Author: bugman
Date: Tue Apr 28 17:59:52 2009
New Revision: 9026
URL: http://svn.gna.org/viewcvs/relax?rev=9026&view=rev
Log:
Merged revisions
8963,8971-8972,8974,8976-8977,8979-8990,8997-9003,9010-9011,9015-9017,9019-9024
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
................
r8963 | semor | 2009-03-10 20:52:43 +0100 (Tue, 10 Mar 2009) | 7 lines
Fix for bug 13163 : latex_mf_table.py sample script broken.
Discussion on this topic is in a thread at:
https://mail.gna.org/public/relax-devel/2009-03/msg00007.html
(Message-id: <49B6A6B1.4080305@xxxxxxxxx>)
................
r8971 | bugman | 2009-03-12 10:37:49 +0100 (Thu, 12 Mar 2009) | 3 lines
Modified the full_analysis.py script to perform 500 MC sims and turned on
automatic looping.
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r8972 | bugman | 2009-03-12 11:25:53 +0100 (Thu, 12 Mar 2009) | 5 lines
Added a line with the relax URL (http://nmr-relax.com) in the script
docstring.
This is in case someone has the script and not relax.
................
r8974 | semor | 2009-03-12 18:17:30 +0100 (Thu, 12 Mar 2009) | 7 lines
Fix for bug 13162: Rex values in XML results file not in s-1.
The units are now correctly given in the XML results fiel as discussed in a
thread at:
https://mail.gna.org/public/relax-devel/2009-03/msg00010.html
(Message-id: <20090310-141629.sv7147.79009@xxxxxxx>)
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r8976 | semor | 2009-03-12 18:56:28 +0100 (Thu, 12 Mar 2009) | 10 lines
Reverted r8974.
This follows a remark by Ed at:
https://mail.gna.org/public/relax-devel/2009-03/msg00033.html
(Message-id: <7f080ed10903121024h7a0a3808m3c268ca1f276ee4a@xxxxxxxxxxxxxx>)
The command used was:
svn merge -r8974:8973 .
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r8977 | semor | 2009-03-12 19:01:24 +0100 (Thu, 12 Mar 2009) | 7 lines
Now correctly fixed bug 13162: Rex values in XML results file not in s-1.
This follows a remark by Ed at:
https://mail.gna.org/public/relax-devel/2009-03/msg00033.html
(Message-id: <7f080ed10903121024h7a0a3808m3c268ca1f276ee4a@xxxxxxxxxxxxxx>)
................
r8979 | semor | 2009-03-16 19:52:15 +0100 (Mon, 16 Mar 2009) | 9 lines
Fix for bug 13032: Bug in structure.create diff tensor pdb
The Dz unit in dependency_generator() were erroneous, inputing 'alpha' and
'beta' instead of 'beta' and 'gamma'.
This had the effect of creating a weird shaped ellipsoid diffusion tensor
representation when 'alpha' and 'beta' were set to unequal values.
This is now fixed, yielding properly shaped diffusion tensor
representations for any angles 'alpha', beta' and 'gamma'.
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r8980 | semor | 2009-03-16 19:59:34 +0100 (Mon, 16 Mar 2009) | 11 lines
Changed units of model-free parameters in the test suite results file
according to r8977.
ns -> seconds
ps -> seconds
Angstrom -> meters
x MHz -> sigma_ex = Rex / omega**2
ppm -> unitless
The bzipped file was changed directly with vim. The system tests now pass
without error,
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r8981 | bugman | 2009-03-18 15:48:09 +0100 (Wed, 18 Mar 2009) | 5 lines
Bug fix!
Debugged intensity_sparky() to handle a Sparky assignment such as '004N-H'.
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r8982 | bugman | 2009-03-20 09:49:03 +0100 (Fri, 20 Mar 2009) | 5 lines
Added the Bruker ncproc parameter to handle Topspin's integer scaling of
FID intensities.
The data is now internally scaled by 2**ncproc.
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r8983 | bugman | 2009-03-20 11:28:13 +0100 (Fri, 20 Mar 2009) | 3 lines
RMSD of baseplane noise is now scaled by NC_proc.
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r8984 | bugman | 2009-03-20 15:22:14 +0100 (Fri, 20 Mar 2009) | 3 lines
Fixed a bad apostrophe character causing the script to fail.
