relax SVN archive

Removal of the BMRB branch as it is now merged into the main 1.3 line.

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/bmrb

Removed the Numeric module from the --info print out as it is completely unused now.

The BMRB system tests are now skipped if the bmrblib cannot be found.

Fix for the diffusion tensor module.

This was also destroyed in the merger of the bmrb branch.

Fix for the badly merged data.data_classes module.

Due to the age of the branch, this was quite heavily damaged. However the file in the bmrb branch
is identical to that of the 1.3 line, prior to merging of the branch back in.

Merged revisions 12532-12534,12576 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb

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r12532 | bugman | 2011-02-17 10:21:43 +0100 (Thu, 17 Feb 2011) | 3 lines

Fix for the _bmrb_model_map() method - the bad models must come first in the list!
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r12533 | bugman | 2011-02-17 10:23:31 +0100 (Thu, 17 Feb 2011) | 3 lines

The error tags from the Order_parameters saveframe are only used if they exist.
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r12534 | bugman | 2011-02-17 10:41:36 +0100 (Thu, 17 Feb 2011) | 5 lines

The Modelfree software problem of calling ts te is now handled correctly.

The te parameter is now converted to ts, and the te parameter and error in relax are set to None.
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r12576 | bugman | 2011-02-18 18:29:53 +0100 (Fri, 18 Feb 2011) | 3 lines

Fix for the PDC system tests - the generic_fns.relax_data.pack_data() args are different in the branch.
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Merged revisions 11691-11693,11699,11921,12076-12079,12419,12461-12513,12515-12516,12521-12530 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb

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r11691 | bugman | 2010-11-22 18:17:49 +0100 (Mon, 22 Nov 2010) | 3 lines

The spheroid theta and phi angles are now taken from the BMRB input file.
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r11692 | bugman | 2010-11-22 19:12:19 +0100 (Mon, 22 Nov 2010) | 5 lines

The version 3.0 BMRB system test now skips the local_tm and diffusion data.

The old NMR-STAR definition cannot support this data.
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r11693 | bugman | 2010-11-22 19:21:45 +0100 (Mon, 22 Nov 2010) | 3 lines

Comment expansion in the BMRB system tests.
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r11699 | bugman | 2010-11-27 23:57:58 +0100 (Sat, 27 Nov 2010) | 3 lines

The NMR spectrometer and relaxation experiment saveframes are now created.
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r11921 | bugman | 2010-12-20 17:17:50 +0100 (Mon, 20 Dec 2010) | 6 lines

Fix for the molecule.type() user function due to the addition of the type arg to molecule.create().

The molecule.type() user function now uses a different naming of molecules. These are translated
to BMRB names when creating BRMB deposition files.
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r12076 | bugman | 2010-12-31 15:08:13 +0100 (Fri, 31 Dec 2010) | 3 lines

The BMRB system test now checks for the bond length in the spin containers.
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r12077 | bugman | 2010-12-31 15:09:33 +0100 (Fri, 31 Dec 2010) | 3 lines

The bond length is now placed in the temporary tag Model_free.Val_bond_length in the BMRB file.
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r12078 | bugman | 2010-12-31 15:16:57 +0100 (Fri, 31 Dec 2010) | 3 lines

The bond length is now read from the BMRB files created by relax.
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r12079 | bugman | 2010-12-31 15:26:27 +0100 (Fri, 31 Dec 2010) | 3 lines

The bond length is not in the NMR-STAR v3.0 file!
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r12419 | bugman | 2011-01-21 14:46:36 +0100 (Fri, 21 Jan 2011) | 3 lines

ContainerList has been replaced by RelaxListType in the latest svnmerge.py update.
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r12461 | bugman | 2011-01-31 14:50:05 +0100 (Mon, 31 Jan 2011) | 3 lines

Spin names are not used in the spin ID strings as the AtomName tag is not compulsory.
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r12462 | bugman | 2011-01-31 14:51:21 +0100 (Mon, 31 Jan 2011) | 5 lines

Removed the molecule name generation from the entity data, as the entity data is not always there.

This fixes a crash when reading BMRB files with no entity saveframe.
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r12463 | bugman | 2011-01-31 15:07:25 +0100 (Mon, 31 Jan 2011) | 5 lines

The number of spins is now constructed from the 's2' var if 'data_ids' does not exist.

This allows v2.1 model-free saveframes to be read.
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r12464 | bugman | 2011-01-31 15:19:03 +0100 (Mon, 31 Jan 2011) | 6 lines

Reverted r12461 as this was the wrong way to do this.

