relax SVN archive

Added a PDB file containing the N, H, and calcium atoms of Bax's 1J7P structure.

This will be used in the creation and testing of optimisation of alignment tensors from RDCs and
PCSs.

Fix for the __linear_constraints() method.

The last probability N is not in the scaling matrix! Therefore don't scale.

The __linear_constraints() method now handles the N-state models without probabilities.

Merged revisions 8714,8717,8723,8725-8732,8734-8746 via svnmerge from
svn+ssh://semor@.../svn/relax/1.3

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r8714 | bugman | 2009-02-02 04:58:41 -0500 (Mon, 02 Feb 2009) | 3 lines

Added some printouts stating which file the relax saved state is placed in when in Debug mode.
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r8717 | bugman | 2009-02-02 05:30:54 -0500 (Mon, 02 Feb 2009) | 11 lines

Fixed an annoying bug in the RelaxError debugging mode.

The problem here is that the relax state was being saved in the __init__() methods if in debug mode.
The result was that in try statements which catch and allow for RelaxErrors, the relax state was
being saved even though the error message and exception was suppressed. The fix was to shift the
state saving code into the __str__() method.

A side effect of this change is a simplification of all the RelaxError classes as the debug code is
no longer duplicated in each class.
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r8723 | bugman | 2009-02-03 12:05:58 -0500 (Tue, 03 Feb 2009) | 6 lines

Wrote 2 new system tests for the new structural data design.

In test_read_pdb_internal6(), 2 different structures are loaded as 2 molecules. In
test_read_pdb_internal7(), 2 identical structures are loaded as 2 molecules.
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r8725 | bugman | 2009-02-04 04:33:25 -0500 (Wed, 04 Feb 2009) | 3 lines

Duplicated 5 systems tests of the internal PDB reader for the Scientific python PDB reader.
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r8726 | bugman | 2009-02-04 04:37:40 -0500 (Wed, 04 Feb 2009) | 5 lines

Bug fix for the load_pdb() method.

When set_model_num is None, this is now handled properly.
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r8727 | bugman | 2009-02-04 04:51:40 -0500 (Wed, 04 Feb 2009) | 6 lines

Fixes for the test_read_pdb_mol_2_model_scientific() system test.

The Scientific python PDB reader somehow decided to split the single structures in
'lactose_MCMM4_S1_*.pdb' into 2.
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r8728 | bugman | 2009-02-04 09:55:49 -0500 (Wed, 04 Feb 2009) | 5 lines

Fixes for the load_pdb() method.

Previously loaded structures were not being taken into account.
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r8729 | bugman | 2009-02-04 10:16:25 -0500 (Wed, 04 Feb 2009) | 5 lines

More fixes for load_pdb().

Collapsing 2 models into 1 was failing.
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r8730 | bugman | 2009-02-04 11:22:01 -0500 (Wed, 04 Feb 2009) | 5 lines

Another fix for the load_pdb() method.

The mol_offset value should be calculated at all times!
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r8731 | bugman | 2009-02-04 11:22:38 -0500 (Wed, 04 Feb 2009) | 3 lines

Added error checking to load_pdb() for when the number of molecules exceeds the set_mol_name list.
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r8732 | bugman | 2009-02-04 11:24:47 -0500 (Wed, 04 Feb 2009) | 3 lines

The read_mol arg now does something in load_pdb()!!!
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r8734 | bugman | 2009-02-04 11:32:36 -0500 (Wed, 04 Feb 2009) | 6 lines

Fix for the test_read_pdb_complex_scientific() system test.

Retarded Scientific python splitting a perfectly good molecule into 2 when it can't recognise a
residue type!
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r8735 | bugman | 2009-02-05 04:00:21 -0500 (Thu, 05 Feb 2009) | 6 lines

Modified test_read_pdb_internal1() to catch a molecule name identification bug.

The test_read_pdb_scientific1() was similarly modified, but there is no bug in the Scientific python
code.
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r8736 | bugman | 2009-02-05 04:18:17 -0500 (Thu, 05 Feb 2009) | 5 lines

Bug fix for the atom_loop() method.