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r8985 | bugman | 2009-03-20 15:28:37 +0100 (Fri, 20 Mar 2009) | 3 lines
Comment fix - missing data and error column args.
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r8986 | bugman | 2009-03-20 15:39:45 +0100 (Fri, 20 Mar 2009) | 3 lines
Removed a check disallowing multiple NOE data sets at the same spectrometer
frequency.
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r8987 | bugman | 2009-03-20 16:55:06 +0100 (Fri, 20 Mar 2009) | 5 lines
Bug fix for the results reading from_xml() method.
The molecule name was being evaluated?!?
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r8988 | bugman | 2009-03-20 17:35:00 +0100 (Fri, 20 Mar 2009) | 3 lines
Allowed vectors() to generate vectors even if the spin numbers are
different (for different PDBs).
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r8989 | bugman | 2009-03-20 17:35:55 +0100 (Fri, 20 Mar 2009) | 3 lines
Also removed the molecule name (for different PDBs).
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r8990 | bugman | 2009-03-20 17:44:37 +0100 (Fri, 20 Mar 2009) | 5 lines
Made the call to cdp.structure.bond_vectors() more fault tolerant.
The molecule name, residue name, and spin number are removed to allow for
different structures!
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r8997 | bugman | 2009-03-25 21:49:55 +0100 (Wed, 25 Mar 2009) | 5 lines
Modified the model elimination print out to show the data pipe name.
This was picked up while trying to debug bug #13259
(https://gna.org/bugs/index.php?13259).
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r8998 | bugman | 2009-03-25 22:26:06 +0100 (Wed, 25 Mar 2009) | 3 lines
Clean up of the model_loop() checking.
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r8999 | bugman | 2009-03-25 22:42:30 +0100 (Wed, 25 Mar 2009) | 6 lines
Removed the check for spin selection so that determine_model_type() works
with nothing selected.
This is a partial response to bug #13259
(https://gna.org/bugs/index.php?13259) reported by
Pierre-Yves Savard (pierre-yves dot savard att bcm dot ulaval dot ca).
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r9000 | bugman | 2009-03-26 00:21:17 +0100 (Thu, 26 Mar 2009) | 3 lines
Fixes for the MC sim methods for deselected spins.
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r9001 | bugman | 2009-03-26 00:42:14 +0100 (Thu, 26 Mar 2009) | 5 lines
Modified the structure.vectors() user function to fail if no vectors are
found.
This saves a lot of sanity when debugging a user script which fails.
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r9002 | bugman | 2009-03-26 15:10:14 +0100 (Thu, 26 Mar 2009) | 7 lines
Bug fix for bug #13259 (https://gna.org/bugs/index.php?13259).
This bug was reported by Pierre-Yves Savard (pierre-yves dot savard att bcm
dot ulaval dot ca).
The bug may not be completely gone yet.
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r9003 | bugman | 2009-03-26 16:40:57 +0100 (Thu, 26 Mar 2009) | 6 lines
Fix for the regression of bug #12607 (https://gna.org/bugs/?12607).
The determine_model_type() method now handles the strange case where no
spins are selected
(gracefully).
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r9010 | bugman | 2009-04-15 14:33:53 +0200 (Wed, 15 Apr 2009) | 5 lines
Expanded the test_read_pdb_internal3() and test_read_pdb_scientific3()
system tests.
Now the reading of atomic positions from different models is tested.
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r9011 | bugman | 2009-04-15 15:28:15 +0200 (Wed, 15 Apr 2009) | 6 lines
Removed a test in load_spins() causing a bug.
This test is totally unnecessary as the structures are not created if they
already exist. This was
causing only the position from the first model to be extracted, if ave_pos
was False.
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r9015 | bugman | 2009-04-27 15:26:25 +0200 (Mon, 27 Apr 2009) | 5 lines
Bug fix.
The PyMOL code was failing because of the new design of the structural data
object.
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r9016 | bugman | 2009-04-28 13:47:51 +0200 (Tue, 28 Apr 2009) | 3 lines
Added a catch for bug #13442 (https://gna.org/bugs/index.php?13442) to the
test suite.
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r9017 | bugman | 2009-04-28 14:02:02 +0200 (Tue, 28 Apr 2009) | 6 lines
Fix for bug #13442 (https://gna.org/bugs/index.php?13442).
The problem was that global minimisation objects were being accessed when
the do not exist. These
are now skipped.