The command used was:
svn merge -r12461:12460 .
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r12465 | bugman | 2011-01-31 15:38:28 +0100 (Mon, 31 Jan 2011) | 5 lines

Shifted the sequence generation code into the BMRB specific generate_sequence() function.

This is to allow for strangeness in the BMRB entries :S
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r12466 | bugman | 2011-01-31 15:46:36 +0100 (Mon, 31 Jan 2011) | 3 lines

The reading of BMRB model-free saveframes will now generate sequence data if needed.
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r12467 | bugman | 2011-01-31 15:48:09 +0100 (Mon, 31 Jan 2011) | 3 lines

Removed a debugging print out from generate_sequence().
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r12468 | bugman | 2011-01-31 16:06:26 +0100 (Mon, 31 Jan 2011) | 3 lines

Better handling of missing data in the BMRB model-free saveframes.
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r12469 | bugman | 2011-01-31 16:31:56 +0100 (Mon, 31 Jan 2011) | 3 lines

The relaxation data pack_data() function can now handle missing errors.
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r12470 | bugman | 2011-01-31 16:33:17 +0100 (Mon, 31 Jan 2011) | 3 lines

Some missing imports.
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r12471 | bugman | 2011-01-31 16:36:54 +0100 (Mon, 31 Jan 2011) | 3 lines

The model-free model is only created if there is one in the BMRB file now.
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r12472 | bugman | 2011-01-31 16:48:53 +0100 (Mon, 31 Jan 2011) | 5 lines

Added a catch for broken sequence information in the BMRB file.

This will result in no spin being found.
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r12473 | bugman | 2011-01-31 17:02:11 +0100 (Mon, 31 Jan 2011) | 3 lines

Fixes for the BMRB system tests - the install path is now in the status object and not __main__.
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r12474 | bugman | 2011-01-31 18:06:50 +0100 (Mon, 31 Jan 2011) | 5 lines

Fixes for the experimental info data structures.

The element_name and element_desc are now simply name and desc in the Element container.
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r12475 | bugman | 2011-01-31 18:44:11 +0100 (Mon, 31 Jan 2011) | 3 lines

Fix for the model-free _model_setup() which was not merged from the main 1.3 line.
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r12476 | bugman | 2011-01-31 19:39:54 +0100 (Mon, 31 Jan 2011) | 3 lines

The BMRB generate_sequence() function can now handle if no molecule name is given.
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r12477 | bugman | 2011-01-31 19:52:37 +0100 (Mon, 31 Jan 2011) | 3 lines

The BMRB generate_sequence() function can now handle args of None.
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r12478 | bugman | 2011-01-31 19:57:00 +0100 (Mon, 31 Jan 2011) | 3 lines

Model-free saveframes without any data are now skipped.
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r12479 | bugman | 2011-02-01 10:50:44 +0100 (Tue, 01 Feb 2011) | 3 lines

Fixed a RelaxError in _model_map() so that a model-free model of None will raise the correct error.
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r12480 | bugman | 2011-02-01 10:53:32 +0100 (Tue, 01 Feb 2011) | 3 lines

Fixed the print out of a RelaxError and Warning for the model-free model from the BMRB file.
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r12481 | bugman | 2011-02-01 11:01:22 +0100 (Tue, 01 Feb 2011) | 3 lines

Added a catch to _bmrb_model_map() for Modelfree4 model names in the BMRB files.
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r12482 | bugman | 2011-02-01 14:20:22 +0100 (Tue, 01 Feb 2011) | 3 lines

Expanded the conversion of Modelfree4 model numbers to include all of the relax model numbers as well.
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r12483 | bugman | 2011-02-01 14:43:41 +0100 (Tue, 01 Feb 2011) | 3 lines

The Python round() function is now used to create the MHz frequency label for the relaxation data.
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r12484 | bugman | 2011-02-01 15:51:49 +0100 (Tue, 01 Feb 2011) | 5 lines

The molecule number from EntityID is now being used to fill in the model-free data.

