Author: bugman
Date: Sat Feb 19 15:17:02 2011
New Revision: 12586
URL: http://svn.gna.org/viewcvs/relax?rev=12586&view=rev
Log:
Merged revisions
11691-11693,11699,11921,12076-12079,12419,12461-12513,12515-12516,12521-12530
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/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ContainerList has been replaced by RelaxListType in the latest svnmerge.py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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Modified:
1.3/ (props changed)
1.3/data/exp_info.py
1.3/generic_fns/bmrb.py
1.3/generic_fns/diffusion_tensor.py
1.3/generic_fns/mol_res_spin.py
1.3/generic_fns/relax_data.py
1.3/prompt/bmrb.py
1.3/prompt/molecule.py
1.3/specific_fns/api_base.py
1.3/specific_fns/model_free/bmrb.py
1.3/specific_fns/model_free/main.py
1.3/test_suite/system_tests/bmrb.py
1.3/test_suite/system_tests/scripts/bmrb_rw.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: 1.3/data/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/exp_info.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/bmrb.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/diffusion_tensor.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/mol_res_spin.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/relax_data.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/bmrb.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/molecule.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/specific_fns/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/api_base.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/bmrb.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/main.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/test_suite/system_tests/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/bmrb.py?rev=12586&r1=12585&r2=12586&view=diff
Modified: 1.3/test_suite/system_tests/scripts/bmrb_rw.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/bmrb_rw.py?rev=12586&r1=12585&r2=12586&view=diff
r12586 - in /1.3: ./ data/ generic_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/system_tests/ test_suite/s...