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r9019 | bugman | 2009-04-28 14:05:30 +0200 (Tue, 28 Apr 2009) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-8161" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/ave_noe
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r9020 | bugman | 2009-04-28 14:28:05 +0200 (Tue, 28 Apr 2009) | 321 lines
Merged revisions
8162-8179,8181-8182,8643-8655,8657-8668,8671-8672,8674,8677,8679-8680,8689-8695,8700-8701,8710-8713,8716,9005-9009,9013
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/ave_noe
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r8162 | bugman | 2008-12-08 16:41:32 +0100 (Mon, 08 Dec 2008) | 5 lines
Fix for the noe.read_constraints() user function.
The noe object is called noe_obj.
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r8163 | bugman | 2008-12-08 16:46:53 +0100 (Mon, 08 Dec 2008) | 7 lines
The noe.read_constraints() user function now calls
generic_fns.noesy.read_constraints().
The noe user functions need not all point to the specific NOE object!
Maybe later the steady-state
NOE can be separated from the NOESY, but for now it isn't too illogical
for both to be in the same
user function class.
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r8164 | bugman | 2008-12-08 16:48:34 +0100 (Mon, 08 Dec 2008) | 3 lines
Created an empty module for NOESY data.
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r8165 | bugman | 2008-12-09 10:30:36 +0100 (Tue, 09 Dec 2008) | 3 lines
Wrote a stub function generic_fns.noesy.read_constraints().
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r8166 | bugman | 2008-12-09 10:37:16 +0100 (Tue, 09 Dec 2008) | 3 lines
Added a directory to the test-suite for holding NOE restraint data.
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r8167 | bugman | 2008-12-09 10:39:00 +0100 (Tue, 09 Dec 2008) | 5 lines
Added an RNA H-bond Xplor restraint file.
This comes from http://bass.chem.yale.edu/labdocs/packages/xplor.html.
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r8168 | bugman | 2008-12-09 10:45:58 +0100 (Tue, 09 Dec 2008) | 5 lines
Added the system test framework for NOE restraint reading tests.
This includes one test for the reading of RNA H-bond restraints from an
Xplor formatted input file.
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r8169 | bugman | 2008-12-09 10:47:29 +0100 (Tue, 09 Dec 2008) | 3 lines
Renamed 'constraints' to 'restraints' for the NOEs.
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r8170 | bugman | 2008-12-09 11:04:24 +0100 (Tue, 09 Dec 2008) | 3 lines
The RNA sequence of the noe_rna_hbond.dat file is now generated through a
new class method.
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r8171 | bugman | 2008-12-09 11:06:01 +0100 (Tue, 09 Dec 2008) | 3 lines
Renamed all the noe.read_constraints() references in the unit tests to
noe.read_restraints().
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r8172 | bugman | 2008-12-09 13:31:47 +0100 (Tue, 09 Dec 2008) | 5 lines
Completed the test_read_xplor_rna() system test.
Checks for the restraint list have now been added.
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r8173 | bugman | 2008-12-09 13:32:57 +0100 (Tue, 09 Dec 2008) | 3 lines
Activated the Noe_restraints system test framework.
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r8174 | bugman | 2008-12-09 13:33:19 +0100 (Tue, 09 Dec 2008) | 3 lines
Bug fix in the rna_seq() method.
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r8175 | bugman | 2008-12-09 13:36:17 +0100 (Tue, 09 Dec 2008) | 3 lines
Another bug fix for the rna_seq() sequence generation method.
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r8176 | bugman | 2008-12-09 13:49:38 +0100 (Tue, 09 Dec 2008) | 3 lines
Final fixes for the rna_seq() sequence generation method.
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r8177 | bugman | 2008-12-09 13:50:30 +0100 (Tue, 09 Dec 2008) | 3 lines
Fix for the call to noe.read_restraints() in test_read_xplor_rna().
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r8178 | bugman | 2008-12-09 13:57:32 +0100 (Tue, 09 Dec 2008) | 3 lines
Removed the non-existent frq arg and a docstring clarification about the
relax formatted file.
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r8179 | bugman | 2008-12-09 14:02:53 +0100 (Tue, 09 Dec 2008) | 3 lines
Missing import!
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r8181 | bugman | 2008-12-10 14:30:44 +0100 (Wed, 10 Dec 2008) | 3 lines
Added a missing import.