This is necessary for multiple molecule entries in BMRB files.
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r12485 | bugman | 2011-02-01 16:26:23 +0100 (Tue, 01 Feb 2011) | 3 lines

The isotope number is now being guessed from the atom name if not given in the BMRB file.
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r12486 | bugman | 2011-02-01 16:41:04 +0100 (Tue, 01 Feb 2011) | 3 lines

Better handling of the EntityID tag in the model-free saveframe.
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r12487 | bugman | 2011-02-01 16:42:33 +0100 (Tue, 01 Feb 2011) | 3 lines

The relaxation frequency label is now rounded to the nearest factor of 10.
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r12488 | bugman | 2011-02-01 17:00:01 +0100 (Tue, 01 Feb 2011) | 3 lines

The correlation times are now being scaled based on the TauEValUnits tag value.
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r12489 | bugman | 2011-02-01 17:33:03 +0100 (Tue, 01 Feb 2011) | 3 lines

The relax model-free model name in the BMRB file can now be handled.
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r12490 | bugman | 2011-02-01 17:37:35 +0100 (Tue, 01 Feb 2011) | 3 lines

The correlation time errors are now scaled as well.
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r12491 | bugman | 2011-02-01 20:03:23 +0100 (Tue, 01 Feb 2011) | 3 lines

Shifted some of the code out of specific_fns/model_free/bmrb.py for use in generic_fns/relax_data.py.
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r12492 | bugman | 2011-02-01 20:04:57 +0100 (Tue, 01 Feb 2011) | 3 lines

Fixes for the new generic_fns.bmrb functions molecule_names() and num_spins().
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r12493 | bugman | 2011-02-01 20:07:46 +0100 (Tue, 01 Feb 2011) | 3 lines

specific_fns.model_free.bmrb now uses the generic_fns.bmrb functions derived from itself.
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r12494 | bugman | 2011-02-01 20:10:30 +0100 (Tue, 01 Feb 2011) | 3 lines

Shifted the spin ID generation code into generic_fns.bmrb.generate_sequence().
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r12495 | bugman | 2011-02-01 20:11:36 +0100 (Tue, 01 Feb 2011) | 3 lines

Fix for molecule_names(), the list is now being returned.
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r12496 | bugman | 2011-02-01 20:24:54 +0100 (Tue, 01 Feb 2011) | 3 lines

The Rex value read from the BMRB file is now scaled to the correct value.
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r12497 | bugman | 2011-02-01 20:29:43 +0100 (Tue, 01 Feb 2011) | 3 lines

A fix for BMRB files with no relaxation data - Rex cannot be scaled to the correct value!!!
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r12498 | bugman | 2011-02-01 20:44:06 +0100 (Tue, 01 Feb 2011) | 3 lines

Missing spaces in the BMRB model-free model name are now accepted.
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r12499 | bugman | 2011-02-01 20:59:41 +0100 (Tue, 01 Feb 2011) | 3 lines

Atom names can now be missing from the model-free saveframes.
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r12500 | bugman | 2011-02-01 21:10:47 +0100 (Tue, 01 Feb 2011) | 3 lines

Added 'S2, te, S2f' as a BMRB 'm5' model-free model.
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r12501 | bugman | 2011-02-01 21:34:55 +0100 (Tue, 01 Feb 2011) | 3 lines

Brackets are now removed from the molecule name - this kills the spin IDs.
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r12502 | bugman | 2011-02-01 21:37:39 +0100 (Tue, 01 Feb 2011) | 3 lines

Atom types of '.' in the model-free saveframes can now be handled.
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r12503 | bugman | 2011-02-02 13:26:24 +0100 (Wed, 02 Feb 2011) | 3 lines

The default version of 3.1 in all the BMRB user functions has been turned off.
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r12504 | bugman | 2011-02-02 13:27:46 +0100 (Wed, 02 Feb 2011) | 3 lines

The BMRB user function version args can now be None to allow Bmrblib decide on the default version.
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r12505 | bugman | 2011-02-02 13:43:13 +0100 (Wed, 02 Feb 2011) | 3 lines

The model-free bmrb module is now using the new bmrblib create_nmr_star() interface.
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r12506 | bugman | 2011-02-02 16:47:02 +0100 (Wed, 02 Feb 2011) | 3 lines

Created the BMRB list_sample_conditions() function to return a list of sample condition names.
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r12507 | bugman | 2011-02-02 16:53:10 +0100 (Wed, 02 Feb 2011) | 3 lines

The model-free bmrb_read() now accepts a sample conditions arg and checks that only one is loaded.
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r12508 | bugman | 2011-02-02 17:01:31 +0100 (Wed, 02 Feb 2011) | 3 lines

The bmrb.read() user function now accepts the sample_conditions arg.
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r12509 | bugman | 2011-02-02 18:25:45 +0100 (Wed, 02 Feb 2011) | 3 lines

The back-end of the bmrb.read() user function is now recognising the sample_conditions arg.
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r12510 | bugman | 2011-02-02 19:19:53 +0100 (Wed, 02 Feb 2011) | 5 lines

The sample_conditions arg to bmrb.read() is now set to None.