The molecule name was not being checked!
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r8737 | bugman | 2009-02-05 04:22:02 -0500 (Thu, 05 Feb 2009) | 3 lines

Added a check for the molecule name.
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r8738 | bugman | 2009-02-05 04:22:35 -0500 (Thu, 05 Feb 2009) | 3 lines

Modified a print out to make it clearer.
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r8739 | bugman | 2009-02-05 05:30:37 -0500 (Thu, 05 Feb 2009) | 3 lines

Modified the get_pipe() function to check if a data pipe exists.
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r8740 | bugman | 2009-02-05 05:43:43 -0500 (Thu, 05 Feb 2009) | 3 lines

Modified 2 system tests for the loading of N-Ca vectors.
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r8741 | bugman | 2009-02-05 08:41:36 -0500 (Thu, 05 Feb 2009) | 22 lines

Massive speed up of the bond_vectors() method.

The algorithm used was very, very poorly designed. Now when setting the profile flag to 1 gives the
following. Before in one test:

11168736 function calls (10986641 primitive calls) in 76.750 CPU seconds

ncalls tottime percall cumtime percall filename:lineno(function)
758954 12.160 0.000 51.060 0.000 /home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search)
141 0.890 0.006 67.620 0.480 /home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors)

All other function call info lines have been removed. After the changes:

2586419 function calls (2579305 primitive calls) in 21.370 CPU seconds

ncalls tottime percall cumtime percall filename:lineno(function)
62803 1.180 0.000 5.020 0.000 /home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search)
141 0.060 0.000 12.020 0.085 /home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors)

The difference is that the selection object is no longer used, as it is completely unnecessary.
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r8742 | bugman | 2009-02-05 08:42:51 -0500 (Thu, 05 Feb 2009) | 3 lines

Modified the base API bond_vectors() method.
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r8743 | bugman | 2009-02-05 08:46:28 -0500 (Thu, 05 Feb 2009) | 3 lines

Added the atoms 'NZ' and 'OH' as nitrogens and oxygens of amino acids respectively.
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r8744 | bugman | 2009-02-05 08:54:50 -0500 (Thu, 05 Feb 2009) | 8 lines

Fixes for the bond_vectors() method.

The atom_id string is now generated as it is no longer passed in. This is a temporary fix and this
function is very inefficient, just as the internal object bond_vectors() method was (which was fixed
in r8741).
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r8745 | bugman | 2009-02-05 09:00:36 -0500 (Thu, 05 Feb 2009) | 5 lines

Fix for the test_read_pdb_scientific1() system test.

The current data pipe was not aliased.
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r8746 | bugman | 2009-02-05 09:03:40 -0500 (Thu, 05 Feb 2009) | 3 lines

Removed some debugging print statements.
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Removed some debugging print statements.

Fix for the test_read_pdb_scientific1() system test.

The current data pipe was not aliased.

Fixes for the bond_vectors() method.

The atom_id string is now generated as it is no longer passed in. This is a temporary fix and this
function is very inefficient, just as the internal object bond_vectors() method was (which was fixed
in r8741).

Added the atoms 'NZ' and 'OH' as nitrogens and oxygens of amino acids respectively.

Modified the base API bond_vectors() method.

Massive speed up of the bond_vectors() method.

The algorithm used was very, very poorly designed. Now when setting the profile flag to 1 gives the
following. Before in one test:

11168736 function calls (10986641 primitive calls) in 76.750 CPU seconds

ncalls tottime percall cumtime percall filename:lineno(function)
758954 12.160 0.000 51.060 0.000 /home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search)
141 0.890 0.006 67.620 0.480 /home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors)

All other function call info lines have been removed. After the changes:

2586419 function calls (2579305 primitive calls) in 21.370 CPU seconds

ncalls tottime percall cumtime percall filename:lineno(function)
62803 1.180 0.000 5.020 0.000 /home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search)
141 0.060 0.000 12.020 0.085 /home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors)

The difference is that the selection object is no longer used, as it is completely unnecessary.