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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ContainerList has been replaced by RelaxListType in the latest svnmerge.py update.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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bugman 2011-02-19

changed /1.3
changed /1.3/data/exp_info.py
changed /1.3/generic_fns/bmrb.py
changed /1.3/generic_fns/diffusion_tensor.py
changed /1.3/generic_fns/mol_res_spin.py
changed /1.3/generic_fns/relax_data.py
changed /1.3/prompt/bmrb.py
changed /1.3/prompt/molecule.py
changed /1.3/specific_fns/api_base.py
changed /1.3/specific_fns/model_free/bmrb.py
changed /1.3/specific_fns/model_free/main.py
changed /1.3/test_suite/system_tests/bmrb.py
changed /1.3/test_suite/system_tests/scripts/bmrb_rw.py
/1.3
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/1.3/generic_fns/bmrb.py Diff Switch to side-by-side view
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/1.3/generic_fns/diffusion_tensor.py Diff Switch to side-by-side view
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/1.3/generic_fns/mol_res_spin.py Diff Switch to side-by-side view
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/1.3/generic_fns/relax_data.py Diff Switch to side-by-side view
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/1.3/prompt/bmrb.py Diff Switch to side-by-side view
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/1.3/prompt/molecule.py Diff Switch to side-by-side view
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/1.3/specific_fns/api_base.py Diff Switch to side-by-side view
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/1.3/specific_fns/model_free/bmrb.py Diff Switch to side-by-side view
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/1.3/specific_fns/model_free/main.py Diff Switch to side-by-side view
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/1.3/test_suite/system_tests/bmrb.py Diff Switch to side-by-side view
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/1.3/test_suite/system_tests/scripts/bmrb_rw.py Diff Switch to side-by-side view
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