This is to allow single condition files to be always read.
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r12511 | bugman | 2011-02-03 13:03:58 +0100 (Thu, 03 Feb 2011) | 3 lines

Fix for generic_fns.mol_res_spin.bmrb_read() for when no molecule name is present.
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r12512 | bugman | 2011-02-03 13:30:10 +0100 (Thu, 03 Feb 2011) | 3 lines

Square brackets and commas are now also removed from the BMRB molecule name.
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r12513 | bugman | 2011-02-03 20:34:33 +0100 (Thu, 03 Feb 2011) | 3 lines

Fix for the Rex scaling - the factor was incorrect!
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r12515 | bugman | 2011-02-07 15:05:54 +0100 (Mon, 07 Feb 2011) | 3 lines

The sample conditions label is now being used to select the correct BMRB saveframes to read.
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r12516 | bugman | 2011-02-07 15:17:28 +0100 (Mon, 07 Feb 2011) | 3 lines

Fix for the sample label matching - this is only performed if the sample label is given.
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r12521 | bugman | 2011-02-14 19:43:21 +0100 (Mon, 14 Feb 2011) | 3 lines

Removed a debugging print out.
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r12522 | bugman | 2011-02-15 08:55:04 +0100 (Tue, 15 Feb 2011) | 3 lines

The relaxation values and errors from the BMRB file are being converted from ms to s now.
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r12523 | bugman | 2011-02-15 09:00:39 +0100 (Tue, 15 Feb 2011) | 3 lines

Fixes for pack_data() to allow the errors to be a numpy array.
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r12524 | bugman | 2011-02-15 09:13:40 +0100 (Tue, 15 Feb 2011) | 3 lines

The values are now properly scaled and values and errors are inverted to go from Tx to Rx values.
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r12525 | bugman | 2011-02-15 11:48:51 +0100 (Tue, 15 Feb 2011) | 3 lines

Better handling of missing data in the BMRB relaxation saveframes.
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r12526 | bugman | 2011-02-15 11:57:37 +0100 (Tue, 15 Feb 2011) | 3 lines

Fix for the num_spins() BMRB function - the keys are not always present.
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r12527 | bugman | 2011-02-15 14:48:21 +0100 (Tue, 15 Feb 2011) | 3 lines

All te model-free parameters in BMRB files which should be ts are now being converted.
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r12528 | bugman | 2011-02-15 18:11:21 +0100 (Tue, 15 Feb 2011) | 3 lines

Simplification of the BMRB num_spins() function.
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r12529 | bugman | 2011-02-16 15:38:49 +0100 (Wed, 16 Feb 2011) | 3 lines

Missing model-free parameter error tags in BMRB files can now be handled.
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r12530 | bugman | 2011-02-16 15:40:29 +0100 (Wed, 16 Feb 2011) | 3 lines

Updated the BMRB specific_fns bmrb_read() method to include the sample conditions.
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Merged revisions 11633,11638-11660 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb

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r11633 | bugman | 2010-10-06 18:55:05 +0200 (Wed, 06 Oct 2010) | 5 lines

Bug fix for the BMRB system tests.

The file paths were incorrect.
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r11638 | bugman | 2010-10-15 17:53:49 +0200 (Fri, 15 Oct 2010) | 5 lines

Fixes for the BMRB system tests.

These tests were non-functional!
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r11639 | bugman | 2010-10-15 18:05:22 +0200 (Fri, 15 Oct 2010) | 3 lines

Fixes for the file paths to sync with the 1.3 line.
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r11640 | bugman | 2010-10-15 18:05:59 +0200 (Fri, 15 Oct 2010) | 3 lines

Fix for all the BMRB related user functions - exec_info is now a private variable.
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r11641 | bugman | 2010-10-19 15:33:49 +0200 (Tue, 19 Oct 2010) | 3 lines

Added checks and the RelaxNoModuleInstallError relax error to make sure that bmrblib is installed.
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r11642 | bugman | 2010-10-19 20:05:32 +0200 (Tue, 19 Oct 2010) | 6 lines

The diffusion tensor saveframe is now being created in the BMRB submission file.

This saveframe is not complete and contains no tensor information, as bmrblib does not support this
yet.
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r11643 | bugman | 2010-10-20 20:04:43 +0200 (Wed, 20 Oct 2010) | 5 lines

Removed the v3.2 BMRB imports as these no longer exist.

There is no 3.2 version!
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r11644 | bugman | 2010-10-21 00:17:29 +0200 (Thu, 21 Oct 2010) | 3 lines

Removed the BMRB NMR-STAR v3.2 system test and started to add data checks for the old and new pipes.
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r11645 | bugman | 2010-10-21 20:08:53 +0200 (Thu, 21 Oct 2010) | 6 lines

Advancements for the diffusion tensor support in the BMRB file.

All of the tensor data is now being written out, and a very incomplete bmrb_read() function has been
added.
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r11646 | bugman | 2010-10-21 22:35:20 +0200 (Thu, 21 Oct 2010) | 3 lines

The diffusion tensor bmrb_read() function is now complete and the tensor is being created.
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r11647 | bugman | 2010-10-21 23:42:05 +0200 (Thu, 21 Oct 2010) | 3 lines

The prolate diffusion tensors are now correctly created from the BMRB files.
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r11648 | bugman | 2010-10-22 00:42:54 +0200 (Fri, 22 Oct 2010) | 3 lines

The reading of entity information from the BMRB file is fixed.
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r11649 | bugman | 2010-10-22 01:30:29 +0200 (Fri, 22 Oct 2010) | 5 lines

Fixes for the citations BMRB writing.

The author structure is now split up before sending to the saveframe class.
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r11650 | bugman | 2010-10-22 11:33:46 +0200 (Fri, 22 Oct 2010) | 3 lines

The spectrometer frequency is now converted to MHz before being sent to BMRBlib.
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r11651 | bugman | 2010-10-22 15:18:18 +0200 (Fri, 22 Oct 2010) | 3 lines

The saveframe description for the relax scripts now says that they are relax scripts.
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r11652 | bugman | 2010-10-22 17:59:25 +0200 (Fri, 22 Oct 2010) | 3 lines

The relaxation data reading is functional again, matching the new design of bmrblib.
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r11653 | bugman | 2010-10-22 19:21:54 +0200 (Fri, 22 Oct 2010) | 3 lines

The restoration of the data from BMRB files into data pipes is now fully tested in the system tests.
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r11654 | bugman | 2010-10-22 19:53:19 +0200 (Fri, 22 Oct 2010) | 3 lines

Caught when no diffusion tensor data is yielded by the bmrblib loop() method.
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r11655 | bugman | 2010-10-22 22:11:38 +0200 (Fri, 22 Oct 2010) | 3 lines

A few system and unit test fixes broken by recent rearrangements of the diffusion tensor code.
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r11656 | bugman | 2010-10-22 23:10:00 +0200 (Fri, 22 Oct 2010) | 6 lines

Fix for the test_read() unit test of generic_fns.relax_data.read().

The relaxation data structures are now handled differently in this branch and all data structures
have the same from for all spins, even if data is missing.
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r11657 | bugman | 2010-10-25 09:56:03 +0200 (Mon, 25 Oct 2010) | 3 lines

Restored the reversal of the rotation matrix when determining Euler angles for a tensor in the PDB frame.
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r11658 | bugman | 2010-10-25 10:04:58 +0200 (Mon, 25 Oct 2010) | 5 lines

Shifted the core of the model-free _select_model() method into _model_map().

This allows other parts of the code to translate model names to model-free equations and parameters.
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r11659 | bugman | 2010-10-25 10:07:51 +0200 (Mon, 25 Oct 2010) | 5 lines

Removed the model-free and CSA info from the blacklisted spin variables.

This is to test the implementation of model-free and CSA BMRB saveframe reading.
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r11660 | bugman | 2010-10-25 10:08:53 +0200 (Mon, 25 Oct 2010) | 3 lines

Implemented the reading of model-free and CSA BMRB saveframes from NMR-STAR files.
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Merged revisions 9795-9798,9801-9811,9813-9828,9833,9835-9862,9865-9869,9990,10116,10874,10876-10877,10880,10885,11264 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb

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r9795 | bugman | 2009-10-27 14:07:24 +0100 (Tue, 27 Oct 2009) | 3 lines

Removed the artificial constraint for there being only 1 entity allowed.
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r9796 | bugman | 2009-10-27 14:41:42 +0100 (Tue, 27 Oct 2009) | 3 lines

Relaxation values and errors of ? are now handled and converted to None.
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r9797 | bugman | 2009-10-27 14:42:19 +0100 (Tue, 27 Oct 2009) | 3 lines

Missing relaxation data is now handled when creating the BMRB file.
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r9798 | bugman | 2009-10-27 15:12:27 +0100 (Tue, 27 Oct 2009) | 3 lines

The entity ID tag is now present in the general relaxation saveframe.
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r9801 | bugman | 2009-10-27 15:29:50 +0100 (Tue, 27 Oct 2009) | 3 lines

The translate function now handles numpy arrays.
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r9802 | bugman | 2009-10-27 15:46:54 +0100 (Tue, 27 Oct 2009) | 3 lines

Entity ID numbers are now supported throughout the relaxation data and model-free saveframes.
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r9803 | bugman | 2009-10-27 15:52:18 +0100 (Tue, 27 Oct 2009) | 3 lines

Molecule names are converted to entity IDs and vice versa for BMRB writing and reading.
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r9804 | bugman | 2009-10-27 15:56:39 +0100 (Tue, 27 Oct 2009) | 3 lines

An entity IDs fix for the general relaxation saveframe reading.
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r9805 | bugman | 2009-10-27 15:57:41 +0100 (Tue, 27 Oct 2009) | 3 lines

Removed a test for duplicated data - data can be duplicated!!!
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r9806 | bugman | 2009-10-27 15:58:11 +0100 (Tue, 27 Oct 2009) | 3 lines

Entity IDs are going into the model-free saveframe and missing parameter errors are now handled.
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r9807 | bugman | 2009-10-27 16:14:33 +0100 (Tue, 27 Oct 2009) | 3 lines

All the relaxation data saveframes now contain all the equivalent data as in general relaxation.
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r9808 | bugman | 2009-10-27 16:20:35 +0100 (Tue, 27 Oct 2009) | 3 lines

Added a catch for Rex error values of None.
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r9809 | bugman | 2009-10-27 16:34:45 +0100 (Tue, 27 Oct 2009) | 3 lines

Expansion of the chemical shift anisotropy saveframe.
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r9810 | bugman | 2009-10-27 16:42:02 +0100 (Tue, 27 Oct 2009) | 3 lines

Updated the v3.1 and earlier T1 and T2 saveframes for all the new info.
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r9811 | bugman | 2009-10-27 16:49:45 +0100 (Tue, 27 Oct 2009) | 3 lines

The entity IDs are being passed into the CSA saveframe.
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r9813 | bugman | 2009-10-27 20:58:05 +0100 (Tue, 27 Oct 2009) | 3 lines

Modified the citation label so that the multiple entries wouldn't have the same name.
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r9814 | bugman | 2009-10-27 21:12:56 +0100 (Tue, 27 Oct 2009) | 3 lines

The relax citation ID is now going in as the BMRB citation label.
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r9815 | bugman | 2009-10-27 21:20:21 +0100 (Tue, 27 Oct 2009) | 5 lines

The SfFramecode tag is now being created for the citation saveframes.

This fixes deposition issues due to all citations having the same entry_citation name.
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r9816 | bugman | 2009-10-27 21:23:57 +0100 (Tue, 27 Oct 2009) | 3 lines

Added a dummy title for the Sparky citation as this must be supplied.
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r9817 | bugman | 2009-10-27 22:59:45 +0100 (Tue, 27 Oct 2009) | 3 lines

The SfFramecode tag is now going into the heteronuclear NOE saveframe.
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r9818 | bugman | 2009-10-27 23:02:37 +0100 (Tue, 27 Oct 2009) | 3 lines

The base class add() methods are now receiving all args.
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r9819 | bugman | 2009-10-27 23:12:53 +0100 (Tue, 27 Oct 2009) | 3 lines

All the relaxation data info can now be set through the add() method.
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r9820 | bugman | 2009-10-27 23:14:19 +0100 (Tue, 27 Oct 2009) | 3 lines

The element name is now being placed into the relaxation data saveframes.
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r9821 | bugman | 2009-10-27 23:20:02 +0100 (Tue, 27 Oct 2009) | 3 lines

Added the SfFramecode tag to the general relaxation saveframe.
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r9822 | bugman | 2009-10-27 23:20:29 +0100 (Tue, 27 Oct 2009) | 3 lines

Variable renaming.
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r9823 | bugman | 2009-10-27 23:22:45 +0100 (Tue, 27 Oct 2009) | 3 lines

Fix for the previous variable change.
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r9824 | bugman | 2009-10-27 23:36:49 +0100 (Tue, 27 Oct 2009) | 5 lines

The DataFileName tag is being created for the CSA saveframe.

This doesn't seem to be read by the ADIT-NMR system.
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r9825 | bugman | 2009-10-27 23:50:51 +0100 (Tue, 27 Oct 2009) | 3 lines

Fix for the _Vendor.Electronic_address tag (previously incorrectly named).
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r9826 | bugman | 2009-10-28 11:05:19 +0100 (Wed, 28 Oct 2009) | 3 lines

Fix for the _General_Relaxation_list.Sf_category tag.
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r9827 | bugman | 2009-10-28 11:34:59 +0100 (Wed, 28 Oct 2009) | 5 lines

The tags for the 2 heteronuclNOE atoms are now supported.

