

This is redundant as R1rho data is always single quantum.
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r22016 | bugman | 2014-01-16 16:19:10 +0100 (Thu, 16 Jan 2014) | 6 lines

Backported the relax 3.1.3 CHANGES file addition to trunk.

The command used was:
svn merge -r22014:22015 svn+ssh://bugman@.../svn/relax/tags/3.1.3 .
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r22024 | bugman | 2014-01-17 11:51:16 +0100 (Fri, 17 Jan 2014) | 12 lines

Created the Frame_order.test_generate_rotor2_distribution system test.

This is to test the Frame Order distribution generating base script, used for creating the synthetic
Frame Order test data, and to demonstrate a failure in handling back-calculated RDC data.

To implement this, the test_suite/shared_data/frame_order/cam/ path has been converted into a Python
package (with the addition of the __init__.py files). The base data generation script
test_suite/shared_data/frame_order/cam/generate_base.py has also been modified to use the absolute
path for the data files and its run() method now accepts the save_path argument to allow the files
to be saved into a temporary directory.
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r22025 | bugman | 2014-01-17 11:57:50 +0100 (Fri, 17 Jan 2014) | 6 lines

Fix for bug #21499 (https://gna.org/bugs/?21499), the failure of the rdc.write user function.

The rdc.write user function fails for back-calculated RDC data. The fix was to handle the missing
interatom.rdc_data_types variable.
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r22026 | bugman | 2014-01-17 12:00:43 +0100 (Fri, 17 Jan 2014) | 7 lines

Fixes for the Frame_order.test_generate_rotor2_distribution system test.

The test_suite/shared_data/frame_order/cam/generate_base.py script now saves the program state files
into the self.save_path directory, preventing the system test from attempting to save files into the
relax test suite directories.
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r22027 | bugman | 2014-01-17 12:02:58 +0100 (Fri, 17 Jan 2014) | 7 lines

Another fix for the Frame_order.test_generate_rotor2_distribution system test.

The test_suite/shared_data/frame_order/cam/generate_base.py script no longer prints its progress
indicator to sys.__stderr__ but to sys.stderr instead. This avoids the progress text from appearing
during the relax test suite execution.
........

 2014-01-17 11:23:16 Tree
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