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r8182 | bugman | 2008-12-10 15:18:38 +0100 (Wed, 10 Dec 2008) | 3 lines
Added some more code to the read_restraints() function.
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r8643 | bugman | 2009-01-26 11:52:11 +0100 (Mon, 26 Jan 2009) | 3 lines
Wrote the __file_format() function for determining the NOE restraint file
format.
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r8644 | bugman | 2009-01-26 13:30:06 +0100 (Mon, 26 Jan 2009) | 3 lines
The non-implemented function generic_fns.xplor.parse_noe_restraints() is
now being called.
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r8645 | bugman | 2009-01-26 13:44:06 +0100 (Mon, 26 Jan 2009) | 3 lines
Reverted to calling file.readlines() rather than file.read().
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r8646 | bugman | 2009-01-26 15:01:10 +0100 (Mon, 26 Jan 2009) | 6 lines
Created the Xplor module for handling Xplor formatted files.
The function parse_noe_restraints() has been added to parse the NOE
restraints. The function
strip_comments() has been written to remove Xplor comments from the input
data.
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r8647 | bugman | 2009-01-26 15:24:53 +0100 (Mon, 26 Jan 2009) | 3 lines
Created __convert_to_id() to convert from Xplor atom string to relax atom
id.
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r8648 | bugman | 2009-01-26 15:31:05 +0100 (Mon, 26 Jan 2009) | 3 lines
Added checks to make sure spin containers corresponding to the Xplor atom
strings exist.
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r8649 | bugman | 2009-01-26 16:26:45 +0100 (Mon, 26 Jan 2009) | 3 lines
Typo fix. 'H4' should have been 'N4'!
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r8650 | bugman | 2009-01-26 16:32:49 +0100 (Mon, 26 Jan 2009) | 3 lines
The NOE restraints are now stored in the current data pipe.
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r8651 | bugman | 2009-01-26 16:39:22 +0100 (Mon, 26 Jan 2009) | 3 lines
Fixes for the test_read_xplor_rna() system test.
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r8652 | bugman | 2009-01-26 16:40:32 +0100 (Mon, 26 Jan 2009) | 5 lines
Modified the NOE restraint list so that some restraints are spread across
2 lines.
This should test the Xplor parsing code better.
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r8653 | bugman | 2009-01-26 16:42:12 +0100 (Mon, 26 Jan 2009) | 5 lines
Bug fix for the parse_noe_restraints() function.
Xplor restraints spread across 2 lines are now properly handled.
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r8654 | bugman | 2009-01-26 16:43:23 +0100 (Mon, 26 Jan 2009) | 3 lines
Added a few comments to test the Xplor parsing even more.
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r8655 | bugman | 2009-01-26 18:44:13 +0100 (Mon, 26 Jan 2009) | 3 lines
Shifted the checks of the atom id strings from the Xplor parser to the
NOE restraint reading fn.
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r8657 | bugman | 2009-01-27 09:35:53 +0100 (Tue, 27 Jan 2009) | 3 lines
Missing RelaxError import.
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r8658 | bugman | 2009-01-27 09:44:38 +0100 (Tue, 27 Jan 2009) | 3 lines
Added some test NOEs, in a generic formatted file, for phthalic acid and
testing the NOE reading.
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r8659 | bugman | 2009-01-27 10:01:41 +0100 (Tue, 27 Jan 2009) | 3 lines
Created a system test for the reading of a generically formatted NOE
restraint file.
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r8660 | bugman | 2009-01-27 10:15:15 +0100 (Tue, 27 Jan 2009) | 3 lines
Removed an unused import.
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r8661 | bugman | 2009-01-27 10:16:04 +0100 (Tue, 27 Jan 2009) | 3 lines
The generically formatted NOE restraint file is now being parsed.
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r8662 | bugman | 2009-01-27 11:10:45 +0100 (Tue, 27 Jan 2009) | 3 lines
Modified the phthalic acid NOE restraint reading test to include
pseudo-atoms.
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r8663 | bugman | 2009-01-27 13:45:15 +0100 (Tue, 27 Jan 2009) | 3 lines
Removed the '@' from the pseudo-atom spin names.
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r8664 | bugman | 2009-01-27 13:47:35 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote a unit test for the creation of pseudo-atom spin containers.
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r8665 | bugman | 2009-01-27 13:55:57 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote 5 arg unit tests for the spin.create_pseudo() user function.