The normal relaxation tags for the atom info are duplicated and called *_1 and *_2 for the 2 atoms.
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r9828 | bugman | 2009-10-28 11:38:20 +0100 (Wed, 28 Oct 2009) | 3 lines

Fix for the Seq_ID_2 tag in the heteronuclear NOE saveframe.
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r9833 | bugman | 2009-10-28 12:01:52 +0100 (Wed, 28 Oct 2009) | 5 lines

The attached atom info is been sent into the BMRB NMR-STAR file.

This is used in the heteronuclear NOE saveframe.
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r9835 | bugman | 2009-10-28 18:11:01 +0100 (Wed, 28 Oct 2009) | 5 lines

Expanded the entity saveframe.

The PolymerType, PolymerSeqOneLetterCode, and ThiolState are now supported.
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r9836 | bugman | 2009-10-28 18:20:02 +0100 (Wed, 28 Oct 2009) | 3 lines

Shifted a line of code to the correct place.
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r9837 | bugman | 2009-10-28 18:59:00 +0100 (Wed, 28 Oct 2009) | 5 lines

The polymer type and one letter code sequence are being placed into the BMRB file.

The new molecule.type() user function has been created for this.
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r9838 | bugman | 2009-10-29 11:23:53 +0100 (Thu, 29 Oct 2009) | 3 lines

Added support for the method saveframe.
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r9839 | bugman | 2009-10-29 11:32:52 +0100 (Thu, 29 Oct 2009) | 3 lines

Added a number of new user function calls to the BMRB system test.
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r9840 | bugman | 2009-10-29 11:59:17 +0100 (Thu, 29 Oct 2009) | 3 lines

Created the bmrb.thiol_state() user function.
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r9841 | bugman | 2009-10-29 13:14:53 +0100 (Thu, 29 Oct 2009) | 3 lines

Removed the thiol state check as this can be anything.
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r9842 | bugman | 2009-10-29 13:15:31 +0100 (Thu, 29 Oct 2009) | 3 lines

The thiol state is now being put into the BMRB file.
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r9843 | bugman | 2009-10-29 14:31:33 +0100 (Thu, 29 Oct 2009) | 3 lines

Created the bmrb.script() user function for specifying the scripts used in the analysis.
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r9844 | bugman | 2009-10-29 14:42:57 +0100 (Thu, 29 Oct 2009) | 3 lines

The method saveframes are now accessible from the API.
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r9845 | bugman | 2009-10-29 14:43:56 +0100 (Thu, 29 Oct 2009) | 3 lines

Missing import fix.
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r9846 | bugman | 2009-10-29 14:52:14 +0100 (Thu, 29 Oct 2009) | 3 lines

Fixes for the method saveframe. This should now work correctly.
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r9847 | bugman | 2009-10-29 14:53:14 +0100 (Thu, 29 Oct 2009) | 3 lines

The citation ID strings are now going into the script containers.
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r9848 | bugman | 2009-10-29 14:53:47 +0100 (Thu, 29 Oct 2009) | 3 lines

The scripts are now being placed by relax into the BMRB file.
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r9849 | bugman | 2009-10-29 14:55:05 +0100 (Thu, 29 Oct 2009) | 3 lines

The script name was being overwritten.
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r9850 | bugman | 2009-10-29 15:45:47 +0100 (Thu, 29 Oct 2009) | 5 lines

Changed how the built in citations are handled.

They are now all stored in the CITE dictionary.
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r9851 | bugman | 2009-10-29 15:58:39 +0100 (Thu, 29 Oct 2009) | 3 lines

The setting up of software and its citations is now functional again.
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r9852 | bugman | 2009-10-29 16:02:15 +0100 (Thu, 29 Oct 2009) | 3 lines

The _Method_file and _Method_param tag categories are now free tables.
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r9853 | bugman | 2009-10-29 16:23:02 +0100 (Thu, 29 Oct 2009) | 3 lines

Changed the method saveframe category name.
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r9854 | bugman | 2009-10-29 16:24:04 +0100 (Thu, 29 Oct 2009) | 14 lines

Reverted r9852.

The command used was:
svn merge -r9852:9851 .

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r9852 | bugman | 2009-10-29 16:02:15 +0100 (Thu, 29 Oct 2009) | 3 lines
Changed paths:
M /branches/bmrb/bmrblib/experimental_details/method.py

The _Method_file and _Method_param tag categories are now free tables.
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r9855 | bugman | 2009-10-29 17:26:35 +0100 (Thu, 29 Oct 2009) | 3 lines

Separated the software info from CITE into the SOFTWARE dictionary.
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r9856 | bugman | 2009-10-29 17:31:53 +0100 (Thu, 29 Oct 2009) | 3 lines

The directory info is being stored in the script container.
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r9857 | bugman | 2009-10-29 17:54:26 +0100 (Thu, 29 Oct 2009) | 5 lines

Added the model-free model selection and elimination and set theory papers as citations.

These are also placed into the BMRB file.
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r9858 | bugman | 2009-10-29 17:56:17 +0100 (Thu, 29 Oct 2009) | 3 lines

The method saveframes containing scripts now refer to the citations associated with that script.
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r9859 | bugman | 2009-10-29 18:25:45 +0100 (Thu, 29 Oct 2009) | 3 lines

Sometimes the spin container attached atom variable name is 'attached_proton' and not 'attached_atom'.
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r9860 | bugman | 2009-10-29 18:25:57 +0100 (Thu, 29 Oct 2009) | 3 lines

Fixes for the BMRB system test.
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r9861 | bugman | 2009-10-29 19:12:15 +0100 (Thu, 29 Oct 2009) | 3 lines

Suppressed a retarded warning message in pystarlib.
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r9862 | bugman | 2009-11-02 18:19:53 +0100 (Mon, 02 Nov 2009) | 6 lines

Removed the bmrblib package as this is now its own software project.

The BMRB library package (https://gna.org/projects/bmrblib/) is now a dependency if BMRB file
creation or reading is required.
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r9865 | bugman | 2009-11-04 15:12:10 +0100 (Wed, 04 Nov 2009) | 3 lines

Added the specification of the peak intensity type to the BMRB system test.
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r9866 | bugman | 2009-11-04 15:18:15 +0100 (Wed, 04 Nov 2009) | 5 lines

The peak intensity type is now being passed into the BMRB file.

This doesn't work yet as the user function doesn't exist!
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r9867 | bugman | 2009-11-05 11:52:27 +0100 (Thu, 05 Nov 2009) | 3 lines

Added the interface for the relax_data.peak_intensity_type() user function.
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r9868 | bugman | 2009-11-05 13:23:26 +0100 (Thu, 05 Nov 2009) | 5 lines

The relax_data.peak_intensity_type() user function is now fully operational.

The BMRB system test has been repaired for the user function argument name change.
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r9869 | bugman | 2009-11-05 13:48:57 +0100 (Thu, 05 Nov 2009) | 3 lines

Implemented the get_peak_intensity_type() method for returning that data.
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r9990 | bugman | 2009-11-27 10:50:50 +0100 (Fri, 27 Nov 2009) | 3 lines

Added bmrb_read() and bmrb_write() to the analysis specific base API.
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r10116 | bugman | 2010-01-06 18:15:24 +0100 (Wed, 06 Jan 2010) | 3 lines

Fixes for the rename of prompt.check to the arg_check module.
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r10874 | bugman | 2010-02-23 21:56:34 +0100 (Tue, 23 Feb 2010) | 3 lines

relax now can start without the presence of the bmrblib package (http://gna.org/projects/bmrblib/).
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r10876 | bugman | 2010-02-23 22:02:55 +0100 (Tue, 23 Feb 2010) | 6 lines

Fix for the PipeContainer.from_xml() method.

The experimental information container was been searched for in the wrong node (actually an
undeclared variable).
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r10877 | bugman | 2010-02-23 22:31:03 +0100 (Tue, 23 Feb 2010) | 5 lines

User function fixes to match the changes to the user function framework

The exec_info box is now being used.
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r10880 | bugman | 2010-02-24 00:15:26 +0100 (Wed, 24 Feb 2010) | 5 lines

Shifted to using the Info_box rather than the local CITE variable.

This is for the d'Auvergne and Gooley, 2003, 2006, and 2007 refs. The rest will be converted later.
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r10885 | bugman | 2010-02-24 01:27:24 +0100 (Wed, 24 Feb 2010) | 5 lines

All references are now taken from the Info_box.bib dictionary

The CITE structure has therefore been deleted.
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r11264 | bugman | 2010-06-29 23:16:35 +0200 (Tue, 29 Jun 2010) | 3 lines

Started to create the diffusion tensor saveframe.
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