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r8666 | bugman | 2009-01-27 14:00:37 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote the interface for the spin.create_pseudo() user function.
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r8667 | bugman | 2009-01-27 14:03:18 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the arg unit tests of spin.create_pseudo().
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r8668 | bugman | 2009-01-27 14:06:13 +0100 (Tue, 27 Jan 2009) | 3 lines
Imported the non-existant create_pseudo_spin() function.
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r8671 | bugman | 2009-01-27 16:14:22 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote the create_pseudo_spin() and __linear_ave() functions for
pseudo-atom support.
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r8672 | bugman | 2009-01-27 16:17:07 +0100 (Tue, 27 Jan 2009) | 5 lines
Fix for the phthalic acid NOE restraint reading system test.
Pseudo-atom creation was not correctly called.
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r8674 | bugman | 2009-01-27 16:27:54 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the create_pseudo_spin() and __linear_ave() functions.
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r8677 | bugman | 2009-01-27 16:41:23 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the 2 test_create_pseudo_spin() unit tests.
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r8679 | bugman | 2009-01-27 16:49:58 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the test_create_pseudo_spin() unit test. The atomic positions
are now set.
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r8680 | bugman | 2009-01-27 16:51:47 +0100 (Tue, 27 Jan 2009) | 3 lines
The __linear_ave() now handles the coordinates as numpy arrays.
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r8689 | bugman | 2009-01-28 11:24:04 +0100 (Wed, 28 Jan 2009) | 3 lines
Added some more checks for the test_create_pseudo_spin() unit test.
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r8690 | bugman | 2009-01-28 11:30:24 +0100 (Wed, 28 Jan 2009) | 3 lines
Wrote a second unit test for the creation of a pseudo-spin.
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r8691 | bugman | 2009-01-28 11:38:57 +0100 (Wed, 28 Jan 2009) | 3 lines
Modified the checks for the pseudo-spin creation unit tests.
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r8692 | bugman | 2009-01-28 11:40:14 +0100 (Wed, 28 Jan 2009) | 5 lines
The pseudo-spin name and number is now stored in the member spin
containers.
This gives a mapping between from the spin to the pseudo-spin.
........
r8693 | bugman | 2009-01-28 11:40:50 +0100 (Wed, 28 Jan 2009) | 3 lines
Fixes for test_create_pseudo_spin() and test_create_pseudo_spin2().
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r8694 | bugman | 2009-01-28 11:41:27 +0100 (Wed, 28 Jan 2009) | 3 lines
One more fix for test_create_pseudo_spin().
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r8695 | bugman | 2009-01-28 11:42:32 +0100 (Wed, 28 Jan 2009) | 3 lines
The members list is now stored in the pseudo-spin to map this to the
respective spin containers.
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r8700 | bugman | 2009-01-29 09:42:21 +0100 (Thu, 29 Jan 2009) | 3 lines
Added a call to calc() to test the quadratic potential calculation.
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r8701 | bugman | 2009-01-29 16:40:07 +0100 (Thu, 29 Jan 2009) | 5 lines
Created a module for calculating different optimisation/energy potentials.
The function quad_pot() has been written to provide a flat-bottom
potential.
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r8710 | bugman | 2009-02-02 10:44:48 +0100 (Mon, 02 Feb 2009) | 3 lines
Added tests for the existence of the current data pipe.
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r8711 | bugman | 2009-02-02 10:49:06 +0100 (Mon, 02 Feb 2009) | 3 lines
Modified the RelaxNoModelError print out to be more informative,
especially for the N-state model.
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r8712 | bugman | 2009-02-02 10:51:17 +0100 (Mon, 02 Feb 2009) | 3 lines
Added the start of the calculate() method.
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r8713 | bugman | 2009-02-02 10:51:45 +0100 (Mon, 02 Feb 2009) | 3 lines
The N-state model is now selected in the NOESY system test.
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r8716 | bugman | 2009-02-02 11:05:21 +0100 (Mon, 02 Feb 2009) | 3 lines
Modified __base_data_types() to include NOE restraints.
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r9005 | bugman | 2009-04-09 19:33:13 +0200 (Thu, 09 Apr 2009) | 3 lines
[... 174 lines stripped ...]
r9026 - in /branches/bmrb: ./ data/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ sample_scripts/ specific_fns/